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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

548 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
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
AutoPrimeResource, analysis service resource, data analysis service, service resource, production service resourceServer to rapidly design primers for real-time PCR measurement of eukaryotic expression.primer, real-time pcr, primer designSCR_000097(AutoPrime, RRID:SCR_000097)German Cancer Research Center listed by: OMICtoolsLast checked upOMICS_02333
PROVEANResource, analysis service resource, software resource, data analysis service, service resource, production service resourceA software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.amino acid substitution, indel, function, protein, amino acid, substitution, protein variant, genome variant, next-generation sequencing, insertion, deletionSCR_002182(PROVEAN, RRID:SCR_002182)J. Craig Venter Institute NHGRI, NIHlisted by: OMICtoolsPMID:23056405Last checked upOMICS_01849
Primer3Resource, analysis service resource, software resource, data analysis service, service resource, production service resourceTool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos.primer, primer design, polymerase chain reaction, pcr primer, dna sequence, c, perlSCR_003139(Primer3, RRID:SCR_003139)University of Tartu; Tartu; Estonia NHGRIrelated to: Primer3Plus, Primer-BLAST, listed by: OMICtoolsReferences (2)Last checked upnlx_156833, OMICS_02325http://bioinfo.ut.ee/primer3-0.4.0/, http://sourceforge.net/projects/primer3/, http://frodo.wi.mit.edu/primer3
ngLOCResource, analysis service resource, software resource, data analysis service, service resource, production service resourceAn n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License.subcellular localization, protein, eukaryote, prokaryoteSCR_003150(ngLOC, RRID:SCR_003150)listed by: OMICtoolsLast checked downOMICS_01629
SeqAntResource, analysis service resource, software resource, data analysis service, service resource, production service resourceA free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest.annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genomeSCR_005186(SeqAnt, RRID:SCR_005186) SourceForge , Emory University; Georgia; USA listed by: OMICtoolsPMID:20854673Last checked upOMICS_00182
Functional ROI AtlasResource, atlas, data or information resourceAn effort to provide a set of quasi-probabilistic atlases for established functional ROIs in the human neuroimaging literature. Many atlases exist for various anatomical parcellation schemes, such as the Brodmann areas, the structural atlases, tissue segmentation atlases, etc. To date, however, there is no atlas for so-called functional ROIs. Such fROIs are typically associated with an anatomical label of some kind (e.g. the _fusiform_ face area), but these labels are only approximate and can be misleading inasmuch as fROIs are not constrained by anatomical landmarks, whether cytoarchitectonic or based on sulcal and gyral landmarks. The goal of this project is to provide quasi-probabilistic atlases for fROIs that are based on published coordinates in the neuroimaging literature. This is an open-ended enterprise and the atlas can grow as needed. Members of the neuroscience and neuroimaging community interested in contributing to the project are encouraged to do so.magnetic resonance, nifti, functional roi, region of interest, neuroimagingSCR_009481(Functional ROI Atlas, RRID:SCR_009481)listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnlx_155628
MetaLocGramNResource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resourceA tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice.subcellular localization, protein, prediction, sequence, analysis, gram-negative protein, gram-negative, gram-negative bacteriaSCR_003154(MetaLocGramN, RRID:SCR_003154)International Institute of Molecular and Cell Biology; Warsaw; Poland related to: Biocatalogue - The Life Science Web Services Registry, listed by: OMICtoolsLast checked upOMICS_01626
ChIP-seqResource, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, service resource, software resourceSet of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, cSCR_001237(ChIP-seq, RRID:SCR_001237) Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland , SourceForge listed by: OMICtoolsLast checked upOMICS_02103http://ccg.vital-it.ch/chipseq/
SumsDBResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, atlas, image repository, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figuressegmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomySCR_002759(SumsDB, RRID:SCR_002759)Washington University School of Medicine in St. Louis; Missouri; USA Mental disease, Neurological disorder, NormalHuman Brain Project, NASA, National Partnership for Advanced Computational Infrastructure, NCI, NIMH, NLM, NSFrelated to: Computerized Anatomical Reconstruction and Editing Toolkit, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: Biositemaps, NeuroImaging Tools and Resources Collaboratory (NITRC), re3data.orgLast checked downnif-0000-00016http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb
FunNet - Transcriptional Networks AnalysisResource, data analysis service, data processing software, production service resource, analysis service resource, software application, service resource, software resourceFunctional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblegenome, transcriptional interaction, microarray, gene expression, statistical analysisSCR_006968(FunNet - Transcriptional Networks Analysis, RRID:SCR_006968)Cordelier Research Center related to: Gene Ontology, KEGG, listed by: Gene Ontology ToolsPMID:18208606Last checked upnlx_149243
Genome ProjectorResource, data analysis service, production service resource, analysis service resource, database, service resource, software resource, data or information resourceA searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.genome, plasmid, pathway, dna, mapSCR_011790(Genome Projector, RRID:SCR_011790)Japan Society for the Promotion of Sciencelisted by: OMICtoolsLast checked upOMICS_00912
Code Analysis Repository and Modelling for e-NeuroscienceResource, database, software repository, service resource, storage service resource, software resource, data repository, data or information resourceInfrastructure for sharing data, tools and services, this virtual research environment (VRE) supports e-Neuroscience and is designed to provide services for data and processing of that data. While the system is initially focused on electrophysiology data (neural activity recordings are the primary data types), it is equally applicable to many domains outside neuroscience. The Portal Provides: * User login and customization. * Data upload/download. * Data handling including custom permissions for public, shared or private data. * The ability to invoke custom public, shared or private services that consume and produce data. For example, it would allow spike series to be run through a sorter, producing new data representing the sorted spikes. * The ability to host services written in a number of languages including, but not limited to Matlab, R, Python, Perl, Java. * A system to support metadata for data objects, which provides extensive support for entering metadata at the point of upload, and allows the generation of metadata from services to provide provenance information. * The ability to invoke additional visualization for the data, for example, via the Signal Data Explorer. A core part is the development of: (i) minimum reporting guidelines for annotation of data and other computational resources for the purpose of sharing, and; (ii) intermediate formats and APIs for translation between proprietary and bespoke data types. These recommendations are being implemented and the global community is encouraged both to engage in their specification and make use of them for their own data sharing systems. * MINI: Minimum Information about a Neuroscience Investigation - This framework represents the formalized opinion of the CARMEN consortium and its associates, and identifies the minimum reporting information required to support the use of electrophysiology in a neuroscience study, for submission to the CARMEN system. * NDTF: Neurophysiology Data Translation Format - This framework provides a vendor-independent mechanism for translating between raw and processed neurphysiology data in the form of time and image series. They are implementing NDTF in CARMEN but it may also be useful for third party applications.neural activity recording, signal, image series, neurophysiology, data sharing, metadata standard, collaboration, electrophysiologySCR_002795(Code Analysis Repository and Modelling for e-Neuroscience, RRID:SCR_002795)Newcastle University; Newcastle upon Tyne; United Kingdom EPSRCReferences (2)Last checked upnif-0000-00442
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous PromotersResource, data or information resource, databasePublic database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.gene, alignment, annotation, binding, computational, genome, nucleotide, ortholog, prediction, promoter, sequence, target, transcription, transcriptional factor, binding site, promoter sequence, protein motif, benchmark, transcription factor binding siteSCR_002276(ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters, RRID:SCR_002276)Center for Genomic Regulation; Barcelona; Spain European Union FP6related to: IntegromeDBPMID:16381947Last checked upnif-0000-21006
