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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GEROprotectors Resource Report Resource Website 10+ mentions |
GEROprotectors (RRID:SCR_016737) | data or information resource, database | 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. | geroprotector, data, collection, current, thearpeutic, prevention, aging, disease, geriatic |
uses: PubChem uses: ChemSpider uses: DrugBank uses: ChEMBL uses: CHEBI uses: UniProt uses: GenAge |
Wellcome Trust ; Israel Ministry of Science and Technology ; Fund in Memory of Dr. Amir Abramovich |
PMID:26342919 | Public, Free, Freely available | SCR_016737 | Geroprotectors | 2026-02-11 10:59:31 | 11 | |||||||
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BIGSdb Resource Report Resource Website 1+ mentions |
BIGSdb (RRID:SCR_023551) | data or information resource, database | 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. | sequence data, bacterial isolates, gene-by-gene bacterial population, annotation and analysis, bacterial genome variation, | Wellcome Trust | PMID:21143983 | Free, Freely available | https://bigsdb.readthedocs.io/en/latest/ | SCR_023551 | Bacterial Isolate Genome Sequence Database | 2026-02-11 11:00:42 | 1 | |||||||
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DECIPHER Resource Report Resource Website 1000+ mentions |
DECIPHER (RRID:SCR_006552) | DECIPHER | data or information resource, database | Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes. | chromosomal imbalance, phenotype, chromosome, gene, genome, deletion, duplication, copy number, genotype, polymorphism, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Deciphering Developmental Disorders is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Microdeletion Syndrome, Overgrowth syndrome, Microduplication syndrome, Deletion syndrome, Duplication syndrome, Wolf-Hirschhorn Syndrome, Williams-Beuren Syndrome, Smith-Magenis Syndrome, Etc | Wellcome Trust WT077008 | PMID:19344873 | Acknowledgement required | nlx_151653, OMICS_00265 | SCR_006552 | Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources, Decipher | 2026-02-11 10:57:25 | 1797 | ||||
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Retinal wave repository Resource Report Resource Website |
Retinal wave repository (RRID:SCR_010462) | Retinal wave repository | data or information resource, data set | A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged. | hdf5, development, neural circuit, retina, eye, multielectrode, array recording, spontaneous activity, reproducible research, retinal wave, electrophysiology, multielectrode array, developmental age, genotype |
has parent organization: GigaScience has parent organization: Code Analysis Repository and Modelling for e-Neuroscience has parent organization: University of Cambridge; Cambridge; United Kingdom |
Developing retina, Aging | EPSRC EP/E002331/1; BBSRC BB/H023577/1; BBSRC BB/I000984/1; Wellcome Trust 083205/B/07/Z |
PMID:24666584 | Registration required, (CARMEN), Acknowledgement required, The community can contribute to this resource | nlx_157664 | http://www.damtp.cam.ac.uk/user/eglen/waverepo/ | SCR_010462 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | 2026-02-11 10:58:19 | 0 | |||
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Pavlovia Resource Report Resource Website 100+ mentions |
Pavlovia (RRID:SCR_023320) | software resource, web application | Web application as repository and launch platform for Psychopy experiments and other open-source tools. | Open Science Tools Limited, Psychopy experiments, repository and launch platform, behavioural sciences, | Wellcome Trust ; University of Nottingham; Nottingham; United Kingdom |
Restricted | SCR_023320 | 2026-02-12 09:47:37 | 191 | ||||||||||
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mousebrain.org Resource Report Resource Website 100+ mentions |
mousebrain.org (RRID:SCR_016999) | data or information resource, atlas | 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. | Atlas, brain cell, cell type, single cell RNA seq data, taxon, tissue, gene, marker, anatomical location, data | has parent organization: Karolinska Institute; Stockholm; Sweden | Knut and Alice Wallenberg Foundation ; Swedish Foundation for Strategic Research ; Wellcome Trust ; Swedish Research Council ; SSF ; Cancerfonden ; EU ; Hjärnfonden ; SFO Strat Regen ; European Research Council ; Ollie and Elof Ericssons Foundation ; Åke Wiberg Foundation |
PMID:30096314 | Free, Available for download, Freely available | SCR_018356 | SCR_016999 | Linnarsson lab Mouse Brain Atlas | 2026-02-12 09:46:27 | 111 | ||||||
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Genes to Cognition - Biological Resources Resource Report Resource Website 1+ mentions |
Genes to Cognition - Biological Resources (RRID:SCR_001675) | G2C Biological Resources | biomaterial supply resource, organism supplier, material resource | Biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6J | transgenic, mutant mouse strain, c57bl/6j, 129s5, transgenic mouse line, vector, es cell line, transgenic mouse |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
Free, Freely Available | nif-0000-10163 | http://www.genes2cognition.org/mice_resources/ | http://www.genes2cognition.org/resources.html | SCR_001675 | G2C Mice Resources, G2C Biological Resources, G2C-Biological Resources, G2C - Biological Resources | 2026-02-13 10:54:54 | 2 | ||||
