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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)

Physical Resource or Software Tool Software

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
2DMAPResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for constructing 2-d crossover-based map.gene, genetic, genomic, ms-dosSCR_009036(2DMAP, RRID:SCR_009036)listed by: Genetic Analysis SoftwareLast checked downnlx_154001
2LDResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.gene, genetic, genomic, cSCR_000826(2LD, RRID:SCR_000826)listed by: Genetic Analysis SoftwareLast checked downnlx_154006http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software.htm
2SNPResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. An algorithm resource for scalable phasing method for trios and unrelated individuals.gene, genetic, genomicSCR_009038(2SNP, RRID:SCR_009038)listed by: Genetic Analysis SoftwarePMID:18451440Last checked downnlx_154003https://omictools.com/2snp-toolhttp://alla.cs.gsu.edu/~software/2SNP/
3D-Genomics DatabaseResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Database containing structural annotations for the proteomes of just under 100 organisms. Using data derived from public databases of translated genomic sequences, representatives from the major branches of Life are included: Prokaryota, Eukaryota and Archaea. The annotations stored in the database may be accessed in a number of ways. The help page provides information on how to access the database. 3D-GENOMICS is now part of a larger project, called e-Protein. The project brings together similar databases at three sites: Imperial College London , University College London and the European Bioinformatics Institute . e-Protein''s mission statement is To provide a fully automated distributed pipeline for large-scale structural and functional annotation of all major proteomes via the use of cutting-edge computer GRID technologies. The following databases are incorporated: NRprot, SCOP, ASTRAL, PFAM, Prosite, taxonomy, COG The following eukaryotic genomes are incorporated: Anopheles gambiae, protein sequences from the mosquito genome; Arabidopsis thaliana, protein sequences from the Arabidopsis genome; Caenorhabditis briggsae, protein sequences from the C.briggsae genome; Caenorhabditis elegans protein sequences from the worm genome; Ciona intestinalis protein sequences from the sea squirt genome; Danio rerio protein sequences from the zebrafish genome; Drosophila melanogaster protein sequences from the fruitfly genome; Encephalitozoon cuniculi protein sequences from the E.cuniculi genome; Fugu rubripes protein sequences from the pufferfish genome; Guillardia theta protein sequences from the G.theta genome; Homo sapiens protein sequences from the human genome; Mus musculus protein sequences from the mouse genome; Neurospora crassa protein sequences from the N.crassa genome; Oryza sativa protein sequences from the rice genome; Plasmodium falciparum protein sequences from the P.falciparum genome; Rattus norvegicus protein sequences from the rat genome; Saccharomyces cerevisiae protein sequences from the yeast genome; Schizosaccharomyces pombe protein sequences from the yeast genomestructure database, protein structureSCR_007430(3D-Genomics Database, RRID:SCR_007430)Imperial College London; London; United Kingdom Last checked downnif-0000-00553
3OmicsResource, software resource, web applicationTHIS RESOURCE IS NO LONGER IN SERVICE, documented October 19, 2016. A web tool for visualizing and integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for transcripts, proteins and metabolites.metabolomics, metabolomics tool, transcriptomics, proteomics, inter-omic, correlation, network, relationship visualizationSCR_014678(3Omics, RRID:SCR_014678)listed by: Metabolomics WorkbenchPMID:23875761Last checked down
ACD/ NMR ProcessorResource, software resource, software toolkitTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports.metabolomics, metabolomics tool, structure verification, data analysis, nmr, nmr processingSCR_014679(ACD/ NMR Processor, RRID:SCR_014679)listed by: Metabolomics WorkbenchLast checked up
AceViewResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER SUPPORTED, documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standardSCR_002277(AceView, RRID:SCR_002277)NCBI Last checked downnif-0000-21007http://www.ncbi.nih.gov/IEB/Research/Acembly/
A Comprehensive Resource Base for C. elegans K+ ChannelsResource, reagent supplier, material resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Supplies potassium channel cDNA clones in vectors suitable for functional expression and stocks of gene knockout strains. Supporting this resource base are studies showing the basic biophysical properties of the channels, studies showing the phenotypes of mutants, and information on the cell-type expression patterns of potassium channels. Studies of potassium channel cell-type expression patterns and functional properties; studies of behavioral phenotypes; generation of knockout mutants. Full-length cDNAs encoding C. elegans potassium channels in a vector suitable for functional expression in Xenopus oocytes and mammalian cell lines are available on request. Information is also provided describing the cell-type expression patterns and basic biophysical properties of potassium channels. And data on behavioral phenotypes are also available. C. elegans strains carrying knockouts of potassium channels are also generated and deposited at the C. elegans stock center at the University of Minnesota.expression, gene, behavioral, biophysical, cdna, c. elegans, cell, clone, ion channel, knockout, mammalian, mutant, oocyte, phenotype, potassium, vector, xenopusSCR_008360(A Comprehensive Resource Base for C. elegans K+ Channels, RRID:SCR_008360)Washington State University; Washington; USA NCRRLast checked downnif-0000-25471
