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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
Neurodatabase.orgResource, service resource, data or information resource, data repository, storage service resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented on June 09, 2015. A repository of neurophysiology data conforming to BrainML data models and protocols: BrainML-formatted experimental data submissions are published in searchable, browsable form. Registered users may submit new experiments. The site contains spike trains, voltage time series, and some derived histograms from single cell and multi-unit activity. The database focuses on in vivo somatosensory and visual activity during task performance. This resource contains only a few datasets, but they are of high quality and have been used for reanalysis by several parties. There are three primary interfaces for querying data from this repository: a web-based browse interface, a web-based HTML query form, and a Java web start desktop application. In addition, there is an XML interface useful for direct access by software clients. To download the source code, please read and acknowledge the license agreement.neurophysiology, source code, spike train, voltage time series, histogram, single cell, multi-unit, in vivo, somatosensory, visual, task, data setSCR_007091(Neurodatabase.org, RRID:SCR_007091)Weill Cornell Medical College; New York; USA used by: NIF Data Federation, uses: BrainMLLast checked downnif-0000-00001http://neurodatabase.org/dataserver/goto.do?page=.home
ModelDBResource, software resource, software repository, data or information resource, databaseCurated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate the simulation results from which authors derived their published insights and conclusions.repository, collection, network, neuron, computational, neuroscience, model, simulation, neural, dataSCR_007271(ModelDB, RRID:SCR_007271)Yale University; Connecticut; USA Human Brain Project, NCI, NIDCD, NIMH, NINDSrelated to: SimToolDB, NeuronDB, NeuronVisio, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: 3DVC, Biositemaps, Integrated Models, lists: ModelRun, works_with: MicrocircuitDBReferences (3)Last checked upnif-0000-00004
NeuroMorpho.OrgResource, service resource, data or information resource, data repository, storage service resource, databaseCentrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurologySCR_002145(NeuroMorpho.Org, RRID:SCR_002145)George Mason University; Virginia; USA MURI, NINDSrelated to: DONE: Detection of Outlier NEurons, NIF Literature, Computational Neurobiology and Imaging Center, Integrated Manually Extracted Annotation, used by: NIF Data Federation, recommended by: National Library of Medicine, BRAIN Initiative, listed by: re3data.org, NeuroImaging Tools and Resources Collaboratory (NITRC)References (3)Last checked downnif-0000-00006http://www.nitrc.org/projects/neuromorpho_org
Cell Centered DatabaseResource, database, service resource, storage service resource, image repository, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.electron microscope, light microscopy, electron tomography, electron microscopy, image, cell, microscopy, tomographySCR_002168(Cell Centered Database, RRID:SCR_002168)University of California at San Diego; California; USA related to: Cell Image Library (CIL), Cell Image Library (CIL), Whole Brain Catalog, Integrated Manually Extracted Annotation, used by: NIF Data Federation, Integrated Datasets, listed by: re3data.orgReferences (2)Last checked upnif-0000-00007
Cerebellar Development Transcriptome DatabaseResource, atlas, database, data or information resourceTranscriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains.gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal developmentSCR_013096(Cerebellar Development Transcriptome Database, RRID:SCR_013096)RIKEN Brain Science Institute Brain development, Brain disorderINCF Japan Node, Japanese Ministry of Education Culture Sports Science and Technology MEXT, Japan Science and Technology Agency, Japan Society for the Promotion of Sciencerelated to: Gene Ontology, RIKEN integrated database of mammalsPMID:18603407Last checked upnif-0000-00008
GenePaintResource, atlas, expression atlas, data or information resource, reference atlas, databaseDigital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution.gene expression, adult mouse, annotated, c57bl6, mouse, mouse embryo, mrna, non radioactive in situ hybridization, light microscopy, molecular neuroanatomy resource, in situ hybridization, embryonic, postnatal, adult, brain, head, annotation, rna probe, sequence, anatomical structureSCR_003015(GenePaint, RRID:SCR_003015)Max Planck Institute for Biophysical Chemistry; Gottingen; Germany BMBF, Burroughs Wellcome Fund, European Union, Max Planck Society, Merck Genome Research Institute, NINDS, Romansky EndowmentReferences (2)Last checked upnif-0000-00009, SCR_017526
