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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
Neuron RegistryResource, database, service resource, registry, storage service resource, knowledge environment, data repository, data or information resourceRepository of neuron types characterized by machine-readable part-relation-value triple-based neuron properties. A Curator Interface facilitates the direct knowledge transfer of information from the participating neuroscientist for entry into the Neuron Registry.neuron, registry, neuron property, data repository, knowledge environment, database, registry, neuroinformaticsSCR_000094(Neuron Registry, RRID:SCR_000094) International Neuroinformatics Coordinating Facility , George Mason University; Virginia; USA International Neuroinformatics Coordinating Facility, under the Program on Ontologies of Neural Structures PONSrelated to: Neuron Registry Annotated Corpus, Program on Ontologies of Neural StructuresLast checked downnif-0000-00540http://incfnrci.appspot.com
INCF DataspaceResource, service resource, data set, data repository, storage service resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017.\\n\\nRepository for sharing of neuroscience data, text, images, sounds, movies, models and simulations.neuroscience, text, image, sound, video, model, simulation, data sharing, preservationSCR_000158(INCF Dataspace, RRID:SCR_000158)International Neuroinformatics Coordinating Facility Last checked downnlx_157665
iOMICSResource, software resource, service resourceA genomics data analysis platform which generates decision models for healthcare organizations and medical research. This service is meant to utilize data through machine learning methods.genomic, decision model, machine learning, healthcare, machine learning, medical researchSCR_000239(iOMICS, RRID:SCR_000239)listed by: OMICtoolsLast checked downOMICS_02159http://www.iomics.in/overview
NeuroBaseResource, data or information resource, databaseA database of gene transcription in neurons derived from Next Gen sequencing. Transcriptomes hosted on this database were designed and constructed at the University of Florida.database, neuron, transcriptome, gene transcription, next gen, sequencingSCR_000922(NeuroBase, RRID:SCR_000922)Last checked downnlx_44174
Nonalcoholic Steatohepatitis Clinical Research Network Resource, disease-related portal, topical portal, resource, research forum portal, portal, clinical trial, data or information resourceClinical research network to focus on the etiology, contributing factors, natural history, complications, and therapy of nonalcoholic steatohepatitis. They research the nature and underlying cause of Nonalcoholic Steatohepatitis (NASH) and conduct clinical studies on prevention and treatment. Approximately 1,500 pediatric and adult participants throughout the United States and Canada with nonalcoholic fatty liver disease (NAFLD) have enrolled into a database. The NASH CRN has recently reopened the database to enroll additional pediatric and adult participants with NAFLD. Serum, liver tissue, and genomic DNA samples are being collected and stored in the NIDDKrepository for ongoing as well as future studies. A three-arm randomized, placebo-controlled clinical trial of pioglitazone versus vitamin E completed enrollment in 2009. In addition to this adult trial, a similar trial in pediatric NASH patients randomized 180 children to receive treatment with vitamin E, metformin, or placebo.prevention, treatment, pediatric, child, adult human, serum, liver tissue, dna, placebo, pioglitazone, vitamin e, metformin, etiology, contributing factor, natural history, complication, therapy, young human, database, clinical trial, bibliography, patient registrySCR_001519( Nonalcoholic Steatohepatitis Clinical Research Network , RRID:SCR_001519)Johns Hopkins University; Maryland; USA Nonalcoholic steatohepatitis, Nonalcoholic fatty liver diseaseNIDDKlisted by: One Mind Biospecimen Bank Listing, NIDDK Information Network, NIDDK Central Repository, submitted by: NIDDK Information NetworkLast checked downnlx_152845https://www.nashcrn.com
Drug-Induced Liver Injury Network Resource, disease-related portal, topical portal, resource, research forum portal, biomaterial supply resource, people resource, bibliography, portal, patient registry, material resource, clinical trial, data or information resourceProspective and retrospective registry of well-characterized cases of drug-induced liver disease. The goals of Network include the development of standardized procedures to identify and fully characterize bona fide cases of drug- and complementary and alternative medicines (CAM)-induced liver injury, and to conduct controlled, clinical studies that will include extensive collection of data, serum, DNA, and tissue specimens. Cases of liver injury due to herbal medications are also included. The network will also develop terminology and standardized definitions for DILI, and to develop causality assessment instruments that are sensitive, specific, and reproducible. DILIN is funded by a cooperative agreement and includes five clinical centers and a central data coordinating center. The research goals of DILIN are to: * Create a registry of carefully documented DILI cases * Identify clinical, immunological, and environmental risk factors for drug- and CAM-mediated hepatotoxicity * Create a bank of biological specimens consisting of DNA, plasma, and immortalized lymphocytes to facilitate