Adenoma Polyp Tissue BankResource, biomaterial supply resource, material resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York.blood, serum, white blood cell, adenoma tissue, tissue, whole blood, block, slide, colorectal adenoma, celecoxib, adenoma, cancer, colorectal cancer, clinical trial, polyp, risk factorSCR_005366(Adenoma Polyp Tissue Bank, RRID:SCR_005366)Human Tissue Resource Network Increased risk for colorectal carcinomaNCIlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144435
AGEINFResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application used to infer the age of a rare, selectively-neutral mutation.gene, genetic, genomic, cSCR_009039(AGEINF, RRID:SCR_009039)Aginglisted by: Genetic Analysis SoftwarePMID:10978301Last checked downnlx_154004http://www.math.sfu.ca/~jgraham/Papers/Programs/AgeCode/
Allen Institute NeurowikiResource, wiki, data or information resource, database, narrative resource, ontology, controlled vocabularyTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. The Allen Institute Neurowiki is a joint project between Vulcan Inc. and the Allen Institute to build a Semantic Wiki mapping genetic instances. It is a finished prototype testing the import pipelines and display componenets for combining 5 major RDF datasets from 4 different sources. Current planning includes mapping complete datasets, curating a better ontology, and creating multiple ontology management for a user class. Biological Linked Data Map: * Open, public online access * Data from multiple RDF data stores * Complete import pipeline using LDIF framework * Outlines of each imported instance embedding inline wiki properties and providing views of imported properties from original RDF datasets * Charting tools that ''''pivot'''' SPARQL queries providing several views of each query * Navigation and composition tools for accessing and mining the data Where did we get the data? * KEGG: Kyoto Encyclopedia of Genes and Genomes: KEGG GENES is a collection of gene catalogs for all complete genomes generated from publicly available resources, mostly NCBI RefSeq * Diseasome: The Diseasome website is a disease / disorder relationships explorer and a sample of an innovative map-oriented scientific work. Built by a team of researchers and engineers, it uses the Human Disease Network dataset. * DrugBank: The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. * Sider: Sider contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. Every piece of content on every instance page is generated by Semantic Result Formatters interpreting SPARQL results.gene, disease, drug, effect, pathway, sparql, triplestore, probe, structureSCR_005042(Allen Institute Neurowiki, RRID:SCR_005042)Allen Institute for Brain Science related to: KEGG, Diseasome, DrugBank, SIDERLast checked downnlx_144032
Alzheimers Research CenterResource, topical portal, portal, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The main site for the Medical Shool of Georgia's Alzheimer's research.SCR_007309(Alzheimers Research Center, RRID:SCR_007309)Medical College of Georgia; Georgia; USA Last checked downnif-0000-00166http://www.mcg.edu/centers/alz/
AlzSWAN Knowledge BaseResource, portal, knowledge environment, community building portal, knowledgebase, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A community-driven knowledgebase of Alzheimer disease, in which researchers can annotate scientific claims, data, and information, putting these into the context of testable hypotheses and treatment discovery. This SWAN project adds a collection of hand-curated hypotheses to a research paper, which are then related through a set of discourse relationships. They can be browsed and relations between claims, as well as support networks for a specific claim, are made and visualized. AlzSWAN is where you explore scientific knowledge about Alzheimer disease and share your own ideas, comments and questions in a semantically structured system. AlzSWAN is enabled by Semantic Web technology, a new standard for knowledge organization and transfer on the Web. AlzSWAN organizes and manages knowledge using formal knowledge descriptions called ontologies. Using these formal knowledge descriptions, they can tie statements made in scientific publications or on the Web to scientific evidence, biological terminologies, and knowledgebases, and to claims and counterclaims made by other researchers.hypothesis, claim, research paper, relationship, semantics, annotationSCR_003017(AlzSWAN Knowledge Base, RRID:SCR_003017)Alzheimer's Research Forum Alzheimer's diseasealz.org, Ellison Medical Foundationrelated to: Semantic Web Applications in Neuromedicine (SWAN) Ontology, listed by: FORCE11PMID:17510163Last checked downnif-0000-00524
