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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Sal-Site
 
Resource Report
Resource Website
50+ mentions
Sal-Site (RRID:SCR_002850) Sal-Site portal, data analysis service, database, organism-related portal, service resource, production service resource, data or information resource, image collection, topical portal, analysis service resource Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network. gene, genomic, expressed sequence tag, blast, model organism, genome, salamander, animal model, genetic map, genetic marker, gene expression, limb regeneration, microarray, quantitative-pcr, rna-seq, nanostring, husbandry, embryo, limb, mutant, strain, neural, olfaction, phentotype, regeneration, renal, retina, sequence, vision, human, chicken, xenopus tropicalis, FASEB list has parent organization: University of Kentucky; Kentucky; USA NSF OB0242833;
NSF DBI0443496;
NCRR R24 RR016344;
NIH Office of the Director R24 OD010435
PMID:16359543 Free, Freely available nif-0000-25309 https://orip.nih.gov/comparative-medicine/programs/vertebrate-models SCR_002850 Ambystoma Resources for Model Amphibians Database 2026-02-15 09:18:25 92
Special Mouse Strains Resource
 
Resource Report
Resource Website
Special Mouse Strains Resource (RRID:SCR_002885) SMSR organism supplier, material resource, biomaterial supply resource Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains. strain panel, frozen, cryopreserved, recombinant inbred mouse, chromosome substitution mouse, consomic strain, gene, disease, strain is listed by: One Mind Biospecimen Bank Listing
is related to: One Mind Biospecimen Bank Listing
is related to: Mouse Phenome Database (MPD)
has parent organization: Jackson Laboratory
Recombinant inbred mouse, Chromosome substitution mouse, Consomic strain NCRR P40 RR016049;
NIH Office of the Director P40 OD011102
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25593 SCR_002885 Special Mouse Strains Resource (SMSR) 2026-02-15 09:18:24 0
BrainInfo
 
Resource Report
Resource Website
10+ mentions
BrainInfo (RRID:SCR_003142) portal, database, atlas, data or information resource, narrative resource, standard specification, topical portal Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures. brain, neuroanatomy is used by: NIF Data Federation
is listed by: Biositemaps
is related to: INIA19 Primate Brain Atlas
has parent organization: University of Washington; Seattle; USA
has parent organization: University of California at San Diego; California; USA
The Human Brain Project ;
NIBIB ;
NLM LM/OD-06243;
NIH Office of the Director LM/OD-06243;
NIMH MHO69259;
NCRR RR-00166
PMID:21789500
PMID:21163300
PMID:18368361
PMID:15055392
Free, Freely available nif-0000-00019 SCR_003142 Brain Info 2026-02-15 09:18:27 16
LUMPY
 
Resource Report
Resource Website
100+ mentions
LUMPY (RRID:SCR_003253) software application, data processing software, software resource, standalone software, simulation software, data analysis software Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed. probabilistic, framework, structural, variant, discovery is listed by: OMICtools
is listed by: Debian
has parent organization: University of Virginia; Virginia; USA
NHGRI R01 HG006693;
NIH Office of the Director DP2 OD006493;
Burroughs Wellcome Fund Career Award
PMID:24970577 Free, Available for download, Freely available OMICS_04674 https://sources.debian.org/src/lumpy-sv/ SCR_003253 lumpy-sv, LUMPY Express 2026-02-15 09:18:28 447
University of Pittsburgh Department of Neuroscience
 
Resource Report
Resource Website
University of Pittsburgh Department of Neuroscience (RRID:SCR_007985) organization portal, department portal, data or information resource, portal The Department of Neuroscience in the School of Arts and Sciences at the University of Pittsburgh provides outstanding undergraduate and graduate education with innovative independent and collaborative research, a well-rounded curriculum, and a seminar series by the world''s most renowned leaders in the field of neuroscience. The Department has become successful and prominent based on the determination, energy, imagination, and skills of its faculty as investigators and as mentors, and on the support of the institution and the funding agencies. Consequently, morale is high and so is our optimism that we will continue to develop and maintain a world-class department. NIH Office of the Director P40 OD010996 nif-0000-04000 SCR_007985 U Pitt, UPitt Department of Neuroscience, UPitt Neuroscience 2026-02-15 09:19:40 0
Bloomington Drosophila Stock Center
 