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Flybrain at Stanford Resource Report Resource Website 1+ mentions |
Flybrain at Stanford (RRID:SCR_001877) | Flybrain(at)Stanford, FlybrainatStanford | data processing software, image collection, data or information resource, software application, software resource, image analysis software | Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer. | brain, cell, neuron, neuropil, olfactory, pheromone, confocal image, antennal lobe, axon trace, forum, neuronal tracing, image registration tool, analysis script, single-cell labeling, image registration, mushroom body, lateral horn, olfactory receptor neuron | has parent organization: Stanford University; Stanford; California | Wellcome Trust WT076726; Damon Runyon Cancer Research Foundation DRG-1766-03; NIAAA AA05965; NIAAA AA13521; NIDCD R01-DC005982 |
PMID:17382886 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10437 | SCR_001877 | Flybrain (at) Stanford - A warped brain is a good thing, Flybrain (at) Stanford | 2026-02-13 10:54:56 | 6 | |||||
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OME-TIFF Format Resource Report Resource Website |
OME-TIFF Format (RRID:SCR_002636) | OME-TIFF | data or information resource, narrative resource, standard specification | A standardized file format for multidimensional microscopy image data. OME-TIFF maximizes the respective strengths of OME-XML and TIFF. It takes advantage of the rich metadata defined in OME-XML while retaining the pixel structure in multi-page TIF format for compatibility with many image-processing applications. An OME-TIFF dataset has the following characteristics: * Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible. * A complete OME-XML metadata block describing the dataset is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a dataset are misplaced, the metadata remains intact. * The OME-XML metadata block may contain anything allowed in a standard OME-XML file. * OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent files, instead of encoding pixels as base64 chunks within the XML. Since TIFF is an image format, it makes sense to only use OME-TIFF as opposed to OME-XML, when there is at least one image plane. | microscopy, format, archiving, data management, annotation, mark up, metadata standard, standard, tiff, ome-xml |
is listed by: FORCE11 is related to: JCB DataViewer is related to: Cell Image Library (CIL) is related to: HMS LINCS Database is related to: Stowers Original Data Repository is related to: Bio-Formats has parent organization: OME - Open Microscopy Environment |
Wellcome Trust 68046 | PMID:15892875 | Free, Available for download, Freely available | nlx_156061 | SCR_002636 | OME-TIFF: Open Microscopy Environment Tagged Image File Format, Open Microscopy Environment Tagged Image File Format | 2026-02-13 10:55:05 | 0 | |||||
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International HapMap Project Resource Report Resource Website 5000+ mentions |
International HapMap Project (RRID:SCR_002846) | HapMap | data or information resource, experimental protocol, narrative resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project. | genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosome, bio.tools |
is used by: BioSample Database at EBI is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SNAP - SNP Annotation and Proxy Search is related to: Haploview is related to: NHGRI Sample Repository for Human Genetic Research is related to: DistiLD - Diseases and Traits in LD is related to: SNP at Ethnos is related to: GBrowse has parent organization: NCBI |
Chinese Academy of Sciences ; Chinese Ministry of Science and Technology ; Delores Dore Eccles Foundation ; Genome Canada ; Genome Quebec ; Hong Kong Innovation and Technology Commission ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; National Natural Science Foundation of China ; SNP Consortium ; University Grants Committee of Hong Kong ; Wellcome Trust ; W. M. Keck Foundation ; NIH |
PMID:14685227 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02940, biotools:int_hapmap_project, r3d100011835, OMICS_00273 | http://www.hapmap.org/ https://bio.tools/int_hapmap_project https://doi.org/10.17616/R3H06Q |
http://snp.cshl.org | SCR_002846 | HapMap Project | 2026-02-13 10:55:08 | 6817 | |||
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HumanIslets Resource Report Resource Website 1+ mentions |
HumanIslets (RRID:SCR_025719) | data or information resource, portal, project portal | 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. | human islet data, data access and analysis, molecular profiles, islet function, donor phenotypes, metabolism, diabetes | Canadian Institutes of Health Research ; BCCHRI Child Health Integrative Partnership Strategy Funding ; NIDDK U01 DK 120447; NIDDK U01-DK-123716; NIDDK U01-DK105535; NIDDK U01-DK085545; NIDDK UM-1DK126185; Wellcome Trust ; UBC Life Sciences Institute ; Canada Foundation for Innovation ; BC Knowledge Development Fund ; Genome Canada |
PMID:38948734 | Free, Freely available | SCR_025719 | 2026-02-12 09:49:03 | 9 | |||||||||
