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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
3DSwapResource, data or information resource, databaseCurated knowledegbase of protein structures that are reported to be involved in 3-dimensional domain swapping. 3DSwap provides literature curated information and structure related information about 3D domain swapping in proteins. Information about swapping, hinge region, swapped region, extent of swapping, etc. are extracted from original research publications after extensive literature curation.protein structure, protein, structure, 3d domain swapping, function, sequence, domain swap, 3d spatial imageSCR_004133(3DSwap, RRID:SCR_004133)Tata Institute of Fundamental Research; Mumbai; India National Centre for Biological Sciences, Tata Institute of Fundamental Research; Mumbai; India, Wellcome TrustReferences (2)Last checked upnlx_143564
Accessible Resource for Integrated Epigenomics StudiesResource, topical portal, data access protocol, web service, portal, software resource, data or information resourcePortal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time.Epigenomic, human, tissue, DNA, methylation, data, peripheral, bloodSCR_017492(Accessible Resource for Integrated Epigenomics Studies, RRID:SCR_017492)BBSRC, Medical Research Council, University of Bristol, Wellcome Trustsubmitted by: Resource Identification PortalPMID:25991711Last checked uphttp://www.bristol.ac.uk/alspac/
ACT: Artemis Comparison ToolResource, software resourceA free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.dna sequence, genome, synteny, pairwise comparisonSCR_004507(ACT: Artemis Comparison Tool, RRID:SCR_004507)Wellcome Trust Sanger Institute; Hinxton; United Kingdom Wellcome Trustlisted by: OMICtoolsPMID:15976072Last checked upnlx_48986, OMICS_00928
Africa Centre for Health and Population StudiesResource, data set, data or information resourceLongitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present.medicine, hiv infection, economic, demography, biology, social, longitudinalSCR_008964(Africa Centre for Health and Population Studies, RRID:SCR_008964)University of KwaZulu-Natal; Durban; South Africa HIVAgence Nationale de Recherches sur le Sida et les Hepatites Virales, CIDA, CSIR, Department for International Development, EDCTP, National Research Foundation, South African MRC, UNFPA, USAID, Wellcome Trustlisted by: re3data.org, DataCiteLast checked downnlx_152006
Alien-hunterResource, software resource, software applicationSoftware for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer.software, gene, transfer, interpolated, variable, motif, prediction, hgt, ivomSCR_015967(Alien-hunter, RRID:SCR_015967)Wellcome Trustworks_with: Artemis: Genome Browser and Annotation ToolPMID:16837528Last checked up
ALSPACResource, project portal, portal, data or information resourceA long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.longitudinal, study, parent, child, health, research, mother, development, research, disease, genetic, environmentalSCR_007260(ALSPAC, RRID:SCR_007260)University of Bristol; Bristol; United Kingdom UK Medical Research Council, University of Bristol, Wellcome TrustLast checked upnif-0000-30224
AribaResource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkitAnalysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlstSCR_015976(Ariba, RRID:SCR_015976)Biotechnology and Biological Sciences Research Council, Wellcome TrustPMID:29177089Last checked up
ARNIEResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.network, orthologue, paralogue, gene, orthologue, protein interaction, protein, blast, extracellular, expression profiling, interaction network, ligand, interaction, signalingSCR_000514(ARNIE, RRID:SCR_000514)Wellcome Trust Sanger Institute; Hinxton; United Kingdom MRC, Wellcome Trustlisted by: OMICtoolsPMID:20802085Last checked upOMICS_01529
Artemis: Genome Browser and Annotation ToolResource, software resourceA free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.training tool, genome browser, gene annotation, javaSCR_004267(Artemis: Genome Browser and Annotation Tool, RRID:SCR_004267)Wellcome Trust Sanger Institute; Hinxton; United Kingdom Wellcome Trustrelated to: DNAPlotter, listed by: OMICtools, 3DVC, works_with: Alien-hunterPMID:11120685Last checked upnlx_28554, OMICS_00903
Bio-eagleResource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkitSoftware package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probabilitySCR_015991(Bio-eagle, RRID:SCR_015991)Broad Institute of MIT and Harvard Austrian Science Fund, Dutch Brain Foundation, Fannie and John Hertz Foundation, NCRR, NHGRI, NHLBI, NIMH, NWO, Wellcome TrustReferences (2)Last checked uphttps://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/
Bio-FormatsResource, data processing software, software library, software application, software resource, software toolkit, image processing softwareA standalone Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard. (Dec. 2013)write, read, life science, image, format, microscopy, standard, javaSCR_000450(Bio-Formats, RRID:SCR_000450)OME - Open Microscopy Environment Wellcome Trustrelated to: OMERO, OME-TIFF Format, listed by: FORCE11PMID:20513764Last checked upnif-0000-30175http://www.force11.org/node/4810
BioLexiconResource, data or information resource, databaseA large-scale English terminological database that contains over 2.2.M lexical entries (3.3M semantic relations), terminological variants and rich linguistic information (subcategorization frames) which supports text mining systems. It is primarily intended to support text mining and information retrieval in the biomedical domain. The BioLexicon provides specific information to help determine the relevant facts to be extracted. BioLexicon is available in a relational database format (MySQL dump format) and it adheres to the EAGLES/ISO standards for lexical resources.text mining, biomedical, terminology, semantics, terminological variant, linguistic, information retrieval, computational linguisticsSCR_000589(BioLexicon, RRID:SCR_000589)National Centre for Text Mining Economic and Social Research Council, Europe PubMed Central, Wellcome Trustused by: Europe PubMed Central, uses: MEDIE, listed by: FORCE11References (2)Last checked upnlx_54008