detailed genetic analyses * Characterize the natural history of drug- and CAM-induced DILI for at least six months following enrollment * Develop the capability to recontact these individuals over an extended period of time so that additional studies exploring DILI mechanisms can be performed Two studies are being initiated by the network. In the Retrospective Study, the implicated drugs are restricted to isoniazid, phenytoin, combination clavulanic acid/amoxicillin, and valproic acid (Depakote), Nitrofurantoin, Trimethoprim-sulfamethoxazole, Minocycline, and Quinolone antibiotics. These drugs were chosen because they are frequently administered to patients not receiving other hepatotoxic drugs, making it easier to establish causality. Patients must be alive, and the date of onset of the DILI episode must be on or after January 1, 1994. In the Prospective Study, all incident cases of drug- and CAM-induced liver injury are being considered. Initial presentation to a healthcare professional must be within the previous six months. A detailed medication history of the implicated DILI drug together with all prescription, OTC, and herbal medications is being recorded. Liver and serological tests are being performed to characterize the injury and to exclude competing causes of liver injury. A blood sample is also being drawn for plasma storage and DNA isolation. These cases will be followed longitudinally to characterize the long-term effects of the DILI episode. For both studies, documented, clinically significant DILI must be recorded in the patient's medical charts so that a causal determination can be made. Patients will be excluded if they are unwilling or unable to provide a blood sample or participate in the genetics component. Children under two years of age at the time of enrollment are excluded due to blood-volume requirements. If you have patients who are eligible to participate in either study, please contact one the DILIN clinical sites. As a general policy, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) invites investigator-initiated research project applications for ancillary studies to ongoing, large-scale clinical trials, epidemiological studies, and disease databases supported by the Institute. These studies are focused on a wide range of diseases and conditions including diabetes, obesity, acute and chronic liver disease, chronic kidney disease, and benign prostatic hyperplasia, among others.prescription drug, over-the-counter drug, alternative medicine, herbal product, supplement, serum, dna, tissue, blood, immortalized lymphocyte, drug, medication, quinolone antibiotic, isoniazid, phenytoin, clavulanic acid, amoxicillin, valproic acid, depakote, nitrofurantoin, trimethoprim-sulfamethoxazole, minocycline, diagnosis, hepatotoxicity, risk factor, genetic analysisSCR_001524( Drug-Induced Liver Injury Network , RRID:SCR_001524)Duke University; North Carolina; USA Liver injury, Hepatic injury, Drug-induced liver diseaseNIDDKlisted by: One Mind Biospecimen Bank Listing, NIDDK Information Network, Diabetes Research Centers, submitted by: NIDDK Information NetworkLast checked downnlx_152822
BigBrain LORIS DatabaseResource, model, dynamic model, data or information resourceAn ultrahigh-resolution 3D human brain model at nearly cellular resolution of 20 micrometers, based on the reconstruction of 7404 histological sections. BigBrain is a free, publicly available tool that provides considerable neuroanatomical insight into the human brain, thereby allowing the extraction of microscopic data for modeling and simulation. BigBrain enables testing of hypotheses on optimal path lengths between interconnected cortical regions or on spatial organization of genetic patterning, redefining the traditional neuroanatomy maps such as those of Brodmann and von Economo.brain, neuroanatomy, cortical region, model, 3d spatial imageSCR_001593(BigBrain LORIS Database, RRID:SCR_001593)McGill University; Montreal; Canada related to: Human Brain Project EUDOI:10.1126/science.1235381, PMID:23788795Last checked downnlx_153840
Sample of ScienceResource, data or information resource, service resource, journal article, access service resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE.\\n\\nFree access service resource dedicated to connect researchers creating scientific samples with scientists who need samples for their experiments. With Sample of Science researchers can submit samples, or contact scientists proposing sample for dissemination. Each disseminated sample also gets its description published in Sample of Science Bulletin, a dedicated open access journal. It acquires a Digital Object Identifier (DOI) and becomes a fully citable item. Because both adequate sample descriptions and mutually-agreed dissemination conditions are key factors for a fruitful dissemination that respects mutual interest, Sample of Science provides tools to elaborate, communicate, discuss, and refine both sample description and dissemination conditions. This process, termed peer-adoption process, results in the publication of disseminated sample descriptions in Sample of Science Bulletin, a dedicated open access publication. The publication in Sample of Science Bulletin is useful to provide adequate recognition to Sample Authors who contribute to the development of science by offering visibility to their disseminated samples. To the adopter it provides experimental details regarding the sample under the form of a citable reference useful for any future publications involving this sample. To a larger scientific community interested in material science, it provides a useful tool to stay abreast the activity of sample providers in their respective field of expertise.nanorod, nanoprobe, imaging, biomedical, fluorescence, nanostructure, graphene, nanomaterial, magnetic material, metal-organic framework, community building portalSCR_001656(Sample of Science, RRID:SCR_001656)Last checked downnlx_153937https://www.sampleofscience.net/