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Structural Genomics Consortium Resource Report Resource Website 50+ mentions |
Structural Genomics Consortium (RRID:SCR_003890) | SGC | data or information resource, organization portal, portal, consortium | Charity registered in United Kingdom whose mission is to accelerate research in new areas of human biology and drug discovery.Not for profit, public-private partnership that carries out basic science of relevance to drug discovery whose core mandate is to determine 3D structures on large scale and cost effectively targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets. | basic science, drug discovery, drug, structural genomics, genomics, 3d structure, protein, human parasite, drug target, structure, human protein, protocol, phylogenetic tree, histone tail, high-throughput protein crystallization, lex bubbling system, reagent, epigenetic probe, antibody, vector, plasmid, construct |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Addgene uses: GenBank is related to: AbbVie is related to: Canada Foundation for Innovation is related to: Canadian Institutes of Health Research is related to: Genome Canada is related to: Janssen Research and Development is related to: Ontario Ministry of Economic Development Employment and Infrastructure is related to: Pfizer Animal Genetics is related to: Wellcome Trust has parent organization: University of Oxford; Oxford; United Kingdom has parent organization: University of Toronto; Ontario; Canada |
Cancer, Diabetes, Obesity, Psychiatric disorder, Altzheimer | AbbVie ; Boehringer Ingelheim ; Canada Foundation for Innovation ; Canadian Institutes of Health Research ; Genome Canada ; GlaxoSmithKline ; Janssen ; Lilly Canada ; Novartis Research Foundation ; Ontario Ministry of Economic Development Employment and Infrastructure ; Pfizer ; Takeda ; Wellcome Trust |
Restricted | nlx_158220 | SCR_003890 | Structural Genomics Consortium | 2026-02-13 10:55:19 | 61 | |||||
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PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions |
PDBe - Protein Data Bank in Europe (RRID:SCR_004312) | PDBe | data repository, storage service resource, data or information resource, service resource, database | The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules. | x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline |
European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4 |
PMID:21045060 PMID:21460450 PMID:19858099 |
r3d100012791, biotools:pdbe, nlx_32372 | https://bio.tools/pdbe https://doi.org/10.17616/R3J226 |
SCR_004312 | Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database | 2026-02-13 10:55:24 | 52 | |||||
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GeneDB Lmajor Resource Report Resource Website 1+ mentions |
GeneDB Lmajor (RRID:SCR_004613) | GeneDB_Lmajor, GeneDB Lmajor, GeneDB L. major, | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries. | genome, gene, rna gene, rna, pseudogene, protein-coding, function, host-pathogen interaction, interaction, proteolytic enzyme, glycoconjugate, sequence annotation |
is used by: NIF Data Federation is related to: AmiGO is related to: TriTrypDB has parent organization: GeneDB |
Wellcome Trust | PMID:16020728 | nlx_60997 | SCR_004613 | Leishmania major strain Friedlin, Leishmania major strain Friedlin homepage on GeneDB, GeneDB Leishmania major, Leishmania major strain Friedlin on GeneDB | 2026-02-13 10:55:28 | 7 | ||||||
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Eukaryotic Pathogen Database Resources Resource Report Resource Website 10+ mentions |
Eukaryotic Pathogen Database Resources (RRID:SCR_004512) | EuPathDB, ApiDB | data repository, storage service resource, web service, portal, data or information resource, service resource, data access protocol, software resource, topical portal, database | EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens. | Data, Apicomplexa, parasitic, protozoa, Cryptosporidium, Plasmodium, Toxoplasma, database, pathogen, dataset, FASEB list |
is listed by: NIH Data Sharing Repositories is related to: ApiDots is related to: NIH Data Sharing Repositories is related to: AmoebaDB is related to: MicrobiomeDB has parent organization: University of Georgia; Georgia; USA is parent organization of: FungiDB is parent organization of: TriTrypDB is parent organization of: PlasmoDB is parent organization of: ApiDB ToxoDB is parent organization of: ApiDB CryptoDB |
malaria, kala-azar, african sleeping sickness, chagas disease, aids-related, aids | NIAID ; Bill and Melinda Gates Foundation ; Wellcome Trust |
PMID:19914931 PMID:17098930 |
nlx_49652, r3d100011557 | http://ApiDB.org https://doi.org/10.17616/R3X06F |
SCR_004512 | EuPath, Apicomplexan Database Resources, Eukaryotic Pathogen Genome Database, EuPathDB, Eukaryotic Pathogen Database Resources, ApiDB, Apicomplexan Database | 2026-02-13 10:55:27 | 39 | ||||
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Seq-Gen Resource Report Resource Website 100+ mentions |
Seq-Gen (RRID:SCR_014934) | software resource, simulation software, software application | 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. | simulator, simulation software, molecular evolution, nucleotide, amino acid, sequence, phylogeny, phylogenetic tree |
is listed by: Debian is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; BBSRC ; Fogarty ; The Royal Society |
