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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.

(last updated: Oct 12, 2019)

Physical Resource or Software Tool Software

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
NIF Data FederationResource, service resource, portal, data or information resourceService that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below.semantics, neuroscience, animal, annotation, antibody, biospecimen, brain activation foci, clinical trial, connectivity, dataset, disease, drug, grant, image, microarray, model, multimedia, negative data, pathway, people, plasmid, registry, software, brain region, cell, gene, molecule, multi-level, nervous system, nervous system function, modelSCR_004834(NIF Data Federation, RRID:SCR_004834)Neuroscience Information Framework NIDA, NIH Blueprint for Neuroscience Research, U.S. Department of Health and Human Servicesrelated to: International Mouse Strain Resource, Internet Brain Volume Database, Resource Identification Portal, Rat Genome Database (RGD), VISTA Enhancer Browser, NIH Human Pluripotent Stem Cell Registry, Zebrafish International Resource Center, Bloomington Drosophila Stock Center, Journal of Comparative Neurology Antibody database, used by: SciCrunch, NIDDK Information Network, uses: MNI Podcasts, Educational Resources in Neuroscience, Mind Hacks, BAMS Nested Regions, Indeed, NINDS Disorder Index, Drug Design Data Resource, PubMed Health, This Week In Science, Science Talk, BAMS Connectivity, A Lady Scientist, Psychology Corner, Wired Science, CENtral Science, RetractionWatch.com, The Guardian: Science Weekly, H2SO4Hurts, 60-Second Mind, PLoS Blogs, Monarch Initiative, Clarity resources, Open Source Brain, Diabetic Complications Consortium , Integrated Animals, Kawasaki Disease Dataset, EEGbase, Integrated Models, Lifespan Observations Database, NIF Web Services, NIF Blog, ATCC, Cerebellar Platform, Brain Machine Interface Platform, Rafael Yustes Laboratory, ASAP, NIH VideoCasting, NIDA Data Share, Neurofed, Candida Genome Database, Addgene, ASPGD, Glomerular Activity Response Archive, WikiPathways, AmiGO, NeuroMorpho.Org, Cell Centered Database, Integrated, Community Structure-Activity Resource, ClinicalTrials.gov, Ensembl, GeneNetwork, Avian Brain Circuitry Database, EcoCyc, Entrez Gene, Zebrafish Information Network, Arredondo ANT fNIRS dataset1, Grants.gov, T3DB, Simtk.org, PharmGKB, DrugBank, Aging Genes and Interventions Database, Gene Expression Nervous System Atlas, SumsDB, bioDBcore, BioNumbers, Gene Ontology, Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat, Gramene, Retina Project, HomoloGene, ArrayExpress, Journal of Visualized Experiments, Allen Mouse Brain Atlas, Gene Weaver, Visiome Platform, Developmental Therapeutics Program, NeuroMab, WormBase, NeuronDB, Integrated Grants, studyforrest.org, BrainInfo, Mouse Phenome Database (MPD), NCBI Taxonomy, NCBI Protein, Psychoactive Drug Screening Program Ki Database, Nuclear Receptor Signaling Atlas , Brede Database, NeuroImaging Tools and Resources Collaboratory (NITRC), Mouse Genome Informatics Transgenes, Reactome, Cell Image Library (CIL), BAMS Cells, Synapse Web, Integrated Videos, NeuroVault, Royal College of Psychiatrists Podcasts, WU-Minn HCP 500 Subjects MR and MEG Release, Data.gov Science and Research Data Catalog, NITRC-IR, One Mind Biospecimen Bank Listing, Integrated Brain Gene Expression, BrainSpan: Exon microarray summarized to genes, All In The Mind, Scientific American Cross-Check, PubChem, NeuroPod, BrainSpan: RNA-Seq exons, Health.Data.gov, Biointeractive, UniProtKB, Gray Matters, dkCOIN , Brain Science Podcast, NIGMS Human Genetic Cell Repository, DISCO, GeneDB Lmajor, TAIR, ScienceNOW, Daily Scan, SGD, Integrated Software, BrainPod, GeneDB Tbrucei, MPO, PANTHER, BrainSpan: Exon microarray summarized to probe sets, Neurology Podcast, Integrated Disease, VMD, UCSF Laboratory for Visual Neuroscience, NIMH Chemical Synthesis and Drug Supply Program, NIH Neuroscience Microarray