Resource Report
Resource Website
1000+ mentions
Bloomington Drosophila Stock Center (RRID:SCR_006457) BDSC organism supplier, material resource, biomaterial supply resource Collects, maintains and distributes Drosophila melanogaster strains for research. Emphasis is placed on genetic tools that are useful to a broad range of investigations. These include basic stocks of flies used in genetic analysis such as marker, balancer, mapping, and transposon-tagging strains; mutant alleles of identified genes, including a large set of transposable element insertion alleles; defined sets of deficiencies and a variety of other chromosomal aberrations; engineered lines for somatic and germline clonal analysis; GAL4 and UAS lines for targeted gene expression; enhancer trap and lacZ-reporter strains with defined expression patterns for marking tissues; and a collection of transposon-induced lethal mutations. RIN, Resource Information Network, disease model, deficiency, deletion, transposon insertion, sequenced strain, duplication, protein trap, human disease model, transposon, fly, gene, genetic, genetic analysis, database, deficiency, germline, insertion, invertebrate, scientist, somatic, stock, transposon, mutation, genetic construct, FASEB list, RRID Community Authority is used by: Integrated Animals
is listed by: One Mind Biospecimen Bank Listing
is listed by: Resource Information Network
is related to: One Mind Biospecimen Bank Listing
is related to: NIF Data Federation
has parent organization: Indiana University; Indiana; USA
Human disease model NIH Office of the Director P40 OD018537 nif-0000-00241 https://orip.nih.gov/comparative-medicine/programs/invertebrate-models http://flystocks.bio.indiana.edu/bloomhome.htm SCR_006457 Bloomington Drosophila Stock Center at Indiana University 2026-02-15 09:19:18 3164
Wake Forest Vervet Research Colony
 
Resource Report
Resource Website
10+ mentions
Wake Forest Vervet Research Colony (RRID:SCR_006678) VRC, WFSM VRC service resource, tissue bank, storage service resource, material resource, biospecimen repository, material storage repository, biomaterial supply resource NIH funded national research resource to provide biomedical research community with access to US born, known age, pedigreed, genomically sequenced, pathogen free Caribbean origin vervet monkeys also known as African green monkeys. Provides access to animals, extensive multisystem clinical phenotyping, sample and data repositories, expertise in use of nonhuman primate models for translational studies, serves as platform for training veterinarians and other professionals in biomedical research, husbandry, clinical care, and the colony behavioral management. blood, tissue, chlorocebus, aethiops, sabaeus, animal, model, green, monkey is listed by: One Mind Biospecimen Bank Listing
has parent organization: Wake Forest Primate Center
NIH Office of the Director OD010965 nif-0000-25872, nlx_146208, SCR_012849 SCR_006678 Wake Forest Vervet Research Colony, Wake Forest School of Medicine Vervet Research Colony, Vervet Research Colony 2026-02-15 09:19:20 10
Mouse Brain Architecture Project
 
Resource Report
Resource Website
1+ mentions
Mouse Brain Architecture Project (RRID:SCR_004683) atlas, data or information resource, reference atlas, d spatial image An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset. atlas, brain, brain architecture, connectivity, mouse brain architecture, neuroanatomy is related to: Brain Architecture Project
has parent organization: Brain Architecture Project
NIH Office of the Director ;
NIMH RC1MH088659;
NIMH R01MH087988
Fully accessible to the neuroscience community as well as interested members of the general public, Acknowledgement requested nlx_146201 http://www.brainarchitecture.org http://www.brainarchitecture.org/mouse/about SCR_004683 MBA Project, Mouse Brain Architecture 2026-02-15 09:18:47 5
Tulane National Biomedical Research Center
 
Resource Report
Resource Website
500+ mentions
Tulane National Biomedical Research Center (RRID:SCR_008167) TNPRC organization portal, portal, data or information resource, topical portal, disease-related portal Center focused on understanding human health problems, including infectious diseases that require the use of nonhuman primates to develop diagnostics, therapeutics and preventive strategies. Primary research interests include developing vaccines, treatments and diagnostic tools for infectious diseases such as AIDS, tuberculosis, CMV, COVID-19, Lyme disease, and malaria. TNPRC has both biosafety level 2 and biosafety level 3 laboratories facilities to accommodate various research needs, and is the only National Primate Research Center with Regional Biosafety Laboratory. NPRC, NPRC Consortium, ORIP, primate research, is listed by: National Primate Research Center Consortium
has parent organization: Tulane University; Louisiana; USA
NIH Office of the Director P51 OD011104;
NIH Office of the Director U42 OD010568;
NIH Office of the Director U42 OD024282
nif-0000-24360 https://orip.nih.gov/comparative-medicine/programs/vertebrate-models SCR_008167 Tulane National Primate Research Center 2026-02-15 09:19:44 853
Caribbean Primate Research Center
 
