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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)

Physical Resource or Software Tool Software

16,796 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
CREATEResource, topical portal, database, international standard specification, standard specification, narrative resource, portal, data or information resourceThe CREATE consortium represents a core of major European and international mouse database holders and research groups involved in conditional mutagenesis, primarily to develop a strategy for the integration and dissemination of Cre driver strains for modelling aspects of complex human diseases in the mouse. Collectively the participants have amassed a significant number of these strains in their respective databases. Therefore one of the goals of CREATE is to provide a unified portal for worldwide access to these critical resources. The portal can either be searched through an advanced BioMart interface, by driver name, or by anatomical site of expression using Embryonic Mouse Anatomy Project (EMAP) and Mouse Anatomy (MA) ontology terms. Search results link back to the original source of the data for more detailed information and to IMSR to order mice if available. The ontology browser is particularly useful as it enables the CREATE consortium to identify cell and tissues that are not currently covered by existing lines. CREATE also aims to coordinate the production of suitable lines by the Cre generation projects described above. Through the CREATE portal, the CREATE consortium aims to develop a strategy for the production, integration and dissemination of new Cre driver strains for modelling aspects of complex human diseases in the mouse. CREATE is also developing a roadmap for harnessing emerging technologies and methods for improving Cre-mediated recombination in vivo through targeted, intensive workshops and discussion forums on the portal. This will entail review of construct design options for classical transgenic constructs (promoter/enhancer used, small size <2025 Kb) vs large transgenic constructs (BAC, P1, YAC etc.); methods used for Cre transgenic lines including random vs targeted integration, position independent expression loci, or replacement of endogenous coding sequences with Cre recombinase under the control of the endogenous locus. CREATE provides a platform for discussion of additional issues specific to inducible Cre strategies including background activity before induction, inducibility (kinetics), efficiency, and protocols used for induction of Cre recombinase activity. Additional components of the technology roadmap will be the cataloguing of other existing methodologies (rtTA, FLP, Dre) of mouse genome modification, sharing information on validated Cre mutant lines as well as identification and assessment of new methods of mutagenesis such as RNAi and other emerging technologies. Other discussion topics addressed through surveys on the CREATE portal include the characterization of Cre lines (specificity of expression/deletion; efficiency of expression/ deletion; reproducibility of deletion from animal to animal for the same floxed allele; reproducibility with different floxed alleles; timing of expression/deletion, etc.), the extent to which Cre expression changes upon backcrossing to specific genetic backgrounds through variegation and silencing; potential phenotypes caused by either integration- mediated mutagenesis or Cre ''toxicity''; and other factors affecting the specificity of Cre-mediated expression/deletion. CREATE regularly integrates common fields from the Cre-X, CreZOO and the MGI recombinase portal resources described below. The data in common consists of: * Transgene or Knock-in name. * MGI ID of allele. * Driver. * Anatomical site of expression. * Pubmed ID. * IMSR strain name and link. * Inducibility (YES/NO).cre driver, mutagenesis, cre, gene, allele, mutant mouse es cell line, mutant mouse, es cell line, phenotype, gene expression, cre recombinase, tissue, organ, cell, mouse mutagenesis, cre lineSCR_006133(CREATE, RRID:SCR_006133)European Bioinformatics Institute European Union FP7related to: Recombinase (cre) ActivityPMID:21195764Last checked upnlx_151617
R and D SystemsResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplier who also provides assay services and products.antibody supplier, assay, serviceSCR_006140(R and D Systems, RRID:SCR_006140)Last checked upnlx_152445
University of Oregon; Oregon; USAResource, university, institutionSCR_006269(University of Oregon; Oregon; USA, RRID:SCR_006269)Last checked upnlx_45503
Laval University; Quebec; CanadaResource, university, institutionSCR_011335(Laval University; Quebec; Canada, RRID:SCR_011335)Last checked upnlx_158567
Vaccine OntologyResource, ontology, data or information resource, controlled vocabularyA biomedical ontology in the vaccine domainowlSCR_006271(Vaccine Ontology, RRID:SCR_006271)used by: Ontology of Vaccine Adverse Events, listed by: BioPortalLast checked upnlx_157621
IRIS DMC FDSNWS station Web ServiceResource, web service, software resource, data access protocolWeb service that returns International Federation of Digital Seismograph Networks (FDSN) station metadata in FDSN StationXML format or as delimited text. Results are available at multiple levels of granularity: network, station, channel and response. Metadata may be selected based on channel descriptors, time ranges, geographic regions, and more. This service is an implementation of the FDSN web service specification version 1.seismology, fdnws, station, metadata, time series, seed, wadlSCR_006177(IRIS DMC FDSNWS station Web Service, RRID:SCR_006177)IRIS DMC Web Services listed by: CINERGILast checked upSciRes_000179