Consortium, SGN, Protocol Online - Your labs reference book, Integrated Podcasts, BrainSpan: RNA-Seq exons summarized to genes, OpenNeuro, National Academy of Sciences Podcasts, Beta Cell Biology Consortium , Naturejobs, Scientific American Guest Blog, jobs.ac.uk, New Scientist Jobs, Science Careers, Access-ScienceJobs.co.uk, ScienceBlogs: Life Science, ScienceBlogs: Brain and Behavior, TheScienceJobs.com, Nature Network Blogs, The Guardian: Science, LabSpaces, ScienceBlogs: Medicine and Health, Scientific American Observations, Scientific American Bering in Mind, QUEST, Daring Nucleic Adventures - genegeek, Oxford Science Blog, Sciblogs, New York Times - Well, SciLogs, Cassandras Tears, BioPortfolio, Now at NEJM, 1000 Functional Connectomes Project, Integrated Jobs, Integrated Blogs, JCVI CMR, SciCrunch Registry, Neuroskeptic, CRCNS, Expression Atlas of the Marmoset, IXI dataset, Integrated Auto-Extracted Annotation, EU Clinical Trials Register, Integrated Clinical Trials, Human Brain Atlas, goCognitive, Law and Neuroscience, IMPC, ClinVar, Integrated Gene-Disease Interaction, Human Phenotype Ontology Annotations, XNAT Central, neuroelectro, Integrated Nervous System Connectivity, Antibody Registry, OMIA - Online Mendelian Inheritance in Animals, OMIM, Science Podcast, Mouse Genome Informatics (MGI), Monster, NCBI, Wired Science Blogs, F1000 Posters, Neurophilosophy, Comparative Toxicogenomics Database, FlyBase, GeneReviews, GeneDB Pfalciparum, Naturally Selected, PomBase, Pseudomonas Genome Database, The Guardian: Science Videos, Orphanet, DictyBase, PeptideAtlas, NeuroSynth, neuropathology blog, Genomes Unzipped, National Institutes of Health Research Portfolio Online Reporting Tool, BrainMaps.org, It Takes 30, Gait in Parkinson's Disease, Physiobank, Gait Dynamics in Neuro-Degenerative Disease Data Base, American Journal of Psychiatry Podcasts, Neurodatabase.org, Brain Architecture Management System, RanchoBiosciences, ModelDB, CoCoMac, Olfactory Bulb Odor Map DataBase (OdorMapDB), Gene Expression Omnibus, Caenorhabditis Genetics Center, Labome, Open Access Series of Imaging Studies, BioGRID, Olfactory Receptor DataBase, T1DBase , Gemma, CellML Model Repository, ResearchCrossroads, Biocompare, BioNOT, Hays, Research Blogging, Discover Magazine, PolygenicBlog, Kawasaki Disease Dataset2, Allen Mouse Brain Connectivity Atlas, Integrated Manually Extracted Annotation, Roadmap Epigenomics Project, Integrated Cell Lines, National Mouse Metabolic Phenotyping Centers , Mendelspod, Integrated Snippets, Integrated Datasets, Nature Podcast, GWAS: Catalog of Published Genome-Wide Association Studies, KEGG, USC Multimodal Connectivity Database, Inside NIA: A Blog for Researchers, Research Collaboratory for Structural Bioinformatics Protein Data Bank, NIF Registry Automated Crawl Data, Genetic Analysis Software, anage, Intestinal Stem Cell Consortium , Animal QTLdb, elements of morphology, Human Life-Table Database, Clinical Genomic Database, NIDDK Central Repository, listed by: 3DVC, lists: AutDB, Drug Related Gene Database, Gene Ontology Tools, CHEBILast checked downnlx_81822http://neuinfo.org/nif/nifgwt.html?query=*
Genes to Cognition: Neuroscience Research ProgrammeResource, blog, topical portal, software application, narrative resource, portal, software resource, training material, data or information resourceA neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers.electrophysiological, es cell, functional, gene, gene-target vector, genetic, 1295s, allele, antibody, behavior, behavioral, brain, c57bl/6j, central nervous system, clone, cognition, computation, connection, deletion, disease, disorder, dlg3, dlg4, domain, genomic, guanylate kinase, hprt gene, hras1, human, knockout, learning, mechanism, memory, model, molecular, mouse, mutation, network, neuron, neuroscience, nmda receptor complex, pathogenesis, phenotyping, protein, proteomics, ptk2, strain, synapse, synaptic plasticity, syngap1, transgenic, modelSCR_007121(Genes to Cognition: Neuroscience Research Programme, RRID:SCR_007121)Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome Trustlisted by: 3DVCLast checked downnif-0000-10235
