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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)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
ADHD-200 SampleResource, disease-related portal, data set, topical portal, portal, data or information resourceA grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU)mri, fmri, brain, neuroimaging, attention deficit-hyperactivity disorder, anatomical, resting state functional mri, child, adolescent, human, young, early adult human, functional imaging, structural imaging, normal, normal controlSCR_005358(ADHD-200 Sample, RRID:SCR_005358)1000 Functional Connectomes Project Attention deficit-hyperactivity disorderrelated to: Neuro Bureau, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked downnlx_144426
MEME Suite - Motif-based sequence analysis toolsResource, source code, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, database, service resource, software resource, data or information resourceSuite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysisSCR_001783(MEME Suite - Motif-based sequence analysis tools, RRID:SCR_001783)National Biomedical Computation Resource NCRRrelated to: Gene Ontology, Glam2, ANNOgesic, listed by: OMICtools, lists: DREMEPMID:19458158Last checked downnif-0000-10298,
SNPperResource, software resourceRetrieve known single-nucleotide polymorphisms (SNPs) by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions.single-nucleotide polymorphism, gene, chromosomeSCR_001963(SNPper, RRID:SCR_001963)University of Florida; Florida; USA listed by: OMICtoolsPMID:12490454Last checked downOMICS_01926
Italian Rett Syndrome databaseResource, biomaterial supply resource, biospecimen repository, data set, service resource, storage service resource, data or information resource, material resource, material storage repositoryData and biospecimen from Rett Syndrome patients shared with the scientific community with the ability to visualize the list of available samples and select those with specific clinical and molecular features. It also contains information on biospecimen samples from x-linked retardation, microdeletion, duplication syndromes, autosomal MR, and retinoblastoma. The bank is active since 1998 and it is located in the Medical Genetics Unit, at the University Hospital of Siena. The bank is divided in three distinct sections: # Rett Syndrome. This section contains samples from patients affected by Rett syndrome, a neurodegenerative disease affecting almost exclusively girls with an estimated frequency of 1:10000-15000 live born. By accessing the section users can see a list of all patients available with their phenotype, the specific MECP2 or CDKL5 mutation if known and the kind of biological samples available for each patient. The availability of this large panel of patients is potentially important for the clarification of the molecular bases of Rett syndrome. In fact, a 20-30 of Rett cases do not have MECP2 or CDKL5 mutations. These patients might bear intronic/promoter MECP2 or CDKL5 mutations or they might have alterations in one or more genes different from MECP2 or CDKL5, as suggested by the identification of various chromosomal rearrangements. To confirm a causative role of these rearrangements, and to identify the relevant gene/s, it is important to collect a great number of patients in which to search for overlapping rearrangements or point mutations in candidate genes. # X-Linked Mental Retardation. This section contains samples collected by the centers belonging to the Italian network on X-linked mental retardation, which includes the laboratory of bank curators (for specific information on the network goals and organization, go to the section page). Mental retardation (MR) is the most frequent cause of serious handicap in humans with an estimated prevalence of 0,3-0,5 for moderate to severe MR (IQ<50) which increases to 1-1,5 when mild MR (IQ 50-70) is included. It is calculated that about 20-25 of mentally retarded males have a mutation in a gene on the X chromosome (X-linked mental retardation). X-linked mental retardation is a genetically heterogeneous condition. This is particularly true for the non-syndromic form (MRX), where MR is the only consistent clinical finding and no distinctive features between patients exist. In this situation the only possibility to group patients from different families is represented by linkage analysis, which needs the availability of large families. However, families linked to the same region demonstrate different causative genes. In these conditions, the number of patients available for analysis is a discriminating factor since a large number of patients need to be tested in order to fully confirm or exclude the involvement of a gene in MRX. # Other. This section of the bank contains biological materials and clinical data of patients with other genetic disorders (different from Rett and X-linked mental retardation). Part of this section is dedicated to Alport syndrome. Services: * Isolation of leukocytes from human peripheral blood samples * Establishment of EBV transformed lymphoblastoid cell lines from human peripheral blood leukocytes. * DNA extraction. * Plasma isolation. * Storage: ** Cryo-preservation of transformed cell lines and primary leukocytes at 135??C ** Storage of DNA at 20 degrees C ** Storage of plasma at 20 degrees C * Distribution of the stored biological samples.duplication syndrome, autosomal mr, microdeletion, retinoblastoma, mecp2, cdkl5, foxg1, clinical, mutation, phenotype, lymphoblastoid cell line, leukocyte, dna, plasma, blood, biomaterial manufactureSCR_002000(Italian Rett Syndrome database, RRID:SCR_002000)University of Siena; Tuscany; Italy Rett Syndrome, Duplication syndrome, Autosomal MR, Microdeletion, Retinoblastoma, X-linked retardationTelethon Foundationlisted by: One Mind Biospecimen Bank ListingLast checked downnif-0000-12492
