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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: Aug 10, 2019)

Physical Resource or Software Tool Software

16,721 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Berkeley-expressResource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkitTHIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018.\\nFrom website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/.\\n\\nSoftware for streaming quantification for high-throughput DNA/RNA sequencing. \\nCan be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.quantification, high-throughput, DNA, RNA, sequencing, target, fragment, analysisSCR_015990(Berkeley-express, RRID:SCR_015990)University of California; Berkeley; USA National Science Foundation Graduate Research Fellowship, NIHLast checked upbio.math.berkeley.edu
xFITOMResource, standalone software, data processing software, software application, sequence analysis software, data analysis software, software resourceA fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two.transcription factor, binding site, information theory, customizable program, sequence analysis softwareSCR_014445(xFITOM, RRID:SCR_014445)related to: CollecTF, uses: GenBankPMID:21346861Last checked uphttp://www.mybiosoftware.com/fitom-1-0-detection-binding-sites-dna-rna-sequences.htmlcompbio.umbc.edu/Software/xFITOM/ http://research.umbc.edu/~erill/
INTEGRAYEDMAPResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A web application and database schema for storing and interactively displaying genetic map data.gene, genetic, genomic, ms-windows, (nt/2000/xp profession/), require either, oracle rdbms, or, mysqlSCR_007489(INTEGRAYEDMAP, RRID:SCR_007489)listed by: Genetic Analysis SoftwareLast checked downnlx_154099ftp://cggc.agtec.uga.edu/IntegratedMap/
MAPMAKER/HOMOZResource, software resource, software applicationSoftware application that calculates multipoint lod scores in pedigrees with inbreeding loops (entry from Genetic Analysis Software)gene, genetic, genomic, c, unixSCR_009282(MAPMAKER/HOMOZ, RRID:SCR_009282)listed by: Genetic Analysis SoftwareLast checked downnlx_154463ftp://ftp-genome.wi.mit.edu/distribution/software/homoz
MAPMAKER/SIBSResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Data analysis software for complete multipoint analysis.gene, genetic, genomic, c, unixSCR_008012(MAPMAKER/SIBS, RRID:SCR_008012)listed by: Genetic Analysis SoftwareLast checked downnlx_154465https://dsgweb.wustl.edu/aldi/software/manuals/mapmaker_sibs/mapmaker_sibs.pdfftp://ftp-genome.wi.mit.edu/distribution/software/sibs
PompepResource, data set, data or information resourceFTP site to access Schizosaccharomyces pombe protein data.schizosaccharomyces pombe, yeast, s. pombeSCR_010536(Pompep, RRID:SCR_010536)European Bioinformatics Institute , PomBase Last checked downnlx_24725ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Protein_data/
BORELResource, software resource, software applicationSoftware application for inference of genealogical relationships from genetic data, including sibship inference. (entry from Genetic Analysis Software)gene, genetic, genomic, c, unix, (dec-unix/..)SCR_013135(BOREL, RRID:SCR_013135)listed by: Genetic Analysis SoftwareLast checked upnlx_154197ftp://ftp.u.washington.edu/pub/user-supported/pangaea/PANGAEA/BOREL
TDT-AEResource, software resource, software applicationSoftware program that computes a likelihood-based transmission disequilibrium test. The data are genotypes on trios (father, mother, affected child) in which random genotyping errors leading to Mendelian inconsistencies may or may not have occurred. This program computes the TDT-AE statistic on all trios (whether Mendelianly consistent or not) and thereby maintains a correct type I error rate in the presence of random genotyping errors. (entry from Genetic Analysis Software)gene, genetic, genomic, c, ms-windows, (2000/dos), unix, (sun solaris), linux, (redhat)SCR_009094(TDT-AE, RRID:SCR_009094)listed by: Genetic Analysis SoftwarePMID:11443542Last checked downnlx_154112ftp://linkage.rockefeller.edu/software/tdtae2
JASPARResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of a curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. It is useful to scientists seeking models for specific factors or structural classes, or if experimental evidence is paramount. The prime difference to similar resources (TRANSFAC, TESS etc) consist of the open data access, non-redundancy and quality: JASPAR CORE is a smaller set that is non-redundant and curated. JASPAR is a collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. JASPAR is the only database with this scope where the data can be used with no restrictions (open-source). The database is complemented by a web interface for browsing, searching and subset selection, an online sequence analysis utility and a suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dnaSCR_003030(JASPAR, RRID:SCR_003030) Karolinska Institutet; Stockholm; Sweden , University of Copenhagen; Copenhagen; Denmark Carlsberg Foundation, EMBRACEa Sixth Framework Network of Excellence, European Union, Novo Nordisk Foundation, Research Council of Norway, Sars Centrerelated to: Babelomics, listed by: OMICtools, re3data.orgReferences (3)Last checked downnif-0000-03061, OMICS_00538http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se