National Center for Earth-Surface DynamicsResource, service resource, data or information resource, data repository, storage service resource, databaseField, laboratory, and model data related to earth-surface dynamics created or compiled by NCED-funded scientists. NCED is a Science and Technology Center developed to predict the coupled dynamics and co-evolution of landscapes and their ecosystems in order to transform management and restoration of the Earth-surface environment.landscape, ecosystem, data setSCR_002195(National Center for Earth-Surface Dynamics, RRID:SCR_002195)University of Minnesota Twin Cities; Minnesota; USA NSFlisted by: CINERGILast checked downnlx_154715
Segmentation Validation EngineResource, data analysis service, production service resource, analysis service resource, software application, service resource, software resourceAn automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site.analyze, dice coefficient, information resource, loni/sve terms of use, magnetic resonance, nifti, os independent, other/proprietary license, overlap metrics, quality metrics, quantification, segmentation, tanomoto coefficient, web environment, web resource, web service, mriSCR_002591(Segmentation Validation Engine, RRID:SCR_002591)University of California at Los Angeles; California; USA listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:19073267Last checked downnlx_155995http://www.nitrc.org/projects/sve
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and AnalysisResource, organization portal, production service resource, analysis service resource, data analysis service, service resource, portal, storage service resource, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.ecology, energy, environment, gene, analysis, bioinformatics, biological, biology, community, cyberinfrastructure, data, dna, genome, genomics, health care, map, marine, metadata, metagenomic, microbial, microbiology, molecular biology, organism, research, scientific, sequence, sequencing, software, tool, training, viralSCR_002676(Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis, RRID:SCR_002676)University of California at San Diego; California; USA Gordon and Betty Moore Foundationrelated to: VIROME, listed by: OMICtoolsPMID:21045053Last checked downnif-0000-23292, OMICS_01476, SCR_011924
Integrated Microbial Genomes with Microbial SamplesResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceTools for analyzing the functional capability of microbial communities based on their metagenome sequence, in the context of reference isolate genomes included from the Integrated Microbial Genomes (IMG) system. IMG/M contains metagenome data generated from 65 microbial community samples that are part of 20 metagenome studies, out of which 19 are new samples and 6 are new studies. This version of IMG/M contains all the isolate genomes from IMG 2.8 as well as genomes from the GEBA project, which provide a comprehensive context for metagenome data analysis. Similar to the genomes in IMG 2.8, the functional characterization of metagenomes has been extended with KEGG Orthology (KO) terms which also serve as the main vehicle for associating IMG/M ER genomes and metagenomes with KEGG pathways. The metagenome datasets have been organized to using the classification proposed in GOLD.genome, gene, function, plasmid, virus, genome fragmentSCR_002965(Integrated Microbial Genomes with Microbial Samples, RRID:SCR_002965)DOE Joint Genome Institute listed by: OMICtoolsLast checked downnif-0000-03010, OMICS_01478http://img.jgi.doe.gov/m
ADNI - Alzheimer's Disease Neuroimaging InitiativeResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase of the results of the ADNI study. ADNI is an initiative to develop biomarker-based methods to detect and track the progression of Alzheimer's disease (AD) that provides access to qualified scientists to their database of imaging, clinical, genomic, and biomarker data.mri, alzheimer’s disease, cognitive assessment, neuroimaging, disease study, disease progression, biomarkerSCR_003007(ADNI - Alzheimer's Disease Neuroimaging Initiative, RRID:SCR_003007)Alzheimer's disease, Mild Cognitive Impairment, Elderly control, Traumatic brain injury, Post-Traumatic Stress Disorder, AgingNIArelated to: alz.org, Alzheimers Drug Discovery Foundation, used by: Biomarkers Across Neurodegenerative Diseases, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC), Consortia-pediaLast checked downnif-0000-00516, SciRes_000144http://adni.loni.usc.edu/, http://www.nitrc.org/projects/adni/, http://www.adni3.org/http://www.loni.ucla.edu/ADNI/
SciCrunchResource, portal, community building portal, data or information resourceCommunity building portal where users can create a portal for their community and choose what resources are related to their community to meet their community's needs. The SciCrunch Registry, formerly the NIF Registry, provides a catalog from which to choose. Adding new resources, or editing existing resources, is welcome.data sharing, communitySCR_003115(SciCrunch, RRID:SCR_003115)University of California at San Diego; California; USA related to: Neuroscience Information Framework, SciScore, SciBot, uses: NIF Data Federation, SciBotLast checked downnlx_156715