pfSNPResource, service resource, data or information resource, data repository, storage service resource, databaseSearch engine integrating various bio-informatic resources and algorithims to produce a one-stop resource for biologists to identify potentially functional SNPs. It caters to different groups of scientists interested in SNPs including those working in the following areas: * Whole-genome association studies * Gene-based association studies * Designing experiments to address the functionality of specific SNPs * Determining potentially functionally significant SNPs that are in LD with non-pfSNPs of interest. Users may add published SNP functions.single nucleotide polymorphism, function, association study, gene, genomeSCR_002167(pfSNP, RRID:SCR_002167)National University of Singapore; Singapore; Singapore listed by: OMICtoolsLast checked downOMICS_01854
LIPID MAPS Proteome DatabaseResource, data or information resource, databaseDatabase of approximately 1200 lipid-related proteins representing human and mouse proteins involved in lipid metabolism. UniProt IDs were obtained based on keyword search of KEGG and GO databases, and this LMPD protein list was then enhanced with annotations from UniProt, EntrezGene, ENZYME, GO, KEGG and other public resources. Associations were also assigned with general lipid categories, based on GO and KEGG annotations. Users may search by database ID or keyword, and filter by species and/or lipid class associations; from the search results, one can then access a compilation of data relevant to each protein of interest, cross-linked to external databases.gene, protein, lipid, metabolism, metabolomicsSCR_003062(LIPID MAPS Proteome Database, RRID:SCR_003062)LIPID Metabolites And Pathways Strategy NIGMSuses: Gene Ontology, KEGG, Universal Protein Resource, Entrez Gene, ENZYMEPMID:16381922Last checked downnif-0000-03085
Mouse Genome Informatics TransgenesResource, data set, data or information resourceData set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available.
Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.
transgene, allele, phenotypeSCR_003468(Mouse Genome Informatics Transgenes, RRID:SCR_003468)Mouse Genome Informatics (MGI) related to: Integrated Manually Extracted Annotation, used by: NIF Data FederationLast checked downnif-0000-34000
Arizona Biospecimen LocatorResource, biomaterial supply resource, tissue bank, data set, cell repository, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.arizona biospecimen, biospecimen bank, biological sample bankSCR_004151(Arizona Biospecimen Locator, RRID:SCR_004151)Diseased, NormalArizona Biomedical Research Commissionlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_17349
Wistar Institute Collection at CoriellResource, biomaterial supply resource, material resource, institution, cell repositoryCollection of cell lines developed by Wistar scientists that includes a group of hybridomas that produce monoclonal antibodies that are useful in influenza research and vaccine development, melanoma cell lines derived from patients with diseases ranging from mild dysplasia to advanced metastatic cancer and a range of human endothelial cell lines.hybridoma, monoclonal antibody, antibody, cell line, melanoma cell line, endothelial cell line, smooth muscle cell line, disease, cancer, dysplasia, metastatic cancerSCR_004660(Wistar Institute Collection at Coriell, RRID:SCR_004660)Coriell Cell Repositories , Wistar Institute Disease, Cancer, Dysplasia, ( Diseases ranging from mild dysplasia to advanced metastatic cancer )listed by: One Mind Biospecimen Bank ListingLast checked downnlx_143856
NeurophilosophyResource, blog, narrative resource, data or information resourceBlog about molecules, minds and everything in between, written by Mo, a molecular and developmental neurobiologist turned science writer. He aims to produce well-written and easily accessible articles about all aspects of neuroscience, so that he might help to improve public understanding of it. This blog has been featured for two consecutive years in the Open Lab annual anthologies of the best science blogging. AFTER four years at, Neurophilosophy has moved to a new home. It is now hosted by The Guardian.neuroscience, philosophy, molecule, mind, neuroscience, brainSCR_006514(Neurophilosophy, RRID:SCR_006514)ScienceBlogs used by: NIF Data Federation, Integrated BlogsLast checked downnlx_61948