DOI:10.1093/bioinformatics/13.3.235 | Available for download | OMICS_15373 | https://sources.debian.org/src/seq-gen/ | SCR_014934 | 2026-02-13 10:57:28 | 155 | ||||||
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IUPHAR/BPS Guide to Pharmacology Resource Report Resource Website 1000+ mentions |
IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) | IUPHAR Database, IUPHAR-DB, IUPHAR GPCR, IUPHAR RECEPTOR | portal, data or information resource, narrative resource, database, standard specification | Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. | pharmacology, drug discovery, portal, guide, physiology, molecular structure, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: NC-IUPHAR |
Wellcome Trust | PMID:21087994 | nif-0000-03056, biotools:iuphar-db, r3d100013308 | https://bio.tools/iuphar-db https://doi.org/10.17616/R31NJMRG |
http://www.iuphar-db.org | SCR_013077 | International Union of Pharmacology Database, International Union of Basic and Clinical Pharmacology Database | 2026-02-13 10:57:03 | 2259 | ||||
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Enzyme Structures Database Resource Report Resource Website 1+ mentions |
Enzyme Structures Database (RRID:SCR_007125) | EC->PDB, EC-PDB | data or information resource, image collection, database | Database of known enzyme structures that have been deposited in the Protein Data Bank (PDB). The enzyme structures are classified by their E.C. number of the ENZYME Data Bank. Browse the classification hierarchy or enter an EC number or search-string. There are currently 45,638 PDB-enzyme entries in the PDB (as at 23 February, 2013) involving 38,109 separate PDB files - some files having more than one E.C. number associated with them. | enzyme, structure, gold standard |
is related to: PDBsum is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute |
Wellcome Trust | nlx_30980 | SCR_007125 | 2026-02-13 10:56:01 | 3 | ||||||||
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Gene3D Resource Report Resource Website 100+ mentions |
Gene3D (RRID:SCR_007672) | Gene3D | data repository, storage service resource, web service, data or information resource, service resource, data access protocol, software resource, database | A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein domain, protein, protein superfamily, hidden markov model, structural domain, genome, sequence, domain assignments, protein structure, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
NIH ; Wellcome Trust ; European Union FP6 ENFIN LSHG-CT-2003-503265; European Union FP6 ENFIN LSHG-CT-2004-512092; European Union FP6 ENFIN LSHG-CT-2005-518254; DOE DE-AC02-065CH11357 |
PMID:19906693 PMID:18032434 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02877, biotools:gene3d | https://bio.tools/gene3d | SCR_007672 | Gene3D - Structures assigned to Genomes | 2026-02-13 10:56:08 | 272 | ||||
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Human Ageing Genomic Resources Resource Report Resource Website 50+ mentions |
Human Ageing Genomic Resources (RRID:SCR_007700) | HAGR | data or information resource, software resource, software toolkit, database | Collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses. A major resource in HAGR is GenAge, which includes a curated database of genes related to human aging and a database of ageing- and longevity-associated genes in model organisms. Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on aging, longevity, and life history that is ideal for the comparative biology of aging. GenDR is a database of genes associated with dietary restriction based on genetic manipulation experiments and gene expression profiling. Other projects include evolutionary studies, genome sequencing, cancer genomics, and gene expression analyses. The latter allowed them to identify a set of genes commonly altered during mammalian aging which represents a conserved molecular signature of aging. Software, namely in the form of scripts for Perl and SPSS, is made available for users to perform a variety of bioinformatic analyses potentially relevant for studying aging. The Perl toolkit, entitled the Ageing Research Computational Tools (ARCT), provides modules for parsing files, data-mining, searching and downloading data from the Internet, etc. Also available is an SPSS script that can be used to determine the demographic rate of aging for a given population. An extensive list of links regarding computational biology, genomics, gerontology, and comparative biology is also available. | gene, gerontology, human, model, senescence, genomics, longevity, genetics, perl, spss, demographic analysis, genome, evolution, gene expression, model organism, human aging, dietary restriction, genetic manipulation |
has parent organization: University of Liverpool; Liverpool; United Kingdom is parent organization of: anage is parent organization of: GenAge |
Aging, Cancer | Ellison Medical Foundation ; Wellcome Trust ME050495MES; European Union FP7 Health Research HEALTH-F4-2008-202047 |
PMID:23193293 | GNU General Public License, Creative Commons Attribution v3 Unported License | nif-0000-02938, r3d100011871 | https://doi.org/10.17616/R34W81 | SCR_007700 | 2026-02-13 10:56:03 | 67 |
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