ShARMResource, organism supplier, database, biomaterial supply resource, biospecimen repository, tissue bank, service resource, portal, storage service resource, data or information resource, material resource, community building portal, material storage repositoryA not for profit organization to accelerate research into aging by sharing resources: providing access to cost and time effective, aged murine tissue through a biorepository and database of live ageing colonies, as well as promoting the networking of researchers and dissemination of knowledge through its online collaborative environment; MiCEPACE. ShARM will provide valuable resources for the scientific community while helping to reduce the number of animals used in vital research into aging. The biobank of tissue and networking facility will enable scientists to access shared research material and data. By making use of collective resources, the number of individual animals required in research experiments can be minimized. The project also has the added value of helping to reduce the costs of research by connecting scientists, pooling resource and combining knowledge. ShARM works in partnership with MRC Harwell and the Centre for Intergrated Research into Musculoskeletal Ageing (CIMA).data sharing, female, male, gut, heart, kidney, livers, lung, mammary fat, muscle, pancreas, bat, bladder, bone, brain, femur, skin, spleen, thymus, tibia, wat, aged tissue, aged mouse, murine modelSCR_003120(ShARM, RRID:SCR_003120)Aging, Control, Young controlWellcome Trustlisted by: One Mind Biospecimen Bank ListingPMID:24085518Last checked downnlx_156767
resExomeDBResource, service resource, data or information resource, data repository, storage service resource, databaseAn online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing.whole-exome sequencing, archiving, data management, mutation, gene, gene-disease association, exome, whole genome sequencing, genome, sequencing, exome sequencingSCR_003224(resExomeDB, RRID:SCR_003224)listed by: FORCE11Last checked downnlx_157263
ABIDEResource, data set, data or information resourceResting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included.phenotype, resting state functional magnetic resonance imaging, mri, image, fmriSCR_003612(ABIDE, RRID:SCR_003612) NeuroImaging Tools and Resources Collaboratory (NITRC) , 1000 Functional Connectomes Project Autism spectrum disorder, NormalJoseph P. Healy, Leon Levy Foundation, NIMH, Stavros Niarchos Foundationlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked downnlx_157761
Arizona Biospecimen LocatorResource, biomaterial supply resource, tissue bank, data set, cell repository, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.arizona biospecimen, biospecimen bank, biological sample bankSCR_004151(Arizona Biospecimen Locator, RRID:SCR_004151)Diseased, NormalArizona Biomedical Research Commissionlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_17349https://abl.azdhs.gov/tissuelocator-web/browse.action
TaxSOMResource, analysis service resource, data analysis service, service resource, production service resourceA tool for taxonomic classification of DNA fragments, as they are typically obtained in metagenome projects. The classification is based on taxon-specific DNA base composition characteristics (genomic signatures). Classification of query sequences is achieved by mapping the query sequences to the genomic signatures of sequences with known taxonomic affiliations. The mapping is done via the Self-Organizing Map (SOM) algorithm. TaxSOM offers two modes of operation: * mapping query sequences to a pre-calculated SOM * mapping query sequences to a custom SOMmetagenome, taxonomic classification, dna fragment, taxonomy, next generation sequencingSCR_004669(TaxSOM, RRID:SCR_004669)Max Planck Institute for Marine Microbiology; Bremen; Germany listed by: OMICtoolsPMID:21160538Last checked downOMICS_01468
Chicken Gene Nomenclature ConsortiumResource, database, international standard specification, standard specification, narrative resource, service resource, storage service resource, data repository, data or information resourceInternational group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated from biocurators and interested contributors. A Human Chicken Ortholog Predictions Search is available. Both resources are part of a united CGNC effort and nomenclature data is shared and co-ordinated between these two resources. They strongly encourage researchers with domain knowledge to participate in this nomenclature effort by requesting a login and providing gene nomenclature for their genes of interest. Please contact them for further information or assistance. The AGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees, including the Chicken Gene Nomenclature Committee (CGNC). The Avian and Chicken nomenclature efforts are co-ordinated and chicken data is shared between these two groups.orthology, ortholog, human, gene, nomenclature, predictionSCR_004966(Chicken Gene Nomenclature Consortium, RRID:SCR_004966)Mississippi State University; Mississippi; USA PMID:19607656Last checked downnlx_93177http://www.agnc.msstate.edu/Default.aspx
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