neuroVIISASResource, data visualization software, data processing software, software application, data analytics software, network graph visualization software, software resource, d visualization softwareAn open framework for integrative data analysis, visualization and population simulations for the exploration of network dynamics on multiple levels. This generic platform allows the integration of neuroontologies, mapping functions for brain atlas development, and connectivity data administration; all of which are required for the analysis of structurally and neurobiologically realistic simulations of networks. What makes neuroVIISAS unique is the ability to integrate neuroontologies, image stacks, mappings, visualizations, analyzes and simulations to use them for modelling and simulations. Based on the analysis of over 2020 tracing studies, atlas terminologies and registered histological stacks of images, neuroVIISAS permits the definition of neurobiologically realistic networks that are transferred to the simulation engine NEST. The analysis on a local and global level, the visualization of connectivity data and the results of simulations offer new possibilities to study structural and functional relationships of neural networks. neuroVIISAS provide answers to questions like: # How can we assemble data of tracing studies? (Metastudy) # Is it possible to integrate tracing and brainmapping data? (Data Integration) # How does the network of analyzed tracing studies looks like? (Visualization) # Which graph theoretical properties posses such a network? (Analysis) # Can we perform population simulations of a tracing study based network? (Simulation and higher level data integration) neuroVIISAS can be used to organize mapping and connectivity data of central nervous systems of any species. The rat brain project of neuroVIISAS contains 450237 ipsi- and 175654 contralateral connections. A list of evaluated tracing studies are available. PyNEST script generation does work using WINDOWS OS, however, the script must be transferred to a UNIX OS with installed NEST. The results file of the NEST simulation can be visualized and analyzed by neuroVIISAS on a WINDOWS OS.platform, simulation, mapping data, connectivity data, central nervous system, tracing, connectivity, java, image modality, pynest, nest, animation, brain, nervous system, brain mapping, neuroimaging, terminology, ontology, connectomics, atlas, population spike analysis, analytics, connectome, 3d visualization, visual analytics, ontologySCR_006010(neuroVIISAS, RRID:SCR_006010)University of Rostock; Mecklenburg-Vorpommern; Germany listed by: 3DVCPMID:22350719Last checked downnlx_151398http://139.30.176.116/index-Dateien/Page455.htm
VoronoiaResource, software resource, software toolkit, data or information resource, databaseVoronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins.SCR_006005(Voronoia, RRID:SCR_006005)University Medicine Berlin; Berlin; Germany Last checked upnif-0000-03641http://141.42.202.21/voronoia/index.php
TAGSResource, software resource, software application, data analysis software, data processing software, time-series analysis softwareSoftware tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows.gene, enrichment analysis, time series, function, structureSCR_004294(TAGS, RRID:SCR_004294)Tsinghua University; Beijing; China Last checked upnlx_31187http://166.111.130.26/member/yliu/TAGS/
Prediction of Activity Spectra for SubstancesResource, data analysis software, data processing software, database, software application, software resource, data or information resourcePASS is a computer program which predicts the biological activity spectrum for a compound on the basis of its structural formula. The result of prediction is displayed for free. PASS Inet predicts 3678 pharmacological effects, mechanisms of action, mutagenicity, carcinogenicity, teratogenicity and embryotoxicity. PASS gives you hits in the following: - Finding most probable new leads with required activity spectra among the compounds from in-house and commercial data bases. - Revealing new effects and mechanisms of action for the old substances in corporate and private data bases. - Providing the basis for selection of the most prospective compounds for high throughput screening from the set of available samples. - Determining the assays that are more relevant for a particular compound. Sponsors: This work is supported by the Russian Foundation for Basic Research (Grant # 03-07-90282).element, embryotoxicity, activity, carcinogenicity, chemical, compound, mechanism, m utagenicity, pharmacological, spectrum, structural formula, teratogenicitySCR_001971(Prediction of Activity Spectra for Substances, RRID:SCR_001971)Last checked upnif-0000-10543http://195.178.207.233/PASS/