ConBBPREDResource, analysis service resource, data analysis service, service resource, production service resourceA web tool for the Consensus Prediction of TransMembrane Beta-Barrel Proteins. Prediction of the transmembrane strands and topology of beta-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing different algorithmic techniques and a number of freely available predictors exist. The methods can be grossly divided to those based on Hidden Markov Models (HMMs), on Neural Networks (NNs) and on Support Vector Machines (SVMs). In this work, we compare the different available methods for topology prediction of beta-barrel outer membrane proteins. We evaluate their performance on a non-redundant dataset of 20 beta-barrel outer membrane proteins of gram-negative bacteria, with structures known at atomic resolution. Also, we describe, for the first time, an effective way to combine the individual predictors, at will, to a single consensus prediction method. We assess the statistical significance of the performance of each prediction scheme and conclude that Hidden Markov Model based methods, HMM-B2TMR, ProfTMB and PRED-TMBB, are currently the best predictors, according to either the per-residue accuracy, the segments overlap measure (SOV) or the total number of proteins with correctly predicted topologies in the test set. Furthermore, we show that the available predictors perform better when only transmembrane beta-barrel domains are used for prediction, rather than the precursor full-length sequences, even though the HMM-based predictors are not influenced significantly. The consensus prediction method performs significantly better than each individual available predictor, since it increases the accuracy up to 4% regarding SOV and up to 15% in correctly predicted topologies.predict, topology, beta-barrel outer membrane protein, outer membrane protein, protein, consensus prediction, gram-negative bacteria, transmembrane, beta-barrel proteinSCR_006194(ConBBPRED, RRID:SCR_006194)University of Athens Biophysics and Bioinformatics Laboratory Greek Ministry of National Education and Religious AffairsPMID:15647112Last checked upnlx_151740
Bentham OPENResource, journal article, organization portal, service resource, portal, data or information resourcePublish over 230 plus peer-reviewed open access journals. These free-to-view online journals cover all major disciplines of science, technology, medicine and social sciences. Bentham OPEN offers its ''Complimentary Membership'' to International R & D organizations, institutes and universities. This opportunity will entitle authors from different member institutes to a special discount of 30% in the open access publication fee for submission of articles to Bentham OPEN journals. Additionally, input and contributions from associate institutes would also be recognized and a link to their respective Website would be displayed on the Bentham OPEN membership page. The member institution''s logo will also be published on the same page. Bentham Open Membership provides the following advantages: * Possibility to explore 73 distinct disciplines by means of publishing in 239 open access journals. * Free access to all provides prospects of higher citations. * Author(s) own the copyrights to their published articles. * High standard criteria for peer-review. * Unbound right to read, download or print open access articles. * Access to a range of articles in printed form such as short communications, full length research articles, reviews or conference proceedings. * Simple steps from submission to publication, leading to fast turn-around. * Possibility of archiving published articles. The complimentary membership is valid for a span of one year and upon completion of the prescribed period, it is renewed by mutual interest and agreement. If you find the above mentioned details relevant, then kindly contact us via e-mail at membership_at_benthamscience.org or oa_at_benthamscience.org.publisher, publish, addiction, agriculture sciences, astronomy, biochemistry, biological sciences, biotechnology, cell biology, structural biology, chemistry, computer science, dentistry, earth science, energy, fuel, engineering, environmental science, ethics, food and nutrition, forest science, genomics, imaging, informatics, marine science, materials science, mathematics, medicine and health, microbiology, nanoscience, pharmaceutical sciences, physics, plant science, proteomics, psychiatry and psychology, social sciences, toxicology, transportation, veterinary sciencesSCR_006202(Bentham OPEN, RRID:SCR_006202)Last checked downnlx_151746
QTL ArchiveResource, data set, service resource, data repository, storage service resource, data or information resourceRaw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.quantitative trait locus, inbred rat strain, phenotype, cross, genetics, inbreeding, genetic marker, quantitative geneticsSCR_006213(QTL Archive, RRID:SCR_006213)Jackson Laboratory NIGMSlisted by: re3data.orgLast checked upnlx_151757http://qtlarchive.org/
Reproductive Trait and Phenotype OntologyResource, ontology, data or information resource, controlled vocabularyOntology for livestock reproductive traits and phenotypesowlSCR_006245(Reproductive Trait and Phenotype Ontology, RRID:SCR_006245)listed by: BioPortalLast checked upnlx_157574
