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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)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
3D surgical atlases of the murine headResource, atlas, data or information resource3D interactive atlas of two mouse brains, 129S1/SvImJ and C57Bl/6J. The aim of this resource is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice. These representations of the murine brain and skull, in conjunction with the resource''s development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate off-axis surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambdabregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system.129s1/svimj, anatomy, brain, c57bl/6j, central nervous system, digital atlas, imaging assay, in vivo, micro-electroporation, morphometric analysis, skull, sterotactic, transgenic, imagingSCR_008039(3D surgical atlases of the murine head, RRID:SCR_008039)University of Toronto; Ontario; Canada Canadian Institute for Health Research, NARSAD Young Investigator award, Ontario Research Development ChallengeLast checked upnif-0000-10249
BrainNavigatorResource, atlas, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.3d, 2d, acetylcholinesterase, anatomy, brain, coronal, reconstruction, sagittal, sterotaxic, visualization, molecular neuroanatomy resource, training resource, connection, literature, gene expression, imageSCR_008289(BrainNavigator, RRID:SCR_008289)Last checked downnif-0000-24037
Research Collaboratory for Structural Bioinformatics Protein Data BankResource, service resource, data or information resource, databaseCollection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standardSCR_012820(Research Collaboratory for Structural Bioinformatics Protein Data Bank, RRID:SCR_012820) Rutgers University; New Jersey; USA , University of California at San Diego; California; USA DOE, NIH, NSFrelated to: pdb-data, PDB2MultiGif, GlyProt, pdb-care, pdb2linucs, GlyVicinity, GlyTorsion, GlySeq, AffinDB, StatAlign, Community Structure-Activity Resource, Binding MOAD, ConSurf Database, glycosciences.de, DOMINE: Database of Protein Interactions, Jenalib: Jena Library of Biological Macromolecules, SynSysNet, EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy, PDBe - Protein Data Bank in Europe, TFinDIT, HOLLOW, ccPDB - Compilation and Creation of datasets from PDB, DOMMINO - Database Of MacroMolecular INteractiOns, InterEvol database, Polbase, PoSSuM, ProtChemSI, RNA CoSSMos, PDBsum, Worldwide Protein Data Bank , canSAR, CAPS Database, Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING, Combinatorial Extension (CE), Metalloprotein Site Database, PDBj - Protein Data Bank Japan, Statistical Torsional Angles Potentials of NMR Refinement Database, Metalloprotein Ligand Interaction Database, CARP, PDBTM, RNA FRABASE - RNA FRAgments search engine and dataBASE, AmiGO, ConsensusPathDB, Biological Magnetic Resonance Data Bank, DDBJ - DNA Data Bank of Japan, FlyMine, NCBI Protein, NCBI Nucleotide, FunTree, IndelFR - Indel Flanking Region Database, NMR Restraints Grid, Enzyme Structures Database, Electron Microscopy Data Bank at PDBe, Worldwide Protein Data Bank , DDBJ - DNA Data Bank of Japan, PDBe - Protein Data Bank in Europe, MINAS - Metal Ions in Nucleic AcidS, RCSB PDB, PDBj - Protein Data Bank Japan, used by: SGC, Ligand Expo , DARC - Database for Aligned Ribosomal Complexes, FireDB, Protein Data Bank Bind Database, Protein Data Bank Site, NIF Data Federation, ChannelPedia, MobiDB, Protein Database, listed by: re3data.org, affiliated with: EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy, ConSurf-DB, works_with: CellPhoneDBPMID:12037327Last checked upnif-0000-00135, SCR_017379http://www.rcsb.org, http://www.pdb.org
Allen Mouse Brain AtlasResource, atlas, service resource, database, data or information resource3D genome map of gene expression in adult mouse brain. Reveals expression patterns of genes throughout entire adult mouse brain down to cellular level. Interactive, genome wide image database of gene expression with ISH and Nissl images. Combination of RNA in situ hybridization data. Detailed Reference Atlases and informatics analysis tools are integrated to provide searchable digital atlas of gene expression.3D, map, gene, expression, data, adult, mouse, brain, interactive, imageSCR_002978(Allen Mouse Brain Atlas, RRID:SCR_002978)Allen Institute for Brain Science , Allen Brain Atlas related to: BrainStars, PubAnatomy, Integrated Brain Gene Expression, Allen Brain Atlas API, 3DBar, aGEM, CellTax vignette, used by: NIF Data Federation, works_with: MeshView, Brain Gene Expression Analysis toolboxLast checked upnif-0000-00508http://mouse.brain-map.org/
