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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: Sep 14, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
BAMS Nested RegionsResource, data or information resource, databaseBAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationships. THIS RESOURCE IS NO LONGER AVAILABLE. Documented on July 7th, 2019.neural circuitry, brain region, brainSCR_000238(BAMS Nested Regions, RRID:SCR_000238)Brain Architecture Management System NIMH, NINDS, NINDS/NIMH/NIBIBused by: NIF Data FederationLast checked downnif-0000-10175
BAMS ConnectivityResource, data or information resource, databaseDatabase of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions.brain, neural circuitry, connectivity, brain region, neuroanatomy, neuronal tract tracing, connectomeSCR_000561(BAMS Connectivity, RRID:SCR_000561)Brain Architecture Management System related to: Integrated Manually Extracted Annotation, used by: NIF Data FederationLast checked downnlx_144138http://brancusi.usc.edu/bkms/, http://brancusi.usc.edu/
The Guardian: Science WeeklyResource, narrative resource, podcast, data or information resourceAlok Jha and the Guardian's science team bring you the best analysis and interviews from the worlds of science and technology.interview, science, technologySCR_000674(The Guardian: Science Weekly, RRID:SCR_000674)related to: Integrated Podcasts, used by: NIF Data FederationLast checked downnlx_144241
Kawasaki Disease DatasetResource, data set, data or information resourceCollection of data sets on Kawasaki disease, a rare childhood illness that affects the blood vessels. The data includes biochemical measurements of myocardial strain, oxidative stress, and cardiomyocyte injury as well as protein level analysis.kawasaki disease, nt-probnp, sst2, copeptin, ct-proet-1, mr-proadm, mr-proanp, pct, troponin i cardiac muscle, diastolic dysfunction, oxidative stress, myocarditis, coronary artery aneurysm, blood, child, young humanSCR_001451(Kawasaki Disease Dataset, RRID:SCR_001451)University of California at San Diego; California; USA Kawasaki disease, Febrile control, Myocarditisused by: NIF Data Federation, listed by: Monarch InitiativePMID:21777987Last checked downnif-0000-08189https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nif-0000-08189-1 http://neuinfo.org/nif/nifgwt.html?query=%22Kawasaki%20Disease%20Dataset1%22&category=Data%20Type:Dataset, http://neuinfo.org/nif/nifgwt.html?query=nif-0000-08189
Integrated ModelsResource, data or information resource, databaseA virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun.model, integrated, database, nifSCR_001481(Integrated Models, RRID:SCR_001481)Integrated used by: NIF Data Federation, lists: Simtk.org, ModelDB, Open Source Brain, CellML Model RepositoryLast checked downnlx_152726https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-12 https://neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_152726-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-12
NIF Web ServicesResource, web service, software resource, data access protocolRepresentational State Transfer (REST) model based service for accessing a set of Neuroscience Information Framework (NIF) data through a fixed set of operations. They are defined by a WADL file which allows clients to automatically generate code for these services. The services (AnnotateService, FederationService, LdaService, LexicalService, LiteratureService, QueryService, SummaryService, VocabularyService) include the ability to: * Retrieve a federation summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/summary?q=* * Retrieve data records from a NIF federation source for a search, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nif-0000-00007-1?q=purkinje * Retrieve registry data records from NIF, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nlx_144509-1?q=miame * Retrieve a complete search summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/search?q=cortex * Retrieve NIF auto-complete suggestions, e.g., http://nif-services.neuinfo.org/servicesv1/v1/vocabulary?prefix=hippo * Use the NIF annotator for arbitrary text, e.g., http://nif-services.neuinfo.org/servicesv1/v1/annotate?content=The%20cerebellum%20is%20a%20wonderful%20thing These services are documented for developers in the WADL file (and client stubs should have the comments embedded in them). Visit, http://nif-services.neuinfo.org/servicesv1/ for more informationrest, data sharing, wadlSCR_001631(NIF Web Services, RRID:SCR_001631)Neuroscience Information Framework related to: SciCrunch Registry, NIF Literature, OntoQuest, used by: NIF Data FederationLast checked downnlx_153899
ASAPResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points.gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis serviceSCR_001849(ASAP, RRID:SCR_001849)University of Wisconsin-Madison; Wisconsin; USA NIGMS, USDArelated to: AmiGO, used by: NIF Data FederationPMID:12519969Last checked downnif-0000-02571https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
NeurofedResource, people resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The NeuroFed resource is a listing of neuroscience research funding contacts in the Federal government. It is an informal compendium (PDF) of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units of the federal government. An electronic (PDF) version of the most recent update of this list is available on the Society for Neuroscience website at: http://www.sfn.org/index.aspx?pagename=professionalDevelopment_training. The list is updated annually by NIH personnel.SCR_002011(Neurofed, RRID:SCR_002011)National Institutes of Health used by: NIF Data FederationLast checked downnif-0000-10988
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, listed by: re3data.org, NeuroImaging Tools and Resources Collaboratory (NITRC)References (3)Last checked downnif-0000-00006http://www.nitrc.org/projects/neuromorpho_org
IntegratedResource, data or information resource, databaseVirtual database of individual data sources, maintained by SciCrunch participating groups. Database topics are varied, including animals, grants, software, brain gene expression, and clinical trials.database aggregation, integrated scicrunch viewSCR_002187(Integrated, RRID:SCR_002187)Neuroscience Information Framework , SciCrunch , NeuroLex used by: NIF Data FederationLast checked downnlx_154697http://neurolex.org/wiki/Category:Resource:Integrated
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
Developmental Therapeutics ProgramResource, topical portal, service resource, portal, funding resource, data or information resourcePortal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example.cell line, drug discovery, drug development, drug, treatment, therapy, biopharmaceutical, bortezomib, paclitaxel, romidepsin, eribulin, sipuleucel-t, anticancer therapeutic, compound, natural product extract, animal model, in vivo, in vitro, chemical structure, chemical, structure, anti-hiv, anticancer, molecular structure, database, chemotherapeutic agent, testing, drug synthesis, chemistry, grant, contract, information technology, molecular pharmacology, natural product, pharmaceutical, screening technology, toxicology, pharmacology, screeningSCR_003057(Developmental Therapeutics Program, RRID:SCR_003057)National Cancer Institute Cancer, TumorNCIrelated to: Integrated Cell Lines, used by: NIF Data FederationLast checked downnif-0000-30447
Mouse Genome Informatics TransgenesResource, data set, data or information resourceData set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available.
Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.
transgene, allele, phenotypeSCR_003468(Mouse Genome Informatics Transgenes, RRID:SCR_003468)Mouse Genome Informatics (MGI) related to: Integrated Manually Extracted Annotation, used by: NIF Data FederationLast checked downnif-0000-34000
BAMS CellsResource, data or information resource, databaseBAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein.neuroanatomy, cell, neuron, neural circuitry, brainSCR_003531(BAMS Cells, RRID:SCR_003531)Brain Architecture Management System NIBIB, NIMH, NINDSused by: NIF Data FederationLast checked downnif-0000-90175http://brancusi.usc.edu/bkms/
Integrated Brain Gene ExpressionResource, data or information resource, databaseA virtual database currently indexing brain region gene expression data from mice from: Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI).database, brain gene expression, molecular neuroanatomy resource, brain, gene expression, mouse, geneSCR_004197(Integrated Brain Gene Expression, RRID:SCR_004197)Integrated related to: GENSAT, Allen Mouse Brain Atlas, Mouse Genome Informatics (MGI), used by: NIF Data FederationLast checked downnlx_22354https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-4 http://neuinfo.org/nif/nifgwt.html?query=nlx_22354, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_22354-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-4
Gray MattersResource, narrative resource, podcast, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Gray Matters is a radio series on brain topics that has been produced since 1994 by Public Radio International in association with the Dana Alliance. More than 25 programs have been created on topics ranging from stress, neuroethics, learning throughout life and sports, fitness and the Brain. Dana Alliance members serve as advisers to Gray Matters programming and are interviewed during the programs. The transcripts are also available.SCR_004433(Gray Matters, RRID:SCR_004433)The Dana Foundationrelated to: Integrated Podcasts, used by: NIF Data FederationLast checked downnlx_54435
dkCOIN Resource, data or information resource, resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO).gene, adenovirus construct, antibody, co-immunoprecipitation, embryonic stem cell line, functional genomics, histology, mouse strain, pcr primer, protocol, real time pcr, metadata, diabetes, stem cell, metabolism, tissue development, web service, cloud, embryonic stem cellSCR_004438( dkCOIN , RRID:SCR_004438)NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases NIDDKrelated to: Beta Cell Biology Consortium , NIDDK Information Network, National Mouse Metabolic Phenotyping Centers , Nuclear Receptor Signaling Atlas , Diabetic Complications Consortium , T1DBase , OBO, used by: NIF Data Federation, submitted by: NIDDK Information NetworkLast checked downnlx_44256
Integrated SoftwareResource, data or information resource, databaseA virtual database currently indexing software and tools from the SciCrunch Registry, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software (GAS).database, tool, software, integratedSCR_004745(Integrated Software, RRID:SCR_004745)Integrated related to: Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, used by: NIF Data Federation, listed by: Genetic Analysis Software, NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked downnlx_75188https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-10 http://neuinfo.org/nif/nifgwt.html?query=nlx_75188, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_75188-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-10
Integrated DiseaseResource, data or information resource, databaseA virtual database currently indexing authoritative information on disease and treatment options from NINDS Disorder List and PubMed Health.disease, treatment, disorder, health, databaseSCR_004892(Integrated Disease, RRID:SCR_004892)Integrated related to: NINDS Disorder Index, PubMed Health, used by: NIF Data FederationLast checked downnlx_86401https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-6 http://neuinfo.org/nif/nifgwt.html?query=nlx_86401, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_86401-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-6
VMDResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett''''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs.microbial genome sequence, genome, genome sequence, genome model, gene, image, oomycete, fungus, bacteria, phytophthora sojae, phytophthora ramorum, hyaloperonospora arabidopsidis, plantSCR_004905(VMD, RRID:SCR_004905)Virginia Polytechnic Institute and State University; Virginia; USA NSF, USDA Cooperative State Research Education and Extension Servicerelated to: AmiGO, used by: NIF Data FederationPMID:16381891Last checked downnlx_87328http://phytophthora.vbi.vt.edu
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