Leiden Open Variation DatabaseResource, data processing software, database, software application, data storage software, service resource, storage service resource, software resource, data repository, data or information resourceFreely available tool for Gene-centered collection and display of DNA variations. It also provides patient-centered data storage and storage of Next Generation Sequencing (NGS) data, even of variants outside of genes. Please note that LOVD provides a system for storage of information on genes and allelic variants. To obtain information about any genes or variants, do not download the LOVD package. This information should be obtained from the respective databases, http://www.lovd.nl/2.0/index_list.php In total: 2,507,027 variants (2,208,937 unique) in 170,935 individuals in 62619 genes in 88 LOVD installations. (Aug. 2013) LOVD 3.0 shared installation, http://databases.lovd.nl/shared/genes To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer. You can download LOVD in ZIP and GZIPped TARball formats.genetic variation, genomic variant, gene, transcript, disease, next generation sequencing, dna variation, variant, clinical, screening, locus, phenotype, sequence variation, allelic variant, data sharingSCR_006566(Leiden Open Variation Database, RRID:SCR_006566)Leiden University; Leiden; Netherlands European Union FP7related to: Monarch Initiative, listed by: OMICtoolsReferences (2)Last checked upnif-0000-02998, OMICS_00275
Bio-FormatsResource, data processing software, software library, software application, software resource, software toolkit, image processing softwareA standalone Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard. (Dec. 2013)write, read, life science, image, format, microscopy, standard, javaSCR_000450(Bio-Formats, RRID:SCR_000450)OME - Open Microscopy Environment Wellcome Trustrelated to: OMERO, OME-TIFF Format, listed by: FORCE11PMID:20513764Last checked upnif-0000-30175http://www.force11.org/node/4810
BioSig: An Imaging Bioinformatics System for Phenotypic AnalysisResource, data processing software, software library, software application, software resource, software toolkit, image processing softwareAn open source software library for processing of electroencephalogram (EEG) and other biomedical signals like electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis. Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis. It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events.application, autocorrelation, bsd, c, c++, connectivity analysis, correlation, cross-correlation, directed transfer analysis, discriminant analysis, domain independent, eeg, meg, electrocorticography, end event related potential, format conversion, german, gnome, granger causality, information theory, kde, linux, matlab, microsoft, multivariate analysis, partial directed coherence, posix/unix-like, python, regression, spectral analysis, statistical operation, temporal transformation, time domain analysis, win32 (ms windows), windows, electrocorticogram, electrocardiogram, electrooculogram, electromyogram, respiration, signal, processing, biosignalSCR_008428(BioSig: An Imaging Bioinformatics System for Phenotypic Analysis, RRID:SCR_008428)Lawrence Berkeley National Laboratory listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnif-0000-30190http://www.nitrc.org/projects/biosig
EEG / ERP Data SetResource, data set, data or information resourceA collection of 32-channel EEG / ERP data from 14 subjects (7 males, 7 females) acquired using the Neuroscan software (3.6 Gb), made available by the laboratory of Arnaud Delormes, along with electrode files and images presented in the experiment. Subjects are performing a go-nogo categorization task and a go-no recognition task on natural photographs presented very briefly (20 ms). Images are only available for viewing. Each subject responded to a total of 2500 trials. Data is CZ referenced and is sampled at 1000 Hz (total data size is 4Gb). Alternate datasets are also compiled including one from the EEGLAB software tutorial.eeg, event related potential, erp, male, female, electrode file, image, behavior, categorization, task, independent component analysisSCR_004890(EEG / ERP Data Set, RRID:SCR_004890)University of California at San Diego; California; USA PMID:15019707Last checked upnlx_85968http://sccn.ucsd.edu/~arno/indexeeg.html
EEG human categorization dataResource, data set, data or information resourceA collection of 32-channel data from 14 subjects (7 males, 7 females) acquired using the Neuroscan software. Subjects are performing a go-nogo categorization task and a go-no recognition task on natural photographs presented very briefly (20 ms). Each subject responded to a total of 2500 trials. Data is CZ referenced and is sampled at 1000 Hz (total data size is 4Gb; more details are given later).eeg, meg, electrocorticography, male. femaleSCR_009468(EEG human categorization data, RRID:SCR_009468)listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnlx_155616
MriWatcherResource, data visualization software, software application, data processing software, software resourceThis simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time. Very useful for quality control, image comparison.magnetic resonanceSCR_002318(MriWatcher, RRID:SCR_002318)listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnlx_155667
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