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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
Chernobyl Tissue BankResource, biomaterial supply resource, material resourceThe CTB (Chernobyl Tissue Bank) is an international cooperation that collects, stores and disseminates biological samples from tumors and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The main objective of this project is to provide a research resource for both ongoing and future studies of the health consequences of the Chernobyl accident. It seeks to maximize the amount of information obtained from small pieces of tumor by providing multiple aliquots of RNA and DNA extracted from well documented pathological specimens to a number of researchers world-wide and to conserve this valuable material for future generations of scientists. It exists to promote collaborative, rather than competitive, research on a limited biological resource. Tissue is collected to an approved standard operating procedure (SOP) and is snap frozen; the presence or absence of tumor is verified by frozen section. A representative paraffin block is also obtained for each case. Where appropriate, we also collect fresh and paraffin-embedded tissue from loco-regional metastases. Currently we do not issue tissue but provide extracted nucleic acid, paraffin sections and sections from tissue microarrays from this material. The project is coordinated from Imperial College, London and works with Institutes in the Russian Federation (the Medical Radiological Research Centre in Obninsk) and Ukraine (the Institute of Endocrinology and Metabolism in Kiev) to support local scientists and clinicians to manage and run a tissue bank for those patients who have developed thyroid tumors following exposure to radiation from the Chernobyl accident. Belarus was also initially included in the project, but is currently suspended for political reasons.SCR_010662(Chernobyl Tissue Bank, RRID:SCR_010662)Imperial College London; London; United Kingdom Tumor, Normal, Exposure to radioiodine in childhood following the accident at the Chernobyl power plantEuropean Union, NCI, Sasakawa Memorial Health Foundationlisted by: One Mind Biospecimen Bank ListingLast checked upnlx_70828
eVOCResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomySCR_010704(eVOC, RRID:SCR_010704)University of the Western Cape; Bellville; South Africa European Union, South African Department of Arts Culture Science and Technology, South African National Research Foundation, Wellcome Trustrelated to: OBO, Bgee: a dataBase for Gene Expression EvolutionPMID:12799354Last checked downnlx_84448
Colon Therapy Research Consortium (COLTHERES)Resource, organization portal, portal, consortium, data or information resourceThe Colon Therapy Research (COLTHERES) consortium brings together clinical centers and translational researchers funded in the European Union to define and perform biomarker driven clinical trials to improve cancer therapy outcomes. This 4-year consortium will use comprehensively molecularly-annotated colon cancers as a "test-bed" to define specific biomarkers of response or resistance to signaling pathway agents.translational, clinical, colon cancer, colon, biomarkersSCR_013690(Colon Therapy Research Consortium (COLTHERES), RRID:SCR_013690)European UnionLast checked down
BibSonomyResource, software resource, collaboration toolA software application which assists in managing and sharing scientific literature. Users can collect and share publications, collaborate with other researchers, and find new resources and publications for research.software, publications, collaboration tool, scientific literatureSCR_013756(BibSonomy, RRID:SCR_013756)European Union, German Research Foundation, Land Hessenuses: Citation Style LanguageDOI:10.1007/s00778-010-0208-4Last checked up
OpenAIREResource, project portal, portal, data or information resourceA research portal to share and obtain research data and journal articles openly accessible to all disciplines. Established to support the Open Access Policy, as set out by the ERC Scientific Council Guidelines for Open Access and the Open Access pilot launched by the European Commission.open access, Europe, repository networks, project portal, research data, journal articlesSCR_013740(OpenAIRE, RRID:SCR_013740)European Unionrelated to: ZENODOLast checked down
hFiguresResource, data visualization software, software application, network graph visualization software, data processing software, software resourceA Javascript library that aims to deliver a starting point for interactive health data visualization. Examples and demos are available on the site. hFigures was built with d3.js and a copy of the library is included in this repository. All rights and license terms apply to the d3.js library accordingly.health data, visualization, electronic health record, personal health record, health informaticsSCR_014201(hFigures, RRID:SCR_014201)University of Tampere; Tampere; Finland BMC Medical Informatics and Decision Making Health Figures Software Article, European Union, TEKESPMID:26738061Last checked up