Amino Acid-Nucleotide Interaction DatabaseResource, service resource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. AANT, the Amino Acid-Nucleotide Interaction Database, contains information derived from all of the protein/nucleic acid complexes with experimentally determined structures in the Protein Data Bank. You can visualize the AANT models using the simple web interface, which relies on the Chime plug-in. You can also download these models for further analysis using publicly available tools for manipulating PDB structures. The software that generates AANT uses HBPLUS to predict hydrogen bond interactions between single bases and single amino acid residues within these complexes. The AANT software uses this information to break down a single PDB structure into scores of individual interactions between either the base, sugar, or phosphate of a nucleotide and the side chain or peptide backbone of a amino acid. The software then superimposes all the interactions between a particular moiety of a nucleotide and a particular moiety of a amino acid residue into a single 3D model, centering on a particular point in the base, sugar, or phosphate. The AANT software then groups geometrically similar interactions into clusters.SCR_004617(Amino Acid-Nucleotide Interaction Database, RRID:SCR_004617)University of Texas at Austin; Texas; USA PMID:14681388Last checked downnlx_61417
ANCESTRYResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that provides an easy to use web-based user interface to compute individual ancestry estimates using the Maximum Likelihood Estimation method. This website also allows registered users to manage genotype and marker/allele frequency files. Registration is optional.gene, genetic, genomic, ruby on rails, fortran, web-basedSCR_009121(ANCESTRY, RRID:SCR_009121)listed by: Genetic Analysis SoftwareLast checked downnlx_154224
ANFF CharacterisationResource, service resource, core facility, access service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Network of laboratories which provides leading-edge research capability and supports excellence in science. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological materials) and transform these into structures that have various applications.atomic force microscopy, auger electron spectroscopy, chromatography, confocal microscopy, differential scanning calorimetry, electrochemical impedance spectroscopy, electron spin resonance spectroscopy, ellipsometry, film stress measurement, fluorescence microscopy, gas chromatography-mass spectrometry, holographic microscopy, ion beam microscopy, matrix-assisted laser desorption ionization time-of-flight, mass spectrometry, metallographic service, nuclear magnetic resonance spectroscopy, nuclear magnetic resonance, spectroscopy, phase contrast microscopy, raman spectroscopy, rutherford backscattering spectrometry, scanning electron microscopy, scanning near field microscopy, optical imaging, spectrofluorimetry, surface charge measurement, transmission electron microscopy, ultra violet visible spectrophotometry, x-ray diffraction, x-ray photoelectron spectrometry, x-ray tomographySCR_012687(ANFF Characterisation, RRID:SCR_012687)Australian National Fabrication Facility related to: Australian National Fabrication Facility Labs and Facilities, listed by: Science ExchangeLast checked downSciEx_8884
ANFF Specialist Device FabricationResource, service resource, core facility, access service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. The ANFF provides leading-edge research capability and supports excellence in science. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological moieties) and transform these into structures that have application in sensors, medical devices, nanophotonics and nanoelectronics. It has a strong emphasis on service provision to the research community. ANFF seeks to enhance national and international collaborations and enable world-class-research.SCR_012689(ANFF Specialist Device Fabrication, RRID:SCR_012689)Australian National Fabrication Facility related to: Australian National Fabrication Facility Labs and Facilities, listed by: Science ExchangeLast checked downSciEx_8880
Anxiety InsightsResource, blog, narrative resource, data or information resourceTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016.SCR_008717(Anxiety Insights, RRID:SCR_008717)Last checked downnlx_13334
APEResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that extends partially observed genotype data to the whole pedigree. Can be used for generating starting points for MCMC samplers and for checking that the genotype data are consistent with the pedigree structure.gene, genetic, genomic, c, unixSCR_009122(APE, RRID:SCR_009122)listed by: Genetic Analysis SoftwareLast checked downnlx_154227http://www.helsinki.fi/~mpirinen/download
ASH Video LibraryResource, video resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. ASH's video library includes a number of films produced on various topics, including ASH''s history and award winners, Society programs such as the Clinical Research Training Institute, and a trailer and clips from the hematology documentary Blood Detectives, which aired on Discovery Health. These videos were created for educational purposes, and we encourage members of the hematology community to share them with others.hematology, bloodSCR_005777(ASH Video Library, RRID:SCR_005777)American Society of Hematology Blood disease, Blood disorderLast checked downnlx_149395
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