PRODORICResource, data or information resource, databaseDatabase about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. The integrated approach provides information about molecular networks in prokaryotes with focus on pathogenic organisms. In detail this concerns: * transcriptional regulation (transcription factors and their DNA binding sites * signal transduction (two-component systems, phosphylation cascades) * protein interactions (complex formation, oligomerization) * biochemical pathways (chemical reactions) * other regulation events (e.g. codon usage, etc. ...) It aims to be a resource to model protein-host interactions and to be a suitable platform to analyze high-throughput data from proteomis and transcriptomics experiments (systems biology). Currently it mainly contains detailed information about operon and promoter structures including huge collections of transcription factor binding sites. If an appropriate number of regulatory binding sites is available, a position weight matrix (PWM) and a sequence logo is provided, which can be used to predict new binding sites. This data is collected manually by screening the original scientific literature. PRODORIC also handles protein-protein interactions and signal-transduction cascades that commonly occur in form of two-component systems in prokaryotes. Furthermore it contains metabolic network data imported from the KEGG database.gene regulation, transcription factor binding site, promoter structure, gene expression, genome, regulon, network, visualization, gene regulatory network, pathogen, transcriptional regulation, transcription factor, dna binding site, signal transduction, protein interaction, pathway, regulation, protein-protein interaction, signal-transduction cascade, operon, promoter, structure, position weight matrixSCR_007074(PRODORIC, RRID:SCR_007074)Technical University of Braunschweig; Braunschweig; Germany BMBFrelated to: KEGG, listed by: OMICtoolsPMID:18974177Last checked downnif-0000-03343, OMICS_01872
Magnetics Information ConsortiumResource, database, service resource, storage service resource, software resource, data repository, data or information resourceDatabases that accept and provide access to paleomagnetic and rock magnetic data. The paleomagnetic data range from individual measurements to specimen, sample or site level results, including a wide variety of derived parameters or associated rock magnetic measurements. The rock magnetic database includes data collected during rock magnetic experiments on remanence, anisotropy, hysteresis and susceptibility. The MagIC Console Software provides an effective environment in Microsoft Excel where users can collate and prepare their paleomagentic and rock magnetic data for uploading in the Online MagIC Database.paleomagnetism, rock, magnetic, paleomagnetic, geomagnetic, rock magneticSCR_007098(Magnetics Information Consortium, RRID:SCR_007098)San Diego Supercomputer Center NSFlisted by: CINERGILast checked downnlx_154712, SciRes_000151
HPRD - Human Protein Reference DatabaseResource, data or information resource, databaseDatabase that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.protein, disease, network, post-translational, proteome, protein binding, protein s, protein c, pathway, protein-protein interaction, protein expression, subcellular localization, phosphorylation motif, signaling pathway, protein sequence, blast, molecule, domain, motif, post-translational modification, protein isoformSCR_007027(HPRD - Human Protein Reference Database, RRID:SCR_007027)Johns Hopkins University; Maryland; USA , Institute of Bioinformatics; Bangalore; India related to: Human Proteinpedia, MatrixDB, Interaction Reference Index, Pathway Commons, ConsensusPathDB, Gene Ontology, Agile Protein Interactomes DataServer, used by: Mutation Annotation and Genomic Interpretation, Pathway Analysis Tool for Integration and Knowledge Acquisition, GEMINI, listed by: re3data.orgReferences (3)Last checked downnif-0000-00137
Mach2datResource, software resource, software applicationSoftware that performs logistic regression, using imputed SNP dosage data and adjusting for covariates.genetic association, genomic analysis, imaging genomics, snp, gene, imputationSCR_009599(Mach2dat, RRID:SCR_009599)University of Michigan; Michigan; USA related to: MACH 1.0, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)References (2)Last checked downnlx_155801
miRSeqNovelResource, software resourceAn R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.SCR_013257(miRSeqNovel, RRID:SCR_013257)SourceForge listed by: OMICtoolsLast checked upOMICS_00381
ProViDEResource, software resourceA similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences.metagenome, taxonomy, sequence, virusSCR_004709(ProViDE, RRID:SCR_004709)listed by: OMICtoolsPMID:21544173Last checked upOMICS_01463
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
MAIAResource, software resource, software application, data analysis software, data processing softwareSoftware package of programs for complex segregation analysis in animal pedigrees.gene, genetic, genomic, segregation, analysis, animal, pedigreeSCR_007153(MAIA, RRID:SCR_007153)Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia listed by: Genetic Analysis SoftwareLast checked upnlx_154435
MNI PodcastsResource, narrative resource, podcast, data or information resourceA collection of podcasts which features experts of the Montreal Neurological Institute and Hospital talking about their research, along with important issues and current events regarding it.neurology, podcast, montreal neurological institute, montreal neurological institute and hospital, current events, research newsSCR_000021(MNI Podcasts, RRID:SCR_000021)McGill University; Montreal; Canada related to: Integrated Podcasts, used by: NIF Data FederationLast checked upnlx_91897
M(at)CBETHResource, analysis service resource, data analysis service, service resource, production service resourceA web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset.microarray, classificationSCR_000265(M(at)CBETH, RRID:SCR_000265)Catholic University of Leuven; Flemish Brabant; Belgium listed by: OMICtoolsPMID:15890742Last checked upOMICS_02292
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