MINTResource, data or information resource, databaseA database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, orthologSCR_001523(MINT, RRID:SCR_001523)University of Rome Tor Vergata; Rome; Italy AIRC Associazione Italiana per la Ricerca sul Cancro, ENFIN, European Union, HUPO Proteomics Standards Initiative, IMEx - The International Molecular Exchange Consortium, Interaction Proteome Projectrelated to: MPIDB, TissueNet - The Database of Human Tissue Protein-Protein Interactions, InteroPorc, Interaction Reference Index, Pathway Commons, ConsensusPathDB, VirusMINT, PSICQUIC Registry, Agile Protein Interactomes DataServer, uses: IntAct, PSI-MI, listed by: re3data.org, affiliated with: IMEx - The International Molecular Exchange Consortium, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (8)Last checked upnlx_152821
Glyco-CDResource, data set, data or information resourceManually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology.carbohydrate, glycobiology, glycan, lectin, antigen, interaction, protein, cell surface molecule, microarray, carbohydrate recognition, cluster of differentiation, oligosaccharide sequence, glycoprotein, glycosphingolipid, carbohydrate recognition site, leukocyte, antibody, endothelial cell, epithelial cellSCR_001574(Glyco-CD, RRID:SCR_001574)glycosciences.de European UnionPMID:22847935Last checked downnlx_152887http://www.glycosciences.de//Glyco-CD/
PerseusResource, software resource, software application, data analysis software, data processing softwareSoftware that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing.shotgun proteomics data analysis, protein quantification, post-translational modification data, statistical analysis, omics dataSCR_015753(Perseus, RRID:SCR_015753)European Unionsubmitted by: Resource Identification PortalPMID:27348712Last checked uphttp://www.biochem.mpg.de/5111810/perseus
ABACASResource, software resource, software applicationSoftware that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.contiguation, primer, shotgun assembled contig, reference sequence, assembled sequenceSCR_015852(ABACAS, RRID:SCR_015852)European Union, Wellcome Trust Sanger InstituteLast checked uphttps://sourceforge.net/projects/abacas/files/
BsoftResource, software resource, software application, image processing software, data processing softwareSoftware package and a platform for the processing of electron micrographs in structural biology. Supports different image file formats used in electron microscopy (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF).image, processing, structural, biology, electron, microscopy, different, format, supportSCR_016503(Bsoft, RRID:SCR_016503)European Union, NIAMSrelated to: University of Basel, Basel, SwitzerlandDOI:10.1006/jsbi.2001.4339Last checked up
iMITSResource, catalog, data or information resource, databaseSoftware tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products.international, tracking, system, mouse, production, data, store, catalog, phenotype, collection, mutation, molecular, structure, IKMC, IMPCSCR_016552(iMITS, RRID:SCR_016552)European Union, NIHaffiliated with: IMPC, submitted by: Resource Identification PortalLast checked down
Functional Anatomy of the Cerebro-Cerebellar System (FACCS)Resource, data analysis service, production service resource, analysis service resource, database, service resource, storage service resource, data repository, data or information resourcePublic neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.axonal tracer, axon tracing, brain, cerebellum, cerebral cortex, cerebro-cerebellar function, cerebro-cerebellar structure, cerebro-cerebellar system, injection, injection site, labeled cells, labeled fibers, pontine nuclear complex, pontine nuclei, video, cerebellar cortexSCR_001661(Functional Anatomy of the Cerebro-Cerebellar System (FACCS), RRID:SCR_001661)University of Oslo; Oslo; Norway Centre for Molecular Biology and Neuroscience, European Union, Research Council of NorwayReferences (2)Last checked downnif-0000-02317
SCIPIONResource, software resource, software application, image processing software, data processing software, software toolkitSoftware framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. \\n\\nElectron Microscopy (3DEM).\\n\\nwaiting for pdf from Joeimage, processing, data, 3DEM, macromolecular, complex, electron, microscopy, format, conversionSCR_016738(SCIPION, RRID:SCR_016738)Comunidad the Madrid, European Union, Instruct, Spanish Ministry of Economy and CompetitivenessPMID:27108186Last checked uphttps://github.com/I2PC/scipion
