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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
Neuroanatomy and Neuropathology on the InternetResource, topical portal, database, training resource, clinical database, portal, atlas, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A set of human neuroanatomical resources developed at the University of Hungary. Resources include an on-line brain atlas, a neuropathology atlas, functional neuroanatomy for neurologists and an extensive series of links to other neuroanatomy and neurological resources on the web. The original resources developed by this site include a set of neuropathological slides covering many neurological conditions, e.g., Alzheimer's disease, an atlas of normal human neuroanatomy based on unstained brain slices, along with histological images of brainstem and spinal cord. On-line quizzes are also provided. This is an excellent educational site and gateway to neurological resources on the web.neuroanatomy, neuropathology, slide, histology, brainstem, spinal cord, brain, image, brain atlas, functional neuroanatomySCR_007272(Neuroanatomy and Neuropathology on the Internet, RRID:SCR_007272)University of Debrecen; Debrecen; Hungary Alzheimer's diseaseLast checked downnif-0000-00012
BrainInfoResource, topical portal, database, standard specification, narrative resource, portal, atlas, data or information resourcePortal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.brain, neuroanatomySCR_003142(BrainInfo, RRID:SCR_003142) University of California at San Diego; California; USA , University of Washington; Seattle; USA NCRR, NIBIB, NIH Office of the Director, NIMH, NLM, The Human Brain Projectrelated to: INIA19 Primate Brain Atlas, used by: NIF Data Federation, listed by: BiositemapsReferences (4)Last checked upnif-0000-00019
Neurosciences on the InternetResource, topical portal, portal, data or information resourceA searchable and browsable index of neuroscience resources available on the internet including neurobiology, neurology, neurosurgery, psychiatry, psychology, cognitive science sites and information on human neurological diseases. Two categories exist: Best Bets and Cutaneous Fields of Peripheral Nerves.neuroscience, neurobiology, neurology, neurosurgery, psychiatry, psychology, cognitive science, human, neurological disease, peripheral nerveSCR_000478(Neurosciences on the Internet, RRID:SCR_000478)Last checked upnif-0000-00024
Open Annotation CollaborationResource, topical portal, portal, knowledge environment, data or information resourceThe Open Annotation Collaboration project aims to facilitate the emergence of a Web and Resource-centric interoperable annotation environment that allows leveraging annotations across the boundaries of annotation clients, annotation servers, and content collections. To this end, interoperability specifications will be devised. Additionally, this project will demonstrate through implementations an interoperable annotation environment enabled by the interoperability specifications in settings characterized by a variety of annotation client/server environments, content collections, and scholarly use cases and will seed widespread adoption by deploying robust, production-quality applications conformant with the interoperable annotation environment in ubiquitous and specialized services, tools, and content used by scholars -- e.g.: Zotero, AXE, LORE, Co-Annotea, Pliny; JSTOR, AustLit, MONK. Alpha3 Data Model: The Open Annotation Data Model specifies an approach for associating annotations with resources, using a methodology conformant with the Architecture of the World Wide Web and the Linked Data initiative. It draws on the Annotea model, as well as more recent extensions of that model.SCR_006376(Open Annotation Collaboration, RRID:SCR_006376)Last checked upnif-0000-00029
Mouse Brain LibraryResource, topical portal, database, image collection, portal, atlas, video resource, data or information resourceCollection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies.brain, gene, genome, strain, c57bl/6j, dba/2j, a/j, genetic variant, phenotype, hippocampus, cerebellum, striatum, olfactory bulb, thalamus, neocortex, dorsal nucleus of lateral geniculate body, central nervous systemSCR_001112(Mouse Brain Library, RRID:SCR_001112)University of Tennessee Health Science Center; Tennessee; USA NIMHrelated to: VideoscribblerPMID:10857184Last checked upnif-0000-00030
German Neuroinformatics NodeResource, topical portal, portal, data or information resourcePortal used to coordinate activities of the German portion of the INCF group. The main focus is the development and free distribution of software tools for handling and analyzing neurophysiological data.database, literature, metadata, neuroinformatics, ontology, portal, softwareSCR_007279(German Neuroinformatics Node, RRID:SCR_007279)Ludwig-Maximilians-University; Bavaria; Germany German Federal Ministry of Education and ResearchLast checked