EyeBrowseResource, data set, data or information resourceEyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.est, expressed sequence tag, eye, gene, genome, cataract, cdna, chicken, clone, cluster, cornea, cornea disease, cow, data, disease, dog, human, locus, maturation, mouse, myopia, photoreceptor, rat, retina, rhesus, rna polymerase-ii, tag, zebrafish, data analysis software, eye tracking deviceSCR_008000(EyeBrowse, RRID:SCR_008000)University of California at Santa Cruz; California; USA Retinal disease, Cataract, Myopia, Cornea diseaseNEIBanklisted by: 3DVCLast checked upnif-0000-07733
Bacterial GenomesResource, data analysis software, data processing software, database, software application, software resource, data or information resourceThis website includes a list of projects that the Sanger Institute is currently working on or completed. All projects consist of the genomic sequencing of different bacteria. Each description of the bacteria includes its classification, a description, and the types of diseases that the bacteria is likely to cause. The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing users to search the sequences with their own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. The primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences.bacteria, bacterial, classification, description, disease, genomic, model, organism, pathogen, sequence, sequencing, modelSCR_008141(Bacterial Genomes, RRID:SCR_008141)Wellcome Trust Sanger Institute; Hinxton; United Kingdom listed by: 3DVCLast checked upnif-0000-20963
U.S. Pig Genome ProjectResource, topical portal, data or information resource, portal, databaseDatabase and resources on the pig genome.embryo, embryonic, environmental, exercise, exposure, fat, feed, feeding, fibroblast, food, foot and mouth disease, function, genetic, acute, additive, alcohol, alcoholism, atherosclerosis, bed, behavior, biological, bone, breed, cancer, cell, chronic, clone, degenerative, density, deposition, dermal, developmental, diabetes, dietary, digestive, disease, genome, genomic, growth, habit, healing, human, hypertension, kidney, mammal, map, melanoma, metabolism, nephropathy, nuclear, nutrition, obesity, omnivore, organ, organism, parenteral, pathogen, pattern, phenotype, phenotypic, physiology, pig, pollutant, population, porcine, prenatal, pulmonary, reproductive, respiratory, retinal, sex, shock, size, social, somatic, structure, swine, taxon, technique, tissue, tobacco, transplantation, variation, vascular, warfare, xenobiotic, modelSCR_008151(U.S. Pig Genome Project, RRID:SCR_008151)listed by: 3DVCLast checked upnif-0000-20986
DisGeNETResource, data or information resource, databaseDatabase and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature.gene, disease, gene-disease association, gene-disease ontology, gene-disease text mining, text mining, genotype-phenotype, rdf, genotype, phenotype, gene-disease, variant-diseaseSCR_006178(DisGeNET, RRID:SCR_006178)Pompeu Fabra University; Barcelona; Spain EFPIA, Elixir-Excelerate, European Union Horizon 2020, European Union Seventh Framework Programme, Innovative Medicines Initiative Joint Undertaking, Instituto de Salud Carlos III-Fondo Europeo de Desarrollo Regionalused by: HmtPhenome, uses: Comparative Toxicogenomics Database, Genetic Association Database, Universal Protein Resource, Mouse Genome Informatics Database, Reactome, Unified Medical Language System, Entrez Gene, MEDLINE, National Center for Biomedical Ontology, National Cancer Institute Thesaurus, HPO - Human Phenotype Ontology, Semanticscience Integrated Ontology, Cytoscape, Literature-derived human gene-disease network, Rat Genome Database (RGD), National Library of Medicine, PsyGeNET, listed by: 3DVC, affiliated with: Gene-Disease Association Type OntologyReferences (4)Last checked upnlx_151710
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