Exon Domain DatabaseResource, data or information resource, databaseExDom is a unique database developed for the comparative visualization and analysis of exon-intron structure of protein domains in seven eukaryotic genomes (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). The ExDom database integrates 3744 protein domains annotated in the Pfam database to their corresponding exon-intron structures in 40,390 genes annotated in the RefSeq database and provides a unique platform for integrated comparative analysis of exon-domain relationships. The comparative graphical viewer in ExDom, implemented in Flash MX 6, allows users to query for a domain of interest, retrieve all proteins across different organisms which have this common domain, and then, visualize and compare the exon-intron structures of the domain in these proteins. Homo sapien genome, Mus musculus genome, Bos taurus genome, Rattus norvegicus genome, Danio rerio genome, Gallus gallus genome, Arabidopsis thaliana genomeeukaryotic genome editing, eukaryotic protein, exon, gallus gallus genome, arabidopsis thaliana genome, bos taurus genome, danio rerio genome, homo sapien genome, intron, mus musculus genome, rattus norvegicus genomeSCR_012736(Exon Domain Database, RRID:SCR_012736)Last checked upnif-0000-02825http://66.170.16.154/ExDom/
CARTaGENEResource, biomaterial supply resource, data or information resource, material resource, databaseAs both the public health survey of Quebec, and the Quebec resource for scientists interested in personalized medicine, genomics and public health, this public resource operates under a governance framework and consists of a databank and a biobank. The database contains environmental, demographic and health data. The biobank contains DNA, blood and urine samples. Access to CARTaGENE will be granted to researchers who are seeking to better understand how genes interact with other genes, with the environment and with lifestyle factors. They have collected in-depth information on over 20 000 Quebecers, including 446 sociodemographic, life-style and health data, 190 physiological parameters, 22 types of biochemical analyses and 41 types of haematological analyses. They have also collected 11 types of blood, plasma, serum and urine samples from most participants. Genealogical reconstruction of recruited participants, in collaboration with BALSAC Project, is also possible. CARTaGENE data and samples include the following: Health Questionnaire, Physical measures, Biochemical and hematological analysis, Biological samples stored in the Biobank. CARTagene is currently contacting participants (who have agreed to be recontacted) to collect additional data on environmental exposure. Data on dietary habits will be collected during the second phase of this component which will begin soon. Any scientific researcher working in a public or private organization at the national or international level may apply for access to CARTaGENE samples or data.dna, blood, urine, gene, environment, lifestyle, health, questionnaire, physical measure, biochemical analysis, hematological analysis, biological sample, longitudinal, dietSCR_010614(CARTaGENE, RRID:SCR_010614)University of Montreal; Quebec; Canada listed by: One Mind Biospecimen Bank ListingLast checked downnlx_53142http://www.cartagene.qc.ca/http://67.159.214.68/index.php?lang=english
University of Puerto Rico Biomedical Informatics Research CoreResource, this resource is no longer in service, core facility, nif annotation standard, narrative resource, service resource, standard specification, access service resource, availability annotation standard, data or information resourceCore aims to enhance biomedical research in Puerto Rico by providing resources for research, education and training. These resources will work to advance these specific aims: 1. enhance biomedical research in PR by providing researchers with the bioinformatics tools and technical support they require to perform cutting-edge biomedical research; 2. enhance the computational biology research environment in Puerto Rico by establishing research collaborations with biomedical, computational and mathematics researchers; 3. enhance multidisciplinary research by developing new courses and educational materials in computational biology, statistics and bioinformatics in collaboration with research faculty and the Science and Technology Competency Enhancement (STCE) Core; 4. enhance research by promoting advanced networking between PRAABRE member institutions, to enable collaborative research on and off the island; 5. enhance biomedical research by promoting effective access to scientific literature and databases for the biomedical researchers in PRAABRE; and 6. enhance biomedical research by enabling effective management of bibliographic information by fostering the use of bibliographic software and applying it to literature searches, articles and references management and manuscript writing.THIS RESOURCE IS NO LONGER IN SERVCE, documented January 24, 2019.SCR_010119(University of Puerto Rico Biomedical Informatics Research Core, RRID:SCR_010119)University of Puerto Rico; Puerto Rico; USA related to: Puerto Rico Clinical and Translational Research Consortium Core Laboratory, Puerto Rico Clinical and Translational Research Consortium Nursing Services, Puerto Rico Clinical and Translational Research Consortium Patients Coordinator Services, Puerto Rico Clinical and Translational Research Consortium Biostatistic Core Laboratory, Puerto Rico Clinical and Translational Research Consortium Research Subject Advocate, listed by: Eagle ILast checked upnlx_156594http://aabre.hpcf.upr.edu/node/133