Resource Report
Resource Website
1+ mentions
Caribbean Primate Research Center (RRID:SCR_008345) CPRC organism supplier, material resource, biomaterial supply resource Center for the study of non-human primates. Its mission is the study and use of non-human primates as models for studies of social and biological interactions and for the discovery of methods of prevention, diagnosis and treatment of diseases that afflict humans. Through the stewardship of three unique facilities—Cayo Santiago Field Station, Sabana Seca Field Station, and the Laboratory of Primate Morphology supports a diverse range of research programs that enhance understanding of primate biology and behavior, with direct applications in biomedical and translational research. NPRC, NPRC Consortium, ORIP, environment, genetic, antigen, behavior, biological, biomedical, birth, blood, conception, dengue, disease, human, immune system, laboratory, macaca mulatta, macaque, model, monkey, morphology, movement, pathology, primate, reproductive biology, researcher, rh, rhesus, scientific, serological, siv, skeletal system, vaccine, variation, virology is listed by: National Primate Research Center Consortium
has parent organization: University of Puerto Rico; Puerto Rico; USA
NIH Office of the Director P40 OD012217 nif-0000-25870 https://orip.nih.gov/comparative-medicine/programs/vertebrate-models SCR_008345 Caribbean Primate Research Center Program 2026-02-15 09:19:50 1
Xiphophorus Genetic Stock Center
 
Resource Report
Resource Website
100+ mentions
Xiphophorus Genetic Stock Center (RRID:SCR_008340) organism supplier, material resource, biomaterial supply resource Supplier of xiphophorus (platyfish or swordtails) from pedigreed parental lines, representing variety of species. In addition to supplying strains and providing consultation on husbandry and genetic questions, the XGSC produces custom interspecies hybrids (both first generation F1, and backcross hybrid generation BC1) for a variety of projects. RIN, Resource Information Network, est, fish, cryopreservation, microsatellite, swordtail, RRID Community Authority is used by: Integrated Animals
is listed by: Resource Information Network
has parent organization: Texas State University; Texas; USA
NCI P01 CA75137;
NIH Office of the Director R24 OD011120;
University of Texas MD Anderson Center
nif-0000-24971 https://orip.nih.gov/comparative-medicine/programs/vertebrate-models SCR_008340 XGSC 2026-02-15 09:19:47 109
Southwest National Primate Research Center
 
Resource Report
Resource Website
50+ mentions
Southwest National Primate Research Center (RRID:SCR_008292) topical portal, data or information resource, portal Center that supports studies of nonhuman primate models of human diseases, including common chronic diseases and infectious diseases and the effects that genetics and the environment have on physiological processes and disease susceptibility. SNPRC encourages the use of its resources by investigators from the national and international biomedical research communities. NPRC, NPRC Consortium, ORIP, environment, genetic, aids, animal, baboon, biomedical, breeding, chimpanzee, chronic, colony, disease, human, infectious, macaques, marmoset, nonhuman, physiological, population, primate, process, research, rhesus, specie, study, susceptibility, veterinary, spf, specific, pathogen, free is listed by: National Primate Research Center Consortium
has parent organization: Texas Biomedical Research Institute; Texas; USA
NIH Office of the Director P51 OD011133;
NIH Office of the Director U42 OD010442
nif-0000-24359 https://orip.nih.gov/comparative-medicine/programs/vertebrate-models SCR_008292 SNPRC 2026-02-15 09:19:29 85
National Xenopus Resource
 
Resource Report
Resource Website
100+ mentions
National Xenopus Resource (RRID:SCR_013731) NXR organism supplier, material resource, biomaterial supply resource National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). RIN, Resource Information Network, Xenopus, laevis, tropicalis, RRID Community Authority is used by: Integrated Animals
is listed by: Resource Information Network
NIH Office of the Director P40 OD010997;
NIH Office of the Director R24 OD030008
https://orip.nih.gov/comparative-medicine/programs/vertebrate-models SCR_013731 2026-02-15 09:20:45 308
trRosetta
 
Resource Report
Resource Website
50+ mentions
trRosetta (RRID:SCR_021181) software application, simulation software, service resource, software resource 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. protein structure, restraint-guided structure generation, protein structure prediction uses: Rosetta National Natural Science Foundation of China ;
Fok Ying-Tong Education Foundation ;
Key Laboratory for Medical Data Analysis and Statistical Research of Tianjin ;
Thousand Youth Talents Plan of China ;
China Scholarship Council ;
NIGMS R01 GM092802;
NIH Office of the Director DP5 OD026389
PMID:31896580 Free, Freely available https://github.com/gjoni/trRosetta SCR_021181 transformed restrained Rosetta 2026-02-15 09:21:58 67
Appyters
 
