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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
MicroArray and Gene Expression Markup LanguageResource, narrative resource, interchange format, markup language, standard specification, data or information resourceA language / data exchange format designed to describe and communicate information about microarray based experiments that is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. Descriptions using UML have an advantage over direct XML document type definitions (DTDs), in many respects. First they use graphical representation depicting the relationships between different entities in a way which is much easier to follow than DTDs. Second, the UML diagrams are primarily meant for humans, while DTDs are meant for computers. Therefore MAGE-OM should be considered as the primary model, and MAGE-ML will be explained by providing simplified fragments of MAGE-OM, rather then XML DTD or XML Schema. (from the description by Ugis Sarkans) The field of gene expression experiments has several distinct technologies that a standard must include. These include single vs. dual channel experiments, cDNA vs. oligonucleotides. Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. Given the massive amount of data associated with a single set of experiments, it is felt that Extensible Markup Language (XML) is the best way to describe the data. The use of a Document Type Definition (DTD) allows a well-defined tag set, a vocabulary, to describe the domain of gene expression experiments. It also has the virtue of compressing very well so that files in an XML format compress to ten percent of their original size. XML is now widely accepted as a data exchange format across multiple platforms.microarray, gene expression, bioinformaticsSCR_003023(MicroArray and Gene Expression Markup Language, RRID:SCR_003023) MAGE , European Bioinformatics Institute European Union, TEMBLOR projectrelated to: MADAM, MIAME, RNA Abundance Database, listed by: 3DVCLast checked downnif-0000-30390
aneurISTResource, topical portal, production service resource, analysis service resource, data analysis service, standard specification, narrative resource, service resource, portal, knowledge environment, data or information resourceAn IT infrastructure for the management, integration and processing of data associated with the diagnosis and treatment of cerebral aneurysm and subarachnoid hemorrhage. This new paradigm to understand and manage cerebral aneurysms, provides an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. aneurIST benefits patients with better diagnostics, prevention and treatment because it combines efforts of clinicians and industry. Through research clinicians gain a greater insight in aneurysm understanding, while industry will be dragged by these achievements to develop more suitable medical devices to treat the disease. This infrastructure : * Facilitate clinicians the diagnosis and study of the disease, as a result of providing a seamless access to patient data using data fusion and processing of complex information spanning from the molecular to the personal level. * Provide a better planning and personalization of minimally invasive interventional procedures for patients, after linking modern diagnostic imaging to computational tools. * Collaborate in the development, extension and exploitation of standards and protocols at all project stages. * Share biomedical knowledge providing access to a set of software tools and platforms such as aneuLink, aneuFuse, aneuRisk, aneuEndo, aneuCompute and aneuInfo. * Create awareness through scientific dissemination and collaboration. * Explore the business opportunities directly arising from aneurIST. It intends to provide an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. Software: * aneuLink will create an IT environment with the goal of establishing a link between genomics and disease. * aneuFuse will fuse diagnostic, modelling and simulation data into a coherent representation of the patient''s condition. * aneuRisk will provide clinicians with a tool to facilitate the personalized risk assessment and guidelines establishment to treat patients. * aneuEndo will develop computational tools to optimize and customize the design of endovascular devices. * aneuInfo will enable access to clinical and epidemiological data distributed in public and project-specific protected databases. * aneuCompute will provide aneurIST with distributed computing capabilities ensuring secure data transport.gene, genetic, adult, cerebral aneurysm, cerebral brain hemorrhage, cerebral hemorrhage, cerebral parenchymal hemorrhage, cerebral hemorrhage, clinical, genomic, human, intracerebral hemorrhage, intracranial aneurysm, subarachnoid hemorrhage, risk, aneurysm rupture, patient, treatment, infrastructure, platform, genomics, disease, personalized risk assessment, bioinformatics, clinical, data management, data integration, data processing, software tool, cerebrumSCR_007427(aneurIST, RRID:SCR_007427)Pompeu Fabra University; Barcelona; Spain Cerebral aneurysm, Subarachnoid hemorrhage, AgingEuropean Union, Sixth FPPriority 2 of the Information Society Technologies ISTLast checked downnif-0000-00538
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
European Bioinformatics InstituteOrganization, organization portal, portal, data or information resourceNon-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, proteinSCR_004727(European Bioinformatics Institute, RRID:SCR_004727)European Molecular Biology Laboratory BBSRC, EMBL member states, European Union, Industry Programme partners, NIH, UK Research Councils, Wellcome Trustrelated to: AgedBrainSYSBIO, ProteomeXchange, Open PHACTS, RHEA, TraCeR, used by: Blueprint Epigenome, listed by: re3data.orgLast checked upnlx_72386
