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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL 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 image collection, portal, production service resource, data analysis service, organism-related portal, service resource, database, topical portal, analysis service resource, data or information 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 2026-08-03 09:32:09 92
Special Mouse Strains Resource
 
Resource Report
Resource Website
Special Mouse Strains Resource (RRID:SCR_002885) SMSR biomaterial supply resource, material resource, organism supplier 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) 2026-08-03 09:31:52 0
Mouse Brain Architecture Project
 
Resource Report
Resource Website
1+ mentions
Mouse Brain Architecture Project (RRID:SCR_004683) d spatial image, reference atlas, data or information resource, atlas 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 2026-08-03 09:32:40 5
Texas A and M Health Science Center MSC Distribution
 
Resource Report
Resource Website
10+ mentions
Texas A and M Health Science Center MSC Distribution (RRID:SCR_005522) Texas A&M MSC Distribution material resource, biomaterial supply resource, cell repository THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Center for cell line distribution and stock at Texas A&M Health Science Center College of Medicine Institute for Regenerative Medicine. Scott & White have received a grant funded by the NIH to provide well-characterized human adult stem cells, rat stem cells, and mouse stem cells to academic researchers worldwide upon request. stem cell, bone marrow mesenchymal stem cell, multipotent mesenchymal stromal cell, marrow stromal cell, frozen, bone marrow, adult, adult human, adult rat, lewis rat, c57bl/6j, experimental protocol is listed by: One Mind Biospecimen Bank Listing
has parent organization: Texas A and M Health Science Center College of Medicine; Texas; USA
NIH Office of the Director P40 OD011050 THIS RESOURCE IS NO LONGER IN SERVICE. nlx_144619, SCR_013734 SCR_005522 Texas A&M Health Science Center MSC Distribution, Texas A M Health Science Center MSC Distribution, Institute for Regenerative Medicine at Scott & White MSC Distribution, Texas A&M Health Science Center College of Medicine Institute for Regenerative Medicine MSC Distribution, Adult Mesenchymal Stem Cell Resource 2026-08-03 09:32:53 19
Nonhuman Primate Reagent Resource
 
Resource Report
Resource Website
100+ mentions
Nonhuman Primate Reagent Resource (RRID:SCR_012986) NHPRR antibody supplier, material resource, reagent supplier Center that facilitates the optimal use of nonhuman primate models in biomedical research by identifying, developing, characterizing and producing reagents for monitoring or modulating immune responses. They distribute non-human primate-specific antibodies for in vitro diagnostics, as well as develop and produce primate recombinant antibodies for in vivo cell depletion or modulating immune responses. anti-ig, antibody, biomedical, cell, depletion, diagnostic, immune, immunoglobulin, in vitro, in vivo, macaque, monkey, nonhuman, primate, reagent, recombinant, research, response, specie NIH Office of the Director R24 OD010976;
NIH HHSN272200900037C;
NIH HHSN286200400101C;
NIH HHSN2722001300031C;
NIAID AI126683;
NCRR RR016001;
NIAID AI040101;
NIH 272200900037C;
NIH 286200400101C;
NIH AI-126683;
NIH OD-010976;
NIH RR-016001;
NIH 2722001300031C;
NIH 272201300031C;
NIH AI-040101;
NIH NHPRR
nif-0000-24368 https://orip.nih.gov/comparative-medicine/programs/vertebrate-models, http://www.nhpreagents.org/NHP/contact.aspx http://nhpreagents.bidmc.harvard.edu/NHP/default.aspx SCR_012986 nhp reagents, Nonhuman Primate Reagent Resources, Non-human primate repository, Non human Primate Reagent Resources, NHP Reagent Resource, nhpreagents, NIH Nonhuman Primate Reagent Resource, NHP Reagent, nhpreagent, Non-human Primate Reagent Resources 2026-08-03 09:35:07 221
Phenograph
 
Resource Report
Resource Website
100+ mentions
Phenograph (RRID:SCR_016919) PhenoGraph software resource, data processing software, software application, data analysis software 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 2026-08-03 09:36:38 213
Zebrafish International Resource Center
 
Resource Report
Resource Website
100+ mentions
Zebrafish International Resource Center (RRID:SCR_005065) ZIRC biomaterial supply resource, material resource, organism supplier Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species. RIN, Resource Information Network, zebrafish line, expressed sequence tag, cdna, fish, antibody, pathology, research, embryo, adult, 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: ZMP
is related to: NIF Data Federation
is related to: Zebrafish Information Network (ZFIN)
is related to: zfishbook
has parent organization: University of Oregon; Oregon; USA
NICHD HD12546;
NCRR RR12546;
W.M. Keck Foundation ;
NIH Office of the Director P40 OD011021
Restricted nif-0000-00242 http://zebrafish.org/home/guide.php SCR_005065 Zebrafish International Resource Center 2026-08-03 09:32:50 445
National Resource for Aplysia
 