Resource Report
Resource Website
1+ mentions
Appyters (RRID:SCR_021245) web application, software resource 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. Jupyter Notebooks, data-driven web apps collection, Jupyter Notebook results report is used by: Hypothesis Center
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
NCI U24 CA224260;
NHLBI U54 HL127624;
NIH Office of the Director OT2 OD030160
DOI:10.1016/j.patter.2021.100213 Free, Available for download, Freely available https://github.com/MaayanLab/appyter
https://github.com/MaayanLab/appyter-catalog
SCR_021245 2026-02-15 09:22:31 9
Monocle3
 
Resource Report
Resource Website
100+ mentions
Monocle3 (RRID:SCR_018685) software application, data processing software, software resource, software toolkit, data analysis software 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. Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics has parent organization: University of Washington; Seattle; USA NIH Office of the Director DP2 OD00667;
NIGMS P01 GM099117;
NIH Office of the Director DP2 0D008514;
NHGRI P50 HG006193;
Single Cell Genomics initiative
PMID:24658644 Free, Available for download, Freely available https://github.com/cole-trapnell-lab/monocle3 SCR_018685 Monocle, Monocle 3 2026-02-15 09:21:40 270
Phenograph
 
Resource Report
Resource Website
100+ mentions
Phenograph (RRID:SCR_016919) PhenoGraph software application, data processing software, data analysis software, software resource 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. high, dimention, single, cell, data, phenotype, analysis, heterogeneity uses: Python Programming Language
is related to: Rphenograph
NIGMS R00 GM104148;
NICHD DP1 HD084071;
NCI R01 CA164729;
NCI U54 CA121852;
NCI R01 CA130826;
NCI U54 CA143907;
US Department of Health and Human Services HHSN272200700038C;
NIH N01 HV00242;
NCI P01 CA034233;
NIAID U19 AI057229;
NCI U54 CA149145;
US FDA HHSF223201210194C;
US DOD W81XWH1210591;
Entertainment Industry Foundation ;
Rachford and Carlota Harris Endowed Professorship ;
CIRM DR1 01477;
CIRM RB201592;
Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04;
Packard Fellowship for Science and Engineering ;
NIH Office of the Director DP2 OD002414
PMID:26095251 Free, Available for download, Freely available https://github.com/JinmiaoChenLab/Rphenograph https://github.com/jacoblevine/PhenoGraph SCR_016919 2026-02-15 09:21:56 213
Database of Immune Cell Epigenomes
 
Resource Report
Resource Website
50+ mentions
Database of Immune Cell Epigenomes (RRID:SCR_018259) DICE database, software resource, data access protocol, web service, data or information resource 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. Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis has parent organization: La Jolla Institute for Immunology William K. Bowes Jr Foundation ;
NIAID R24 AI108564;
NCRR S10 RR027366;
NIH Office of the Director S10 OD016262
PMID:30449622 Free, Freely available SCR_018259 Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics 2026-02-15 09:22:19 59
Transgenic Huntington's Disease Monkey Resources
 
Resource Report
Resource Website
Transgenic Huntington's Disease Monkey Resources (RRID:SCR_014560) THDMR material resource, biomaterial supply resource 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. monkey, biomaterial supply resource, transgenic, huntington's disease, longitudinal, postmortem, mri, research assistance has parent organization: Emory University; Georgia; USA Huntington's disease NIH Office of the Director R24 OD010930 Biomaterials are available via request https://orip.nih.gov/comparative-medicine/programs/vertebrate-models SCR_014560 Transgenic Huntington's Disease Monkey Resources (THDMR) 2026-02-15 09:20:44 0
University of California at Davis Mutant Mouse Resource and Research Center
 
Resource Report
Resource Website
100+ mentions
University of California at Davis Mutant Mouse Resource and Research Center (RRID:SCR_016448) MMRRC UCD, UCD MMRRC material resource, biomaterial supply resource 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. ABRF, USEDit, mouse, mice, research, genetic, mutant, mutation, transgenic, knockout, research, animal, behavior is listed by: ABRF CoreMarketplace
is related to: USEDit
is organization facet of: Mutant Mouse Resource and Research Center
NIH Office of the Director U42 OD012210;
NIH Office of the Director U42 OD010983
ABRF_1650 https://coremarketplace.org/?FacilityID=1650&citation=1 SCR_016448 Mutant Mouse Resource and Research Center UC Davis, Davis MMRRC, UCD Mutant Mouse Resource and Research Center, UC Davis MMRRC, UC Davis Mutant Mouse Resource and Research Center, Mutant Mouse Resource and Research Center - UCD, Mutant Mouse Resource and Research Center - University of California at Davis, California MMRRC 2026-02-15 09:21:52 186

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