Genes to Cognition - Biological ResourcesResource, biomaterial supply resource, material resource, organism supplierBiological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6Jtransgenic, mutant mouse strain, c57bl/6j, 129s5, transgenic mouse line, vector, es cell line, transgenic mouseSCR_001675(Genes to Cognition - Biological Resources, RRID:SCR_001675)University of Edinburgh; Scotland; United Kingdom BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome Trustlisted by: One Mind Biospecimen Bank ListingLast checked downnif-0000-10163http://www.genes2cognition.org/mice_resources/http://www.genes2cognition.org/resources.html
Proteome 2D-PAGE DatabaseResource, database, service resource, storage service resource, software resource, data repository, data or information resourceThe Proteome 2D-PAGE Database system for microbial research is a curated database for storing and investigating proteomics data. Software tools are available and for data submission, please contact the Database Curator. Established at the Max Plank Institution for Infection Biology, this system contains four interconnected databases: i.) 2D-PAGE Database: Two dimensional electrophoresis (2-DE) and mass spectrometry of diverse microorganisms and other organisms. This database currently contains 4971 identified spots and 1228 mass peaklists in 44 reference maps representing experiments from 24 different organisms and strains. The data were submitted by 84 Submitters from 24 Institutes and 12 nations. It also contains various software tools that are important in formatting and analyzing gels and mass peaks; software include: *TopSpot: Scanning the gel, editing the spots and saving the information *Fragmentation: Fragmentation of the gel image into sections *MS-Screener: Perl script to compare the similarity of MALDI-PMF peaklists *MS-Screener update: MS-Screener can be used to compare mass spectra (MALDI-MS(/MS) as well as ESI-MS/MS spectra) on the basis of their peak lists (.dta, .pkm, .pkt, or .txt files), to recalibrate mass spectra, to determine and eliminate exogenous contaminant peaks, and to create matrices for cluster analyses. *GelCali: Online calibration of the Mr- and pI-axis of 2-DE gels with mathematical regression methods ii.)Isotope Coded Affinity Tag (ICAT)-LC/MS database: Isotope Coded Affinity Tag (ICAT)-LC/MS data for Mycobacterium tuberculosis strain BCG versus H37Rv. iii.) FUNC_CLASS database: Functional classification of diverse microorganism. This database also integrates genomic, proteomic, and metabolic data. iv.) DIFF database: Presentation of differently regulated proteins obtained by comparative proteomic experiments using computerized gel image analysis.microbial research, electrophoresis, mass spectrometry, mycobacterium tuberculosis, protein regulationSCR_001678(Proteome 2D-PAGE Database, RRID:SCR_001678)Max Planck Institute for Infection Biology; Berlin; Germany BMBF, European UnionLast checked upnif-0000-02523
Biocatalogue - The Life Science Web Services RegistryResource, web service, software resource, data or information resource, data access protocol, databaseCrowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services.biological, web, life science, programmatic access, bioinformatics, registry, annotationSCR_001679(Biocatalogue - The Life Science Web Services Registry, RRID:SCR_001679)European Bioinformatics Institute , University of Manchester; Manchester; United Kingdom EMBO, European Unionrelated to: MetaLocGramN, myExperiment, bioDBcorePMID:20484378Last checked upnif-0000-10167
RNAmmerResource, data analysis service, standalone software, data processing software, data access protocol, production service resource, web service, software application, analysis service resource, service resource, data analysis software, software resourceSoftware package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNASCR_017075(RNAmmer, RRID:SCR_017075)Technical University of Denmark; Lyngby; Denmark Danish Center for Scientific Computing, EMBIO at the University of Oslo, European Union, Research Council of NorwayPMID:17452365Last checked up
MatrixDBResource, service resource, data or information resource, production service resource, databaseFreely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interactionSCR_001727(MatrixDB, RRID:SCR_001727)Claude Bernard University Lyon 1; Lyon; France European Unionrelated to: IMEx - The International Molecular Exchange Consortium, Gene Ontology, PSI-MI, HPRD - Human Protein Reference Database, Interaction Reference Index, ConsensusPathDB, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, IntAct, listed by: re3data.orgReferences (2)Last checked upnif-0000-10226http://matrixdb.ibcp.fr/
SynGOResource, data analysis service, production service resource, analysis service resource, service resource, ontology, controlled vocabulary, data or information resourceEvidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotationSCR_017330(SynGO, RRID:SCR_017330)CERCA Program/Generalitat de Catalunya, European Union, German Federal Ministry of Education and Research, NINDS, Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvarduses: Gene Ontology, submitted by: Neuroscience Information FrameworkPMID:31171447Last checked up
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