Neurogenetics OnlineResource, topical portal, portal, data or information resourcePortal to neurogenetic resources: the mouse brain library, digital atlases of the mouse brain, extensive brain microarray data in WebQTL, and internet access to microscopes and stereology tools.Mouse Brain Library. Mouse Brain Library is an expanding collection of high-resolution histological images, atlases, MRIs, and databases on brain structure of more than 120 different lines of mice. Nervenet also includes several useful genetics and gene mapping databases to download (SNP databases, Map Manager databases, and the Portable Dictionary of the Mouse Genome). The publications section includes revised, expanded, and annotated papers, tutorials, and reviews on neurogenetics, gene mapping, complex trait analysis, stereology, and the control of neuron tools, atlas, qtl, neurogeneticsSCR_007280(Neurogenetics Online, RRID:SCR_007280)Last checked upnif-0000-00035
Datasharing.netResource, topical portal, portal, data or information resourceThe U.S. National Institutes of Health Final NIH Statement on Sharing Research Data (NIH-OD-03-032) is now in effect. It specifies that all high-direct-cost NIH grant applications include plans for sharing of research data. To support and encourage collegial, enabling, and rewarding data sharing for neuroscience and beyond, the Laboratory of Neuroinformatics at Weill Medical College of Cornell University has established this site. A source of, and portal to, tools and proposals supporting the informed exchange of neuroscience management, neuroinformatics, data sharingSCR_003312(, RRID:SCR_003312)Weill Cornell Medical College; New York; USA Human Brain Project, NIMH, NINDS, NSFLast checked downnif-0000-00061
Model Organisms for Biomedical ResearchResource, topical portal, portal, data or information resourceInformation about national and international activities and major resources that are being developed to facilitate biomedical research using animal models Mammalian Models: * Mouse * Rat Non-Mammalian Models * S. cerevisiae (budding yeast) * S.pombe (Fission Yeast) * Neurospora (filamentous fungus) * D. discoideum (social amoebae) * C. elegans (round worm) * Daphnia * D. melanogaster (fruit fly) * D. rerio (zebrafish) * Xenopus (frog) * Gallus (chicken) Other Model Organisms: * Arabidopsismammal, model organism, mouse, rat, saccharomyces cerevisiae, saccharomyces pombe, neurospora, dictyostelium discoideum, caenorhabditis elegans, daphnia, drosophila melanogaster, zebrafish, xenopus, gallus, arabidopsis, organism supplierSCR_007282(Model Organisms for Biomedical Research, RRID:SCR_007282)National Institutes of Health Last checked downnif-0000-00062
Function BIRNResource, topical portal, portal, data or information resourceThe FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.fmri, 3d model, data storage, imaging, map, morphology, mri, neuroinformatics, segmentation, software, talairach, volume, warping, analyze, application, c++, csh/tcsh, data, database, database application, data resource, dicom, javascript, linux, magnetic resonance, nifti, ontology, pl/sql, posix/unix-like, python, quality metrics, spatial transformation, statistical operation, tcl/tk, unix shell, visualization, web resource, web service, workflowSCR_007291(Function BIRN, RRID:SCR_007291)Biomedical Informatics Research Network NCRR, NIGMSlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnif-0000-00070
Hereditary Hearing Loss HomepageResource, atlas, topical portal, database, portal, data or information resourceOverview of the genetics of hereditary hearing impairment for researchers and clinicians. The site lists data and references for all known gene localizations and identifications for nonsyndromic hearing impairment, and several for syndromic hearing loss. For syndromic hearing impairment, only a few of the most frequent forms are covered. An atlas of cochlea with genes listed can be accessed from this site.cochlea, syndromic, nonsyndromic, gene, genetics, hearing impairment, hearing, earSCR_006469(Hereditary Hearing Loss Homepage, RRID:SCR_006469) University of Antwerp; Antwerp; Belgium , University of Iowa; Iowa; USA Hereditary hearing impairment, Hearing impairmentrelated to: MITOMAP - A human mitochondrial genome database, listed by: OMICtoolsLast checked upnif-0000-00075, OMICS_01542
Neuroscience Link ListResource, topical portal, portal, data or information resourceA website that provides links to many neuroscience resources on the web as well as links to university neuroscience and neurobiology program list, links, neuroscience resources, topical portalSCR_000130(Neuroscience Link List, RRID:SCR_000130)Weill Cornell Medical College; New York; USA Last checked downnif-0000-00083
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
Neurological Disorder ResourcesResource, disease-related portal, topical portal, portal, data or information resourceOnline portal resource with hierarchically-organized list of links to web resources concerning neurological disorders.portal, neurological disorder, alzheimers, huntingons, parkinsonsSCR_001747(Neurological Disorder Resources, RRID:SCR_001747)University of Washington; Seattle; USA Last checked upnif-0000-00100