MUSC Center on Aging Campbell Neuropathology LaboratoryResource, biomaterial supply resource, biospecimen repository, tissue bank, service resource, brain bank, storage service resource, material resource, material storage repositoryA brain bank and biospecimen repository that provides research materials to clinicians, scientists and pathologists in South Carolina. The bank provides both control and diseased biospecimens and brain tissue needed for research in Alzheimer's disease, Parkinson's disease and other related neurological disorders. The Campbell Laboratory coordinates the brain tissue donation program, provides post-mortem confirmation of a patient having neurological disorders, and leads research trials. Any South Carolina resident can choose to sign up as a tissue donor and have their brain tissue donated post-mortem to be used for neurological disorder research. The tissue bank will process and analyze these tissue samples and send the results to the deceased person's family.brain tissue, brain, tissue, alzheimer's disease, parkinson's disease, neurological disorder, stroke, dementia, normal control, late adult human, clinical trialSCR_008826(MUSC Center on Aging Campbell Neuropathology Laboratory, RRID:SCR_008826)Medical University of South Carolina Center on Aging Alzheimer's disease, Parkinson's disease, Neurological disorder, Stroke, Aging, Dementialisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144505http://academicdepartments.musc.edu/brainbank/
autoSNPdbResource, service resource, data or information resource, data repository, storage service resource, databaseWe have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The implementation of autoSNPdb allows researchers to query the results of SNP analysis to characterize SNPs between specific groups of individuals or within genes with predicted function. The system is flexible and researchers may add additional levels of annotation, and perform novel queries specific to their area of interest. If you have sequence data you'd like to include please contact Dave Edwards.gene, gene function, single nucleotide polymorphismSCR_001927(autoSNPdb, RRID:SCR_001927)University of Queensland; Brisbane; Australia Australian Research CouncilReferences (2)Last checked downnif-0000-02589https://omictools.com/autosnpdb-toolhttp://acpfg.imb.uq.edu.au/autosnpdb.php
AIDS and Cancer Specimen ResourceResource, biomaterial supply resource, material resource, tissue bank, cell repositoryA biorepository for HIV-infected human biospecimens from a wide spectrum of HIV-related or associated diseases, including cancer, and from appropriate HIV-negative controls. The ACSR has formalin-fixed paraffin embedded biospecimens, fresh frozen biospecimens, malignant cell suspensions, fine needle aspirates, and cell lines from patients with HIV-related malignancies. It also contains serum, plasma, urine, bone marrow, cervical and anal specimens, saliva, semen, and multi-site autopsy speicmens from patients with HIV-related malignancies including those who have participated in clinical trials. The ACSR has an associated databank that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. The ACSR database contains more than 300,000 individual biospecimens with associated clinical information. Biospecimens are entered into the ACSR database by processing type, disease category, and number of cases defined by disease category.aids, hiv, cancer, virology, immunology, pathology, epidemiology, tumor, assay development, clinical data, clinical, tumor tissue, biological fluid, bodily fluid, malignant cell suspension, fine needle aspirate, cell line, serum, plasma, urine, bone marrow, cervical specimen, anal specimen, saliva, semenSCR_004216(AIDS and Cancer Specimen Resource, RRID:SCR_004216)University of California at San Francisco; California; USA AIDS, Cancer, HIV-associated malignancy, HIVNCIlisted by: One Mind Biospecimen Bank ListingLast checked upnlx_23946http://acsr.ucsf.edu/Home/tabid/37/Default.aspx
AIDA ToolkitResource, software resource, software toolkit, data access protocol, web serviceA generic set of components that can perform a variety of tasks, such as learn new pattern recognition models, perform specialized search on resource collections, and store knowledge in a repository. W3C standards are used to make data accessible and manageable with semantic web technologies such as OWL, RDF(S), and SKOS. The AIDA Toolkit is directed at groups of knowledge workers that cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. The server offers services for: text indexing and statistics, metadata storage and querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, and model learning.software toolkit, web service, search, learning, storage, workflow, text indexing, text statistics, metadata storage, metadata querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, model learningSCR_005914(AIDA Toolkit, RRID:SCR_005914)related to: TavernaLast checked upnlx_149497http://adaptivedisclosure.org/aida/
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