Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-08-15 11:24:17 | 39 | ||||||
|
Flash Gviewer Resource Report Resource Website 1+ mentions |
Flash Gviewer (RRID:SCR_012870) | Flash GViewer | software resource | Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool | visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Medical College of Wisconsin; Wisconsin; USA |
Free for academic use | nlx_149333 | http://gmod.org/flashgviewer | SCR_012870 | 2026-08-15 11:24:50 | 2 | |||||||
|
GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | analysis service resource, data analysis service, production service resource, service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-08-20 09:27:05 | 114 | ||||||
|
SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | analysis service resource, data analysis service, production service resource, service resource, software resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SeqAnt - Sequence Annotator | 2026-08-21 12:37:31 | 2 | ||||||
|
GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-08-21 12:37:37 | 4535 | |||||
|
GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | 2026-08-21 12:37:46 | 1 | |||||
|
NEMBASE Resource Report Resource Website 10+ mentions |
NEMBASE (RRID:SCR_006070) | NEMBASE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets. | nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigene, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: nematodes.org |
Wellcome Trust ; Hospital for Sick Children ; BBSRC ; MRC ; NERC |
PMID:21550347 PMID:14681449 |
Public | nlx_151476, biotools:nembase4 | https://bio.tools/nembase4 | SCR_006070 | NEMBASE4, NEMBASE4 - Nematode Transcriptome Analyses | 2026-08-21 12:37:55 | 25 | ||||
|
Integrated Animals Resource Report Resource Website |
Integrated Animals (RRID:SCR_001421) | biomaterial supply resource, material resource, organism supplier | Integrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish). | non human animal, mutant, database, integrated, nif, FASEB list |
uses: Mouse Genome Informatics (MGI) uses: Beta Cell Biology Consortium uses: Zebrafish Information Network (ZFIN) uses: International Mouse Strain Resource uses: Bloomington Drosophila Stock Center uses: Rat Genome Database (RGD) uses: Zebrafish International Resource Center uses: Ambystoma Genetic Stock Center uses: Kyoto Stock Center uses: FlyBase uses: Mutant Mouse Resource and Research Center uses: National Swine Resource and Research Center uses: National Xenopus Resource uses: CWRU In Vivo Animal Facilities uses: Sperm Stem Cell Libraries for Biological Research uses: Tetrahymena Stock Center uses: WormBase uses: Xiphophorus Genetic Stock Center is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) has parent organization: Integrated |
Free, Freely Available | nif-0000-08137 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_154697-1 http://neuinfo.org/nif/nifgwt.html?query=nif-0000-08137, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nif-0000-08137-1 | SCR_001421 | NIF Animals, NIF Integrated Animals, Integrated Animal | 2026-08-21 12:36:23 | 0 | |||||||
|
Ancora Resource Report Resource Website 10+ mentions |
Ancora (RRID:SCR_001623) | Ancora | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements. | genome, highly conserved noncoding element, noncoding element, regulatory gene, regulatory domain, regulatory element, developmental regulatory gene, evolution, enhancer |
is related to: MONARCH Initiative has parent organization: University of Bergen; Bergen; Norway |
Research Council of Norway ; Bergen Research Foundation ; Sars Centre |
PMID:18279518 | Free, Freely available | nlx_153891 | SCR_001623 | Atlas of Noncoding Conserved Regions in Animals | 2026-08-21 12:36:32 | 20 | |||||
|
High Throughput Genomic Sequences Division Resource Report Resource Website 1+ mentions |
High Throughput Genomic Sequences Division (RRID:SCR_002150) | HTG Sequences, HTG Division | data or information resource, data repository, database, service resource, storage service resource | Database of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. It was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. Sequences are prepared for submission by using NCBI's software tools Sequin or tbl2asn. Each center has an FTP directory into which new or updated sequence files are placed. Sequence data in this division are available for BLAST homology searches against either the htgs database or the month database, which includes all new submissions for the prior month. Unfinished HTG sequences containing contigs greater than 2 kb are assigned an accession number and deposited in the HTG division. A typical HTG record might consist of all the first-pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, which together make up more than 2 kb and contain one or more gaps. A single accession number is assigned to this collection of sequences, and each record includes a clear indication of the status (phase 1 or 2) plus a prominent warning that the sequence data are unfinished and may contain errors. The accession number does not change as sequence records are updated; only the most recent version of a HTG record remains in GenBank. | gap, gene, accession, arabidopsis, bac, biological, c. elegans, clone, contig, cosmid, dna, genomic, high-throughput, homology, homo sapiens, invertebrate, nematode, nucleotide, p1, plant, primate, sequence, structure, taxonomy, yac, genome, sequence, nucleotide sequence, dna sequence, nucleotide, dna, gold standard |
