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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
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, 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
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 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:, affiliated with: IMEx - The International Molecular Exchange Consortium, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (8)Last checked upnlx_152821
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 up
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 up
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
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 up
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-0000-10226
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
Connection-set algebraResource, software resourceSoftware tool for description of connectivity in small and large scale neuronal network models. It provides operators to form more complex sets of connections from simpler ones and also provides parameterization of such sets. Can be used as component of neuronal network simulators or other tools.Connectivity, neuronal, network, model, simulatorSCR_017397(Connection-set algebra, RRID:SCR_017397)European UnionPMID:22437992Last checked up
Project DAREResource, project portal, organization portal, portal, consortium, data or information resourceEU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously.European Union, infrastructure, workflow, connectivity, layer, methodology, integrated, data, AgileSCR_017538(Project DARE, RRID:SCR_017538)European UnionLast checked up
VideoLectures.NETResource, narrative resource, training material, video resource, data or information resourceAward-winning free and open access educational video lectures repository. The lectures are given by distinguished scholars and scientists at the most important and prominent events like conferences, summer schools, workshops and science promotional events from many fields of Science. The portal is aimed at promoting science, exchanging ideas and fostering knowledge sharing by providing high quality didactic contents not only to the scientific community but also to the general public. All lectures, accompanying documents, information and links are systematically selected and classified through the editorial process taking into account also users' comments.artificial science, machine learning, network, science, semantic, lecture, biology, chemistry, computers, computer science. environment, health sciences, life science, mathematics, medicine, physics, thechnologySCR_001972(VideoLectures.NET, RRID:SCR_001972)Jozef Stefan Institute; Ljubljana; Slovenia European UnionLast checked upnif-0000-10544
InteroPorcResource, source code, data analysis service, data analysis software, data processing software, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resourceAutomatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, proteinSCR_002067(InteroPorc, RRID:SCR_002067)CEA; Gif sur Yvette; France European Union, French Atomic Energy Commission, French National Agency of Research, Marie Curie Fellowshiprelated to: Integr8 : Access to complete genomes and proteomes, IntAct, MINT, Database of Interacting Proteins, PSICQUIC RegistryPMID:18508856Last checked upnif-0000-20816
ConsensusPathDBResource, data or information resource, databaseAn integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.gene regulatory network, pathway, gene regulatory network, molecular interaction, interaction, gene regulation, protein interaction, genetic interaction, biochemical reaction, drug-target interaction, molecule, visualization, gene, protein, complex, metaboliteSCR_002231(ConsensusPathDB, RRID:SCR_002231)Max Planck Institute for Molecular Genetics; Berlin; Germany European Unionrelated to: BIND, BioCarta Pathways, BioGRID, CORUM, Database of Interacting Proteins, DrugBank, HPRD - Human Protein Reference Database, HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism, Integrating Network Objects with Hierarchies, InnateDB, IntAct, KEGG, MINT, MIPS Mammalian Protein-Protein Interaction Database, MatrixDB, NetPath, Research Collaboratory for Structural Bioinformatics Protein Data Bank, PDZBase, Pathway Interaction Database, PIG - Pathogen Interaction Gateway, PINdb, PharmGKB, PhosphoPOINT, PhosphoSitePlus: Protein Modification Site, Reactome, Small Molecule Pathway Database, SignaLink, SPIKE, Therapeutic Target Database, WikiPathways, listed by: OMICtoolsReferences (4)Last checked upnif-0000-02684, OMICS_01903
CYGD - Comprehensive Yeast Genome DatabaseResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceThe MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis.saccharomyces cerevisiae, yeast, yeast genome, genomeSCR_002289(CYGD - Comprehensive Yeast Genome Database, RRID:SCR_002289)DFG, European Union, Federal Ministry of Education Science Research and Technology, Government of the Brussels Region - Belgiumrelated to: FunSpecPMID:15608217Last checked upnif-0000-02713
Current Controlled TrialsResource, service resource, data or information resource, data repository, storage service resource, databaseFree-to-view clinical trials register of clinical trials worldwide, it allows users to search, register and share information about randomized controlled trials. Publication services are also available via the range of open access peer-reviewed journals published by BioMed Central. Current Controlled Trials is run by an editorial and technical in-house team. It receives advice from an international Advisory Group, including academics, doctors and health care specialists of international renown. The Advisory Group provides valuable guidance on the current activities and possible new directions of Current Controlled Trials' two databases, the metaRegister of Controlled Trials (mRCT) and the International Standard Randomised Controlled Trial Number (ISRCTN) scheme.controlled trial, health, public health, science, trial, randomized controlled trial, clinical trialSCR_002325(Current Controlled Trials, RRID:SCR_002325)administrative fee, European Union, Science Navigation Grouprelated to: ISRCTN Registry, uses: ISRCTN RegistryLast checked upnif-0000-21104
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