3DBarResource, production service resource, analysis service resource, reference atlas, software resource, service resource, atlas, data or information resourceSoftware package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML3d, reconstruction, brain structure, brain, algorithm or reusable library, web service, atlas application, three dimensional display, spinal cord, sensory system, waxholm spaceSCR_008896(3DBar, RRID:SCR_008896)Nencki Institute of Experimental Biology; Warsaw; Poland related to: Scalable Brain Atlas, Allen Mouse Brain Atlas, Waxholm Space Atlas, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:22227717Last checked upnlx_151380http://www.nitrc.org/projects/bar3d, http://service.3dbar.org, http://www.3dbar.org:8080/, http://3dbar.org
MRM NeAt (Neurological Atlas) Mouse Brain Database Image GalleryResource, video resource, d spatial image, image collection, data or information resourceImage Gallery of a 3D MRI Atlas of an Adult C57BL/6J Mouse Brain showing Slice Animation and 3D Animation including Axial, Coronal, Sagittal views. RealPlayer or Windows Media Player needs to be installed for viewing these animations.adult mouse, c57bl/6j, brain, slice animation, 3d animation, axial, coronal, sagittal, animationSCR_007032(MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery, RRID:SCR_007032)MRM NeAt (Neurological Atlas) Mouse Brain Database related to: MRM NeAt (Neurological Atlas) Mouse Brain DatabaseLast checked upnlx_46281
High Resolution Mouse Brain AtlasResource, atlas, data or information resource2D mouse brain atlas of high quality coronal Nissl- and myelin-stained sections with labels, 3D images of hippocampal formation and limited other brain structures. The data for this digital atlas are based on the Atlas of the Mouse Brain and Spinal Cord, authored by Richard L. Sidman, Jay. B. Angevine and Elizabeth Taber Pierce, published as a hard cover book by Harvard University Press in 1971 and currently out of print. C57BL/6J strain adult specimens were used in creating the atlas.adult mouse, hippocampal formation, image, leaf lumina camera, mouse, normal, nuclei of the limbic thalamus, c57bl/6, nissel, myelin, neuroanatomy, olfactory bulb, frontal pole, pyriform cortex, septo-striatal, septo-diencephalic, rostral diencephalon, caudal diencephalon, rostral cerebellum, caudal cerebellum, medula, spinal cord, diencephalon, cerebellum, mesencephalonSCR_006063(High Resolution Mouse Brain Atlas, RRID:SCR_006063)Harvard University; Cambridge; United States Human Brain Project, NINDSLast checked upnif-0000-00087
Mammalian Adult Neurogenesis Gene OntologyResource, database, ontology, data or information resource, controlled vocabularyDatabase of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus.adult neurogenesis, adult, neurogenesis, hippocampus, gene, annotation, cell type, processSCR_006176(Mammalian Adult Neurogenesis Gene Ontology, RRID:SCR_006176)Dresden University of Technology; Saxony; Germany Last checked upnlx_151684
Aged Rodent Tissue ArraysResource, biomaterial analysis service, analysis service resource, service resource, production service resource, material analysis serviceOffer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbersaged, biogerontology, caloric restricted, rodent, protein expression, tissue array, tissue core, histology, adult, old, old rodent, c57bl/6, male, female, liver, cardiac muscle, brain, tissue, kidney, skin, frontal cortex, muscle, thigh, white adipose tissue, pancreas, testes, prostate, spleen, lung, heart, dwarf, wild type, early adult, middle adult, late adult, microarray, imageSCR_007332(Aged Rodent Tissue Arrays, RRID:SCR_007332)Aged Rodent Tissue Bank Aged, Old, Control, AgingNCI, NIA, NIH Blueprint for Neuroscience ResearchLast checked upnif-0000-00216http://www.nia.nih.gov/ResearchInformation/ScientificResources/AgedRodentTissueBankHandbook/TissueArrays/
UAB-UCSD Core Center for Acute Kidney Injury Research Pre-Clinical Studies of AKI Resource, service resource, resource, core facility, access service resourceCore that provides services such as expertise in development and training in the use of rodent models of AKI, specifically in the setting of ischemia/reperfusion (I/R) injury, sepsis and renal transplantation, gamma-ray imaging (gamma camera, microSPECT/CT, microPET/CT), metabolic assessments of kidney O2 consumption, and technical expertise in isolation of primary renal and vascular cell in culture.AKI, pre-clinical studies, murine models, imagingSCR_015278( UAB-UCSD Core Center for Acute Kidney Injury Research Pre-Clinical Studies of AKI , RRID:SCR_015278)University of Alabama at Birmingham School of Medicine; Alabama; USA , University of California San Diego School of Medicine; California; USA , UAB-UCSD Core Center for Acute Kidney Injury Research NIDDKlisted by: NIDDK Information NetworkLast checked up
ALEAResource, software resource, software toolkitA computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.allele, epigenomics, analysis, chip-seq, rna-seq, allelic variation, next-generation sequencingSCR_006417(ALEA, RRID:SCR_006417)BC Cancer Agency listed by: OMICtoolsPMID:24371156Last checked upOMICS_02193