Resource Report
Resource Website
10+ mentions
National Resource for Aplysia (RRID:SCR_008361) National Resource for Aplysia biomaterial supply resource, material resource, organism supplier Center where Aplysia californica are cultured and raised for research purposes. Aplysia from the facility serve in research on genomics, human brain function, toxicology for developmental studies, natural products, chemistry for isolation of novel anti-tumor and antibacterial compounds, in the study of transport by digestive tissues and have potential for use in studies of substance addiction and nerve senescence and regeneration. disease, genomics, aplysia californica, research, brain has parent organization: University of Miami; Florida; USA NIH Office of the Director P40 OD010952;
NCRR
nif-0000-25472 http://aplysia.miami.edu/ SCR_008361 2026-08-03 09:33:47 14
SigCom LINCS
 
Resource Report
Resource Website
1+ mentions
SigCom LINCS (RRID:SCR_022275) web service, data access protocol, software resource 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. FAIR data, data and metadata search engine, gene expression signatures, gene expression signature processed, analyzed, and visualized, LINCS, GTEx, GEO, gene expression signatures, NHLBI U54HL127624;
NIDDK R01DK131525;
NIH Office of the Director OT2OD030160
PMID:35524556 Free, Freely available https://github.com/MaayanLab/sigcom-lincs SCR_022275 SigCom Library of Integrated Network-based Cellular Signatures 2026-08-03 09:37:50 7
CRISPOR
 
Resource Report
Resource Website
1000+ mentions
CRISPOR (RRID:SCR_015935) software resource, web application 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. rna, sg, sgrna, crispr, genome, off-target, prediction, accuracy, clone, cas9, coding, exon is related to: UCSC Genome Browser MRC 53658;
NIH Office of the Director U42 OD011174;
NHGRI U41 HG002371;
NCI U54 HG007990;
California Institute of Regenerative Medicine GC1R-06673C;
Agence Nationale pour la Recherche ;
Fondation pour la Recherche Médicale DEQ20140329544
PMID:27380939 Free, Available for download https://github.com/maximilianh/crisporWebsite SCR_015935 2026-08-03 09:36:30 1320
X2K Web
 
Resource Report
Resource Website
10+ mentions
X2K Web (RRID:SCR_023624) X2K web service, data access protocol, software resource 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. predicts involvement of upstream cell signaling pathways, differentially expressed genes, linking expression signatures, upstream cell signaling networks, has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA NHLBI U54 HL127624;
NCI U24 CA224260;
NIH Office of the Director OT3 OD025467
PMID:29800326 Free, Freely available https://github.com/MaayanLab/x2k_web SCR_023624 eXpression2Kinases (X2K) Web 2026-08-03 09:38:27 10
Appyters
 
Resource Report
Resource Website
1+ mentions
Appyters (RRID:SCR_021245) software resource, web application 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 2026-08-03 09:37:23 9
Database of Immune Cell Epigenomes
 
Resource Report
Resource Website
50+ mentions
Database of Immune Cell Epigenomes (RRID:SCR_018259) DICE web service, database, data access protocol, data or information resource, software 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 2026-08-03 09:37:00 59
Monocle3
 
Resource Report
Resource Website
100+ mentions
Monocle3 (RRID:SCR_018685) software toolkit, software application, data processing software, data analysis software, software resource 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 2026-08-03 09:37:04 270
trRosetta
 
Resource Report
Resource Website
50+ mentions
trRosetta (RRID:SCR_021181) simulation software, service resource, software resource, software application 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 2026-08-03 09:37:21 67
Squirrel Monkey Breeding and Research Resource
 
Resource Report
Resource Website
10+ mentions
Squirrel Monkey Breeding and Research Resource (RRID:SCR_006291) SMBRR tissue bank, material resource, portal, biomaterial supply resource, data or information resource, project portal SMBRR maintains the only self-sustaining national research resource of laboratory-born squirrel monkeys, their tissues and other biological materials, as well as the expertise to carry out research on this animal. Scientists with NIH grants utilize squirrel monkeys to study many diseases that threaten human health including Alzheimer's disease and other disorders of the central nervous system, drug addiction, malaria, and viral diseases. Center that carries out research on squirrel monkey biology and its research uses. It meets the needs of the biomedical research community in three ways: providing national resource for laboratory-born squirrel monkeys, having active research component that continues to add new information about the biology of the squirrel monkey with a particular emphasis on reproduction and colony management, and acts as a source of expertise for squirrel monkey biology, management and husbandry. ORIP, Office of Research Infrastructure Programs, reproductive biology, behavior, reproduction, disease, colony management, tissue, live animal, bodily fluid is listed by: One Mind Biospecimen Bank Listing
has parent organization: University of Texas MD Anderson Cancer Center
NIH Office of the Director P40 OD010938 Public nlx_151947 https://reporter.nih.gov/search/oopkAZDMqkCSLpwC7X2hHg/project-details/10558468, https://orip.nih.gov/comparative-medicine/programs/vertebrate-models, http://www.kccmr.org/ SCR_006291 Keeling Center for Comparative Medicine and Research Squirrel Monkey Breeding and Research Resource, KCCMR SMBRR, KCCMR Squirrel Monkey Breeding and Research Resource 2026-08-03 09:32:58 33
WormAtlas
 