is related to: GenBank has parent organization: NCBI |
PMID:9331365 | Free, Freely available | nif-0000-20943 | SCR_002150 | HTG GenBank Division, HTG database, NCBI High-Throughput Genomic Sequences, HTG Sequence, High-Throughput Genomic Sequences | 2026-08-21 12:36:36 | 5 | ||||||
|
Protein Lounge Resource Report Resource Website 10+ mentions |
Protein Lounge (RRID:SCR_002117) | ProteinLounge | analysis service resource, data analysis service, data or information resource, database, narrative resource, production service resource, service resource, training material | Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal. | gene, antigen, bioinformatics, kinase, life science, peptide, phosphatase, signal transduction pathway, sirna, systems biology, protein, biology, cellular network, protein interaction, cell signaling, cell survival, apoptosis, peptide-antigen, kinase-phosphatase, image, pathway | Restricted | nif-0000-20903 | SCR_002117 | Protein Lounge - Redefining Biology | 2026-08-21 12:36:35 | 31 | ||||||||
|
NLSdb: a database of nuclear localization signals Resource Report Resource Website 1+ mentions |
NLSdb: a database of nuclear localization signals (RRID:SCR_003273) | NLSdb | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree | nuclear localization signal, nuclear protein, nucleus, motif, predict, protein | has parent organization: Columbia University; New York; USA | NIGMS 1-P50-GM62413-01; NSF DBI-0131168 |
PMID:12520032 | Free for academic use, Acknowledgement requested, All others should inquire about a commercial license | nif-0000-03191 | http://cubic.bioc.columbia.edu/db/NLSdb/ | SCR_003273 | NLSdb - a database of nuclear localization signals | 2026-08-21 12:37:05 | 4 | ||||
|
Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
European Molecular Biology Laboratory ; European Union FP6 ENFIN LSHG-CT-2005-518254; NHGRI P41 HG003751; NIGMS GM080223; NIGMS R01 GM100039; Ontario Research Fund |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-08-21 12:37:01 | 4810 | |||||
|
GeneSpeed- A Database of Unigene Domain Organization Resource Report Resource Website |
GeneSpeed- A Database of Unigene Domain Organization (RRID:SCR_002779) | analysis service resource, data analysis service, data or information resource, database, production service resource, resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Database and customized tools to study the PFAM protein domain content of the transcriptome for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans tethered to both a genomics array repository database and a range of external information resources. GeneSpeed has merged information from several existing data sets including the Gene Ontology Consortium, InterPro, Pfam, Unigene, as well as micro-array datasets. GeneSpeed is a database of PFAM domain homology contained within Unigene. Because Unigene is a non-redundant dbEST database, this provides a wide encompassing overview of the domain content of the expressed transcriptome. We have structured the GeneSpeed Database to include a rich toolset allowing the investigator to study all domain homology, no matter how remote. As a result, homology cutoff score decisions are determined by the scientist, not by a computer algorithm. This quality is one of the novel defining features of the GeneSpeed database giving the user complete control of database content. In addition to a domain content toolset, GeneSpeed provides an assortment of links to external databases, a unique and manually curated Transcription Factor Classification list, as well as links to our newly evolving GeneSpeed BetaCell Database. GeneSpeed BetaCell is a micro-array depository combined with custom array analysis tools created with an emphasis around the meta analysis of developmental time series micro-array datasets and their significance in pancreatic beta cells. | molecular neuroanatomy resource, drosophila melanogaster, genome, caenorhabditis elegans, c. elegans, genomics, homo sapiens, mus musculus, protein domain, transcriptome |
is related to: Gene Ontology is related to: InterPro is related to: Pfam is related to: UniGene has parent organization: University of Colorado Denver; Colorado; USA |
NIDDK P30DK57516; NIDDK DK61248 |
PMID:17132830 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02887 | http://genespeed.uchsc.edu/, http://genespeed.ccf.org | SCR_002779 | GeneSpeed Database | 2026-08-21 12:36:52 | 0 | |||||
|
Aging Genes and Interventions Database Resource Report Resource Website 1+ mentions |
Aging Genes and Interventions Database (RRID:SCR_002701) | AGEID | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link. | allele, strain, gene function, phenotype, mutant, homolog, mutation, degeneration, gene, intervention, life-span |