Gene Expression Profiling in Spinal Cord InjuryResource, data set, data or information resource, databaseDatabase which provides on-line searching of microarray datasets generated from rat spinal cord after contusion injury. Both the primary injury site and a site 5 mm distal to the injury site were assayed. Tissue was obtained from Long Evans rats subject to spinal cord contusion injury using the MASCIS impactor (formerly known as the NYU impactor). RNA expression was assayed at the site of injury and distal to the site of injury using the Affymetrix Rat Neuro U34 chip.database, spinal cord, contusion, microarray dataSCR_003260(Gene Expression Profiling in Spinal Cord Injury, RRID:SCR_003260)Rutgers University; New Jersey; USA Last checked upnif-0000-00011
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
Public Expression Profiling ResourceResource, data or information resource, databaseAn experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).microarray, expression profiling, affymetrix, metadata standard, gene, time series, data sharing, visualization, data mining, platform, blood, cell, cancer, bone, brain, eye, gut, heart, kidney, liver, lung, muscle, spinal cord, spleen, analysisSCR_007274(Public Expression Profiling Resource, RRID:SCR_007274)NHGRI, NHLBI, NINDS, United States Department of Defenserelated to: Gene Expression Omnibus, listed by: OMICtoolsReferences (2)Last checked downnif-0000-00014, OMICS_00776
SumsDBResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, atlas, image repository, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figuressegmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomySCR_002759(SumsDB, RRID:SCR_002759)Washington University School of Medicine in St. Louis; Missouri; USA Mental disease, Neurological disorder, NormalHuman Brain Project, NASA, National Partnership for Advanced Computational Infrastructure, NCI, NIMH, NLM, NSFrelated to: Computerized Anatomical Reconstruction and Editing Toolkit, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: Biositemaps, NeuroImaging Tools and Resources Collaboratory (NITRC), re3data.orgLast checked downnif-0000-00016http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb
SenseLabResource, organization portal, database, portal, data or information resourceThe SenseLab Project is a long-term effort to build integrated, multidisciplinary models of neurons and neural systems. It was founded in 1993 as part of the original Human Brain Project, which began the development of neuroinformatics tools in support of neuroscience research. It is now part of the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF). The SenseLab project involves novel informatics approaches to constructing databases and database tools for collecting and analyzing neuroscience information, using the olfactory system as a model, with extension to other brain systems. SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharmA pilot Web portal that successfully integrates multidisciplinary neurocience data.neuron, model, olfactory system, brain, disease, neuronal, olfactorySCR_007276(SenseLab, RRID:SCR_007276)Yale University; Connecticut; USA AgingHuman Brain Project, Multidisciplinary University Research Initiative, NIA, NICD, NIDCD, NIMH, NINDSrelated to: Neuroscience Information Framework, International Neuroinformatics Coordinating FacilityLast checked upnif-0000-00017
Brain Architecture Management SystemResource, data repository, ontology, database, service resource, storage service resource, controlled vocabulary, data or information resourceKnowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is\\nassociated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions.neurobiology, vertebrate, nervous, system, database, repository, neural, circuitry, analysis, data, nomenclature, taxonomy, axonal, connection, cellSCR_007251(Brain Architecture Management System, RRID:SCR_007251)University of Southern California; Los Angeles; USA Human Brain Project, NIBIB, NIMH, NINDSrelated to: Integrated Manually Extracted Annotation, used by: NIF Data Federation, Integrated Nervous System ConnectivityLast checked downnif-0000-00018http://brancusi.usc.edu/bkms/
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
BrainWeb - Simulated Brain DatabaseResource, atlas, data or information resource, databaseDatabase of human brain images derived from a realistic phantom and generated using a sophisticated MRI simulator. Custom simulations may be generated to match a user's selected parameters. The goal is to aid validation of computer-aided quantitative analysis of medical image data. The SBD contains a set of realistic MRI data volumes produced by an MRI simulator. These data can be used by the neuroimaging community to evaluate the performance of various image analysis methods in a setting where the truth is known. The SBD contains simulated brain MRI data based on two anatomical models: normal and multiple sclerosis (MS). For both of these, full 3-dimensional data volumes have been simulated using three sequences (T1-, T2-, and proton-density- (PD-) weighted) and a variety of slice thicknesses, noise levels, and levels of intensity non-uniformity. These data are available for viewing in three orthogonal views (transversal, sagittal, and coronal), and for downloading.human brain, human brain image, human brain database, mri simulation, brain imagingSCR_003263(BrainWeb - Simulated Brain Database, RRID:SCR_003263)McGill University; Montreal; Canada used by: TumorSimLast checked upnif-0000-00020