Resource Report
Resource Website
100+ mentions
WormAtlas (RRID:SCR_002861) data or information resource, atlas, database Anatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. Includes links to other major worm websites and databases. Application for viewing and downloading thousands of unpublished electron micrographs and associated data. These images have been generated by several labs in the C. elegans community, including the MRC, the Hall lab (Center for C. elegans Anatomy), and the Culotti and Riddle labs. electron, ganglion, anatomy, caenorhabditis elegan, c. elegan, cell, development, gfpworm, glossary, lineage, microscopy, morphology, video, nematode, nerve cord, nervous system, neuroanatomy, neuron, phenotype, wiring diagram, worm, image, FASEB list has parent organization: Albert Einstein College of Medicine; New York; USA NCRR ;
NIH Office of the Director R24 OD010943
Free, Freely available nif-0000-00098, nif-0000-25470, SCR_007295 https://orip.nih.gov/comparative-medicine/programs/invertebrate-models SCR_002861 , WormImage, Worm Image Database 2026-08-03 09:32:09 161
Human Tissue and Organ for Research Resource (HTORR)
 
Resource Report
Resource Website
Human Tissue and Organ for Research Resource (HTORR) (RRID:SCR_002859) HTORR tissue bank, biomaterial supply resource, material resource NDRI’s Human Tissue and Organs for Research Resource (HTORR) Program has been funded by the National Institutes of Health (NIH) for over 30 consecutive years to support research programs across multiple disciplines. It is through the HTORR program that NDRI provides academic biomedical investigators with donated normal and diseased human tissues and organs recovered from a diverse donor pool using customized procurement, processing, and preservation and distribution protocols. Our HTORR Program supports academic biomedical research investigators needs by providing: Access to a wide array of human biospecimens from any body system * Customized procurement in a variety of preservation formats including fresh, frozen, and fixed suitable for various analytical techniques * Reduced costs for tissue procurement * Technical support to design your studies utilizing human biospecimens * Letters of support and budgetary information for grant applications tissue, organ, nervous system, pulmonary system, cardiovascular system, endocrine system, eye, bone, cartilage, normal, diseased, human immunodeficiency virus, heart, kidney, lung, brain, liver, eye, bone, joint, disease, rare disease, endocrinology, eye bank, immunology, infectious disease, nephrology, nervous system, ophthalmology, pathology, pulmonary system, research, specimen, toxicology, transplantation, catalog is listed by: One Mind Biospecimen Bank Listing
is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology
has parent organization: National Disease Research Interchange
has parent organization: National Center for Research Resources
Normal, Disease, Human immunodeficiency virus, Rare disease NIH Office of the Director U42 OD011158 Free, Freely available nif-0000-25417 https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources http://www.ncrr.nih.gov/clinical%5Fresearch%5Fresources/resource%5Fdirectory/human_tissue_and_organ_resource_for_research/ SCR_002859 Human Tissue Organ Resource for Research, Human Tissues and Organs for Research, Human Tissues and Organs for Research (HTOR), Human Tissues Organs for Research 2026-08-03 09:31:52 0
WormGUIDES
 
Resource Report
Resource Website
1+ mentions
WormGUIDES (RRID:SCR_013733) data or information resource, atlas 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. embryogenesis, development, neural connectivity, diSPIM, 4d atlas, c elegans has parent organization: Yale University; Connecticut; USA NIH Office of the Director R24 OD016474 Free, Public, Requires Java SCR_014203 https://orip.nih.gov/comparative-medicine/programs/invertebrate-models, http://www.wormguides.org/wormguides SCR_013733 Global Understanding in Dynamic Embryonic Systems 2026-08-03 09:35:31 4
EchinoBase
 
Resource Report
Resource Website
100+ mentions
EchinoBase (RRID:SCR_013732) data or information resource, database 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. sea urchins, echinoderms, genome, FASEB list NIH Office of the Director P40 OD010959 PMID:19010966 Free, Public https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources SCR_013732 SpBase, Echinoderm genomic database, Gene Library Resource for the Sea Urchin Strongylocentrotus purpuratus, Sea Urchin Genome Database, Echino Base 2026-08-03 09:35:24 104

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