is used by: Aging Portal is used by: NIF Data Federation has parent organization: University of Washington; Seattle; USA |
Aging, Age-related neurological disease, Neurological disease | Ellison Medical Foundation | PMID:12044961 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23326 | http://sageke.sciencemag.org/highlights/gidb/ | SCR_002701 | Aging Genes DB, Aging Genes Database, Genes/Interventions Database | 2026-08-21 12:36:50 | 2 | |||
|
FlyMine Resource Report Resource Website 100+ mentions |
FlyMine (RRID:SCR_002694) | FlyMine | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API | anopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publication, FASEB list |
is related to: FlyBase is related to: UniProt is related to: Ensembl is related to: InterPro is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Tree families database is related to: IntAct is related to: Gene Ontology is related to: GOA is related to: ArrayExpress is related to: REDfly Regulatory Element Database for Drosophilia is related to: KEGG is related to: Reactome has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust 067205; NHGRI |
PMID:17615057 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02845 | SCR_002694 | 2026-08-21 12:36:50 | 107 | ||||||
|
I2D Resource Report Resource Website 10+ mentions |
I2D (RRID:SCR_002957) | I2D | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available. | interaction, prediction, protein-protein interaction, high-throughput, model organism, mammal, eukaryote, visualization, interolog, protein |
is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: University of Toronto; Ontario; Canada |
National Science and Engineering Research Council RGPIN 203833-02; NIGMS P50-GM62413 |
PMID:17535438 PMID:15657099 |
Free, Available for download, Freely available | nif-0000-03005, r3d100010675 | https://doi.org/10.17616/R3BG8R | SCR_002957 | Interologous Interaction Database, OPHID, I2D - Interologous Interaction Database | 2026-08-21 12:36:51 | 23 | ||||
|
Wnt homepage Resource Report Resource Website 10+ mentions |
Wnt homepage (RRID:SCR_000662) | Wnt homepage | data or information resource, portal, topical portal | A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year. | wnt signaling, wnt, wnt protein, wnt pathway, signaling, pathway, method, protein, reagent, bibliography | has parent organization: Stanford University; Stanford; California | Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156863 | SCR_000662 | the Wnt homepage | 2026-08-21 12:36:14 | 13 | ||||||
|
Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, data set, image repository, production service resource, service resource, software resource, source code, storage service resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01 |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me, http://www.nitrc.org/projects/ocp/ | SCR_004232 | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-08-21 12:37:17 | 7 | ||||
|
BiblioSpec Resource Report Resource Website 10+ mentions |
BiblioSpec (RRID:SCR_004349) | data or information resource, database, software resource | BiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra. This suite of software tools is for creating and searching MS/MS peptide spectrum libraries. BiblioSpec is available free of charge for noncommercial use through an interactive web-site at http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/bibliospec.php The BiblioSpec package contains the following programs: * BlibBuild creates a library of peptide MS/MS spectra from MS2 files. * BlibFilter removes redundant spectra from a library. * BlibSearch searches a spectrum library for matches to query spectra, reporting the results in an SQT file. In addition to the primary programs, the following auxiliary programs are available: * BlibStats writes summary statistics describing a library. * BlibToMS2 writes a library in MS2 file format. * BlibUpdate adds, deletes, or annotates spectra. * BlibPpMS2 processes spectra (bins peaks, removes noise, normalizes intensity) as done in BlibSearch and prints the resulting spectra to a text file. Several reference libraries are available for download. These libraries are updated regularly and are for use under the Linux operating system. You will find libraries for * Escherichia coli * Saccharomyces cerevisiae * Caenorhabditis elegans | has parent organization: University of Washington; Seattle; USA | PMID:18428681 | nlx_36841 | SCR_004349 | 2026-08-21 12:37:24 | 29 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the PRECISE-TBI Resources search. From here you can search through a compilation of resources used by PRECISE-TBI and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that PRECISE-TBI has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on PRECISE-TBI then you can log in from here to get additional features in PRECISE-TBI such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into PRECISE-TBI you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