Prefrontal.orgResource, blog, narrative resource, data or information resourceA personal weblog of developmental cognitive neuroscience by Craig Bennett in the Department of Psychology at the University of California, Santa Barbara.SCR_006247(Prefrontal.org, RRID:SCR_006247)Last checked upnif-0000-06679
WigwamsResource, software resourceA computational tool for analyzing multiple gene expression time series data sets for the same organism. The goal is to determine if there is evidence for gene regulatory mechanisms that are shared by multiple different expression responses.matlab, gene, gene module, co-regulation, time series, gene expression, differential expressionSCR_006400(Wigwams, RRID:SCR_006400)University of Warwick; Coventry; United Kingdom listed by: OMICtoolsPMID:24351708Last checked upOMICS_02214
Genotype-IBD Sharing Test Resource, software resource, software application, resourceSoftware package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.identical by descent, genotype, gene, genetic, genomic, unix, ms-windows, linux, linkage disequilibrium, linkage, associationSCR_006257( Genotype-IBD Sharing Test , RRID:SCR_006257)Vanderbilt University; Tennessee; USA NHGRI, NIDDK, Vanderbilt Diabetes Centerlisted by: Genetic Analysis SoftwarePMID:14872409Last checked downnlx_154133http://phg.mc.vanderbilt.edu/content/gist
ProgenResource, material resource, reagent supplier, commercial organization, antibody supplierAn Antibody supplierSCR_006726(Progen, RRID:SCR_006726)Last checked upnlx_152433
PatientCrossroadsResource, patient registry, topical portal, portal, people resource, data or information resourceA trusted third-party gatekeeper of patient data from participants in a rare disease ecosystem, collecting and managing the information in a scalable, cost-effective manner. Each patient registry provides critical disease knowledge which makes that disease easier to study, increasing the probability a treatment can be developed. PatientCrossroads takes a network approach to patient registry programs. Unlike companies that merely sell registry software, we offer a full range of administration, management, and genetic curation services. What does this consolidated, patient-centric approach to patient registries mean? * Patients can more easily find registries and provide their valuable data (including locations of blood and tissue samples as well as reports of diagnoses, disease symptoms, treatment usage, and lifestyle activities) * Patients can be confident in the privacy of their de-identified data and the knowledge that PatientCrossroads does not sell patient data * Researchers and pharmaceutical companies have a larger, more easily accessible pool of potential patients for research studies and clinical trials targeting specific rare diseases * Pharmaceutical companies can collect post-market surveillance data in a more scalable and cost-effective manner * Rare disease advocacy and research foundations can more easily organize their global patient populations for inclusion in trials and studiesdisease, treatment, clinical, patient, registry, drug discovery, clinical trial, research study, genetics, biorepositorySCR_006279(PatientCrossroads, RRID:SCR_006279)Rare diseaseLast checked downnlx_151889
Global-Multi Resolution Topography Image ServiceResource, web service, software resource, data access protocolAPI for requesting images from Global-Multi Resolution Topography (GRMT).topography, earth, polar, oceanography, image, apiSCR_006347(Global-Multi Resolution Topography Image Service, RRID:SCR_006347)Integrated Earth Data Applications related to: Global-Multi Resolution Topography Grid Service, listed by: CINERGILast checked upSciRes_000176
WebScopeResource, image collection, data or information resourceExpansive collection of high-quality wholeslide imagesSCR_006355(WebScope, RRID:SCR_006355)Last checked upnlx_152089
University of Oviedo; Oviedo; SpainResource, university, institutionSCR_006359(University of Oviedo; Oviedo; Spain, RRID:SCR_006359)Last checked upnlx_53766
Computational Genomics Analysis ToolsResource, software resource, software toolkitA collection of tools for the computational genomicist written in the python language to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. Please note that the tools are part of a larger code base also including genomics and NGS pipelines. Everyone who uses parts of the CGAT code collection is encouraged to contribute. Contributions can take many forms: bugreports, bugfixes, new scripts and pipelines, documentation, tests, etc. All contributions are welcome.computational genomics, genomics, command-line, next-generation sequencing, python, pipeline, functional enrichment, clustering, metagenomic, contig, variant, analysis, filter, compare, conversion, summarization, annotationSCR_006390(Computational Genomics Analysis Tools, RRID:SCR_006390)University of Oxford; Oxford; United Kingdom related to: Galaxy, listed by: OMICtoolsPMID:24395753Last checked downOMICS_02209
Botryllus schlosseri anatomy and development ontologyResource, ontology, data or information resource, controlled vocabularyOntology describing the anatomy and the development of Botryllus schlosseri.oboSCR_006602(Botryllus schlosseri anatomy and development ontology, RRID:SCR_006602)listed by: BioPortalLast checked upnlx_157342
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