European Nucleotide ArchiveResource, service resource, data or information resource, data repository, storage service resource, databasePublic archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.analysis, bioinformatics, dna, nucleotide, sequencing, web service, rna, molecular biology, nucleotide sequence, protein, gene expression, gene, genome, biochemistry, molecular structure, metabolite, protein binding, chemogenomics, gold standardSCR_006515(European Nucleotide Archive, RRID:SCR_006515)European Bioinformatics Institute EMBL, European Union, Wellcome Trustrelated to: NCBI Sequence Read Archive, ENA Sequence Version Archive, VBASE2, DDBJ Sequence Read Archive, ISA Infrastructure for Managing Experimental Metadata, DDBJ - DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan, NCBI, INSDC, INSDC, NCBI Assembly Archive Viewer, used by: BioSample Database at EBI, listed by: 3DVC,, OMICtoolsPMID:20972220Last checked upnif-0000-32981, OMICS_01029
Worldwide Protein Data Bank Resource, data or information resource, resource, databaseA free and public single global PDB archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standardSCR_006555( Worldwide Protein Data Bank , RRID:SCR_006555)BBSRC, DOE, European Molecular Biology Laboratory; Heidelberg; Germany, European Union, Japan Science and Technology Agency, NBDC - National Bioscience Database Center, NCI, NIDDK, NIGMS, NIH, NINDS, NLM, NSF, Wellcome Trustrelated to: Biological Magnetic Resonance Data Bank, Proteopedia - Life in 3D, NRG-CING, Research Collaboratory for Structural Bioinformatics Protein Data Bank, DDBJ - DNA Data Bank of Japan, PDBe - Protein Data Bank in Europe, PDBe - Protein Data Bank in Europe, PDBj - Protein Data Bank Japan, Biological Magnetic Resonance Data Bank, Research Collaboratory for Structural Bioinformatics Protein Data Bank, used by: Ligand ExpoPMID:14634627Last checked upnif-0000-23903
Interaction Proteome ProjectResource, topical portal, software application, portal, software resource, simulation software, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on January 28, 2013. (URL is no longer valid) A platform for high-throughput proteomic analysis. Major objectives of IPP include the establishment of a broadly applicable platform of routine methods for the analysis of protein interaction networks in bio-medical research. A multidisciplinary approach will address; * their validation by cell biological, biochemical and biophysical methods. * their collection in a new type of public database. * their exploitation and use for in silico simulations of protein-interaction networks. The innovations generated in IPP will provide the basis for an efficient analysis and systems modeling of fundamental biological processes in health and disease. It will develop novel technology, including a high-end mass spectrometer with extremely large dynamic range, high-density peptide arrays, and improved visualization technology for light and electron microscopy. Additionally, the novel technologies will be validated with selected model systems of high relevance to medicine and biotechnology. Extensive bioinformatics support is a key element in the project to cope with the massive increase in experimental data on protein interactions obtained using the novel technologies. In particular, the efficient integration of disparate data sets represents a key challenge in proteomics and functional genomics. Therefore, the consortium includes the creator of the only European protein-interactions database, MINT. The multi-disciplinary efforts required in the scientific program of IPP are organized into four sub-projects (SP): * SP1: Tools for interaction analysis - SP1 is dedicated to the development of innovative proteomics technology to map protein-interaction networks and their cellular topology for the interaction analyses in SP2 and SP3. * SP2: Identification of interaction partners for protein domains - SP2 will generate (high throughput) data for important protein-protein interactions defined by bioinformatics and biomedical interest and by SP3, utilizing technology developed in SP1. * SP3: Functional analysis of interactions - SP3 focuses on the validation of technologies and tools developed in SP1. It will perform functional analyses of protein-interactions in medically and biochemically relevant prokaryotic and eukaryotic (mammalian) model systems. * SP4: Interactome database and modelling - SP4 provides the required bioinformatics infrastructure for the project, comprising the improvement of the public MINT database for the collection and dissemination of the interactome data; modelling and simulation of protein-interaction networks characterised in SP2 and SP3; and the dissemination of the technology developments to the scientific community.electron, eukaryotic, biochemical, bioinformatics, biological, biomedical, biophysical, biotechnology, cell, development, disease, domain, genomics, health, interaction, light, mammalian, map, mass spectrometer, medicine, microscopy, model, modeling, network, peptide array, prokayotic, protein interaction, proteome, proteomics, silico, simulation, system, technology, tool, protein interactionSCR_008043(Interaction Proteome Project, RRID:SCR_008043)Max Planck Institute of Biochemistry; Martinsried; Germany European UnionLast checked upnif-0000-10259
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