Genes to Cognition DatabaseResource, data or information resource, databaseDatabase of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.allele, gene list, mouse line, human disease, phenotyping, plasticity, behavior, proteonomics, brain, cognition, cognition disorder, learning, memory, neuroscience, experimental protocol, synapse proteomics, synapseSCR_002735(Genes to Cognition Database, RRID:SCR_002735)BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome TrustLast checked downnif-0000-02864http://www.genes2cognition.org/cgi-bin/SearchView
Aging Genes and Interventions DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseA 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-spanSCR_002701(Aging Genes and Interventions Database, RRID:SCR_002701)University of Washington; Seattle; USA Aging, Age-related neurological disease, Neurological diseaseEllison Medical Foundationrelated to: Monarch Initiative, used by: Aging Portal, NIF Data FederationPMID:12044961Last checked upnif-0000-23326http://sageke.sciencemag.org/highlights/gidb/
ESTHERResource, data or information resource, databaseDatabase and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila.alpha hydrolase, beta hydrolase, cholinesterase, protein, protein superfamily, blast, gene, protein binding, protein-protein interaction, nucleotide, nucleotide sequence, enzyme, genetics, genome, genomics, mutation, disease, gene expression, peptide, chromosomeSCR_002621(ESTHER, RRID:SCR_002621)INRA - French National Institute for Agricultural Research; Paris; France related to: UniProtKB, AceDB, listed by: re3data.orgPMID:23193256Last checked upnif-0000-02817, nif-0000-30526, SCR_008479
Human Transcriptome Database for Alternative SplicingResource, data or information resource, databaseA specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only)alternative splicing, alternative splicing variant, cdna, transcriptome, h-invitational, rna-seq, rna, comparative genomicsSCR_013305(Human Transcriptome Database for Alternative Splicing, RRID:SCR_013305)National Institute of Advanced Industrial Science and Technology listed by: OMICtoolsReferences (2)Last checked downnif-0000-02935, OMICS_01887
HollywoodResource, data or information resource, databaseDatabase built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags for human and mouse. It links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. A query tool allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser.alternative splicing, exon, mrna, splicing, annotation, regulatory element, ortholog, splicing pattern, cdnaSCR_002920(Hollywood, RRID:SCR_002920)Massachusetts Institute of Technology; Massachusetts; USA listed by: OMICtoolsPMID:16381932Last checked upnif-0000-02972, OMICS_01889
EDAS - EST-Derived Alternative Splicing DatabaseResource, data or information resource, databaseDatabases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test.alternative splicing, gene, protein, mrna, est, exon, intron, rat, dogSCR_002449(EDAS - EST-Derived Alternative Splicing Database, RRID:SCR_002449)Moscow State University; Moscow; Russia listed by: OMICtoolsPMID:16909834Last checked upnif-0000-02786, OMICS_01885
Alzheimer's Research ForumResource, disease-related portal, topical portal, discussion, narrative resource, portal, community building portal, data or information resourceA community building portal dedicated to understanding Alzheimer's disease and related disorders, it reports on the latest scientific findings from basic research to clinical trials, creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across disciplines.alzheimer's disease, human, mouse, community building portal, forumSCR_006416(Alzheimer's Research Forum, RRID:SCR_006416)Alzheimer's diseasegrants, individual donationsrelated to: MSGene, ALZPEDIALast checked upnif-0000-00095
PROVEANResource, analysis service resource, software resource, data analysis service, service resource, production service resourceA software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.amino acid substitution, indel, function, protein, amino acid, substitution, protein variant, genome variant, next-generation sequencing, insertion, deletionSCR_002182(PROVEAN, RRID:SCR_002182)J. Craig Venter Institute NHGRI, NIHlisted by: OMICtoolsPMID:23056405Last checked upOMICS_01849
Atlas3DResource, data processing software, software application, data visualization software, software resource, atlas, data or information resourceA multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.analysis, brain, histological, mouse, rat, slicing, structure, 3d, tomographic, visualization, neuroimaging, image, magnetic resonance, visualizationSCR_001808(Atlas3D, RRID:SCR_001808)University of Oslo; Oslo; Norway NCRR, NIBIB, NIH, Research Council of Norwaylisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnif-0000-10373http://www.nitrc.org/projects/incf_atlas3d
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