Computational Neuroscience on the WebResource, topical portal, portal, data or information resourceAnnotated index for computational neurobiology, focusing on compartmental modeling and realistic simulations of biological neural systems. Has resources to find modeling software and software for computational morphology, phase plane and spike train analysis, and web based neuroinformatics. Provides links to major laboratories, researchers, conferences, education and funding for theoretical neurobiology.computational, neuroscience, compartmental, modeling, simulation, biological, neural, system, neuroinformatics, indexSCR_000010(Computational Neuroscience on the Web, RRID:SCR_000010)Last checked upnif-0000-00107
NeuraLinksPlusResource, narrative resource, topical portal, portal, data or information resourceHierarchically-organized annotated list of approximately 2,500 neuroscience-related web resources. Last update August 2009. Major Topics include: Anatomy: Non-primate Anatomy: Primate (including Atlases) Computing: CS, IT, AI Conditions: Affective Conditions: Agnosia, Aphasia, Dyslexia Conditions: Alzheimer Conditions: Autism Spectrum Conditions: Developmental, Learning, Attentional Conditions: Epilepsy Conditions: Miscellaneous Other Conditions: Multiple Sclerosis Conditions: Neuromuscular Conditions: Stroke, Trauma, Tumor General: Dictionaries, Glossaries, Encyclopedias General: Link Lists, Resource Lists, Organizations Mind: Cognitive Science Mind: Consciousness, Philosophy Physiology: Cardiovascular System Physiology: Cellular, Synapse Physiology: Muscle Physiology: Neurochemistry, Pharmacology Physiology: Sleep Physiology: Speech, Language Physiology: Systems Psychology: Behavior, General Psychology: Illusions, Sensory Phenomena, Synesthesia Psychology: Learning Theory Senses: Auditory, Vestibular Senses: Chemical Senses: Somatic, Proprioceptive, Pain Senses: Vision, Art Techniques: Assistive Technology, Rehabilitation Techniques: Data Mining, Data Visualization Techniques: Math Techniques: Microscopy Techniques: Neuroimaging Techniques: Scientific Method Techniques: Virtual Reality, 3D, SL, OS, VRMLSCR_007049(NeuraLinksPlus, RRID:SCR_007049)University of Colorado Boulder; Colorado; USA Last checked upnif-0000-00114
Neuroscience Database GatewayResource, topical portal, portal, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Resource aimed at promoting awareness and facilitating access to online neuroscience databases.SCR_007297(Neuroscience Database Gateway, RRID:SCR_007297)Society for Neuroscience Last checked downnif-0000-00116
PIRResource, topical portal, production service resource, analysis service resource, database, data analysis service, service resource, portal, data or information resourceThe Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. For over four decades the PIR has provided databases and protein sequence analysis tools to the scientific community, including the Protein Sequence Database (PSD), which grew out from the Atlas of Protein Sequence and Structure. Located both at the University of Delaware and Georgetown University, PIR conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. The PIR web sites are freely accessible by researchers worldwide with over 4 million hits per month from over 100,000 unique sites. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PROannotation, genomic, mining, protein, protein bioinformatics, proteomic, research, sequence, structure, systems biology, gold standardSCR_002837(PIR, RRID:SCR_002837) Georgetown University; Washington D.C.; USA , University of Delaware; Delaware; USA NLMrelated to: NCBI Protein, used by: Protein DatabasePMID:12520019Last checked upnif-0000-00143
Allen Institute for Brain ScienceOrganization, atlas, topical portal, portal, data or information resourceSeattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.Institute, embryonic, gene, expression, data, neuroscience, medical, research, neuroanatomySCR_006491(Allen Institute for Brain Science, RRID:SCR_006491)Allen Institute related to: VisiGene Image Browser, Recombinase (cre) Activity, listed by: Brain Architecture ProjectLast checked upnif-0000-00146
HDBaseResource, disease-related portal, data set, topical portal, portal, data or information resourceA community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse modelsdrug, gene expression, huntingtin, mass spectrometry, microarray, protein interaction, protein-protein interaction, y2h, mouse model, treatment, disease, phenotype, brain, striatum, adipose, muscle, gene, protein, antibody, pathwaySCR_007132(HDBase, RRID:SCR_007132)Institute for Systems Biology; Washington; USA Huntington''s disease, ControlHereditary Disease Foundationuses: CytoscapeLast checked downnif-0000-00153
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