CoCoMacResource, data or information resource, databaseOnline access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute.brain, macaque, non-human primate, connectivity, microcircuitry, prefrontal cortex, neural network, structure, function, neuroanatomy, brain circuitry, axonal projection, data repository, visualization, atlas application, computational neuroscience, magnetic resonance, ontology, php, tractography, web environment, softwareSCR_007277(CoCoMac, RRID:SCR_007277)German Neuroinformatics Node DFG, Heinrich-Heine University of Dusseldorf; Dusseldorf; Germany, Wellcome Trustrelated to: Scalable Brain Atlas, used by: NIF Data Federation, Integrated Nervous System Connectivity, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)References (5)Last checked downnif-0000-00022http://www.nitrc.org/projects/cocomac, http://134.95.56.239/home.asphttp://cocomac.org/, http://cocomac.g-node.org/drupal/
fMRI Data CenterResource, service resource, data or information resource, data repository, storage service resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community.fmri, cognitive, cortex, mri, talairach, neuroimaging, cognitive neuroscience, brain, structure, function, magnetic resonance, intellect, image collection, data setSCR_007278(fMRI Data Center, RRID:SCR_007278)University of California at Santa Barbara; California; USA NIMH, NSF, Sun Microsystems Center of Excellence, W. M. Keck Foundationlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC), Biositemaps, re3data.orgPMID:11545705Last checked downnif-0000-00025http://www.nitrc.org/projects/fmridatacenter/
Biomedical Informatics Research NetworkResource, database, software resource, service resource, storage service resource, atlas, data repository, data or information resourceNational initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups.dti, fmri, alzheimer's disease, cognitive impairment, collaborative environment, cyberinfrastructure, data sharing, depressive disorder, information technology, infrastructure, memory dysfunction, microarray, mri, neurodegenerative disease, neuroinformatics, neuroimaging, genetics, biomedical material, neurobiology, electrophysiology, collaboration, biomedical, imaging, imaging system, biomedical engineering, brain, healthSCR_005163(Biomedical Informatics Research Network, RRID:SCR_005163)University of Southern California; Los Angeles; USA NCRR, NIGMS, NIH Blueprint for Neuroscience Researchlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC), Biositemaps, re3data.org, DataCiteReferences (3)Last checked upnif-0000-00027http://www.nitrc.org/projects/birnhttp://www.birncommunity.org/, https://neuroscienceblueprint.nih.gov/factSheet/birn.htm
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
Internet Brain Volume DatabaseResource, data or information resource, databaseA database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.anatomy, volume, dsm-iv, normal, schizophrenia, autistic disorder, bipolar disorder, major depressive disorder, alzheimer's disease, attention deficit-hyperactivity disorder, alcohol dependence, dementia, traumatic brain injury, borderline personality disorder, obsessive-compulsive disorder, asperger syndrome, brain, brain structure, in vivo, ex vivo, male, female, gorilla beringei beringei, pongo pygmaeus, volumetric analysisSCR_002060(Internet Brain Volume Database, RRID:SCR_002060)Harvard Medical School; Massachusetts; USA Normal, Alzheimers disease, Seizure, Complex febrile seizure, Holoprosencephaly, Alcohol dependence, Bipolar Disorder, Traumatic brain injury, SchizophreniaNINDS, The Human Brain Projectrelated to: NIF Data Federation, Integrated Manually Extracted Annotation, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:21931990Last checked downnif-0000-00033http://www.nitrc.org/projects/ibvd
Ligand-Gated Ion Channel DatabaseResource, data or information resource, databaseDatabase providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembraneSCR_002418(Ligand-Gated Ion Channel Database, RRID:SCR_002418)European Bioinformatics Institute Biotech and Biomed contracts, Centre National de la Recherche Scientifique, College of France; Paris; France, European Union, French Ministry of Higher Education and Research, Institut Pasteurlisted by: re3data.orgReferences (2)Last checked upnif-0000-00037
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