BioMart MartViewResource, data set, web service, software resource, data access protocol, data or information resourceA web server interface of BioMart software and provides a unified view over disparate data sources that enable bioscientists to retrieve data from one or multiple sources in a simple and efficient way. This MartView web server features seamless data federation making cross querying of data sources in a user friendly and unified way. Data sources include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase, etc. The web server not only provides access through a web interface, it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services.gold standardSCR_010714(BioMart MartView, RRID:SCR_010714)EMBL, European Union FP6, Ontario Institute for Cancer Research, Wellcome TrustReferences (2)Last checked downnlx_89178
BioMart ProjectResource, software resource, web service, data access protocolA query-oriented data management system that can be used with any type of data and is particularly suited for providing "data mining" like searches of complex descriptive data. BioMart comes with an "out of the box" website that can be installed, configured and customized according to user requirements. Further access is provided by graphical and text based applications or programmatically using web services or API written in Perl and Java. BioMart has built-in support for query optimization and data federation and in addition can be configured to work as a DAS 1.5 Annotation server. The process of converting a data source into BioMart format is fully automated by the tools included in the package. Currently supported RDBMS platforms are MySQL, Oracle and Postgres.biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standardSCR_002987(BioMart Project, RRID:SCR_002987) European Bioinformatics Institute , Ontario Institute for Cancer Research Agence National de la Recherche, Breast Cancer Campaign Tissue Bank, Center for Genome Regulation, Center for Mathematical Modelling, Centre National de la Recherche Scientifique, European Molecular Biology Laboratory, Japanese Ministry of Education Culture Sports Science and Technology MEXT, National Research Foundation of Korea, Sandra Ibarra Foundation for Cancer, Spanish Government, U.S. Department of Energy, Wellcome Trustrelated to: Mouse Genome Informatics (MGI), used by: Blueprint EpigenomeLast checked upnif-0000-30184
Bio-tradisResource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkitAnalysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perlSCR_015993(Bio-tradis, RRID:SCR_015993)Wellcome Trust Sanger Institute; Hinxton; United Kingdom Alexander von Humboldt Stiftung/Foundation, Medical Research Council, Wellcome TrustPMID:26794317Last checked up
BoxPlotRResource, data visualization software, software application, web application, data processing software, software resourceWeb application that allows users to generate customized box plots in a number of variants based on their data. It creates basic box plots based on the data and can be modified to include additional information.box plot, data visualizationSCR_015629(BoxPlotR, RRID:SCR_015629)ERC, Genome Québec International Recruitment Award, Wellcome Trust, WTCCBsubmitted by: Resource Identification PortalPMID:24481215Last checked uphttps://github.com/VizWizard/BoxPlotR.shiny
Burroughs Wellcome FundResource, funding resourceThe Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation.biomedical sciences, research, science, educationSCR_005772(Burroughs Wellcome Fund, RRID:SCR_005772)Wellcome TrustLast checked upnlx_149371
CellML Model RepositoryResource, service resource, data or information resource, data repository, storage service resource, databaseRepository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.cell function, cell model, model, cell, calcium dynamics, cardiovascularc circulation, cell cycle, cell migration, circadian rhythm, electrophysiology, endocrine, excitation-contraction coupling, gene regulation, hepatology, immunology, ion transport, mechanical constitutive law, metabolism, myofilament mechanics, neurobiology, ph regulation, pkpd, signal transduction, synthetic biology, image, exposureSCR_008113(CellML Model Repository, RRID:SCR_008113)CellML Maurice Wilkins Centre for Molecular Biodiscovery, Royal Society of New Zealand, Wellcome Trustrelated to: Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: 3DVC, Integrated ModelsReferences (5)Last checked upnif-0000-20828
CellMLResource, narrative resource, interchange format, markup language, standard specification, data or information resourceThe CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org.biological model, cell, mathematical model, mathematics, metadata, model structure, model, xml, annotation, mark up languageSCR_008061(CellML, RRID:SCR_008061)University of Auckland; Auckland; New Zealand aneurIST, Foundation for Research Science and Technology, International Union of Physiological Sciences: Physiome Project, Maurice Wilkins Centre for Molecular Biodiscovery, NZIMA, VPH NoE, Wellcome Trustrelated to: PathGuide: the pathway resource list, listed by: 3DVCReferences (7)Last checked upnif-0000-10448
ChEMBLResource, data or information resource, databaseCollection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.database, compound, data, bioassay, bioactive, molecule, drug, discoverySCR_014042(ChEMBL, RRID:SCR_014042)EMBL Member States, EU Innovative Medicines Initiative, GSK, Medicines for Malaria Ventures, Pfizer, Syngenta, Wellcome Trustused by: GEROprotectors, PubChemPMID:21948594Last checked up
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