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on page 1 showing 20 out of 205 results

Cite this (3D-footprint, RRID:SCR_015713)

URL: http://floresta.eead.csic.es/3dfootprint

Resource Type: Resource, data or information resource, database

Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.

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Cite this (Adult Wistar Rat Atlas, RRID:SCR_006288)

URL: http://www.civm.duhs.duke.edu/neuro2012ratatlas/

Resource Type: Resource, atlas, data or information resource

Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.

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    agriGO

Cite this (agriGO, RRID:SCR_006989)

URL: http://bioinfo.cau.edu.cn/agriGO/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool

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Cite this (Allen Mouse Brain Atlas, RRID:SCR_002978)

URL: http://mouse.brain-map.org/

Resource Type: Resource, atlas, database, data or information resource

A genome-wide, three-dimensional map of gene expression in the adult mouse brain. Similar in scale to the Human Genome Project, the Atlas reveals the expression patterns of approximately 20,000 genes throughout the entire adult mouse brain down to the cellular level. The Allen Institute's inaugural project, the Atlas was completed in 2006. The Allen Brain Atlas of the mouse brain is an interactive, genome-wide image database of gene expression with ISH and Nissl images. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. Together, these resources present a comprehensive online platform for exploration of the brain at the cellular and molecular level.

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Cite this (Allen Mouse Brain Connectivity Atlas, RRID:SCR_008848)

URL: http://connectivity.brain-map.org/

Resource Type: Resource, atlas, spatially referenced dataset, data or information resource

A high-resolution map of neural connections in the mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, further information about the transgenic mouse lines and genetic tracers used to create the Atlas is also available, thereby allowing other researchers to expand upon the neural connectivity framework from the Atlas. Ultimately, the Atlas will consist of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Tools will be developed to enable 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses. Upon completion the Atlas is expected to include: * Datasets ** Projection Mapping: Axonal projections mapped from ~300 anatomical regions and diverse neuronal populations defined by ~100 different Cre driver lines, labeled by viral tracers and visualized using serial two-photon tomography. ** BDA vs. rAAV Comparison: Axonal projections from 20 representative brain regions labeled by both conventional and viral tracers and imaged using an epifluorescence microscope for direct comparison of the two tracing methods. ** Transgenic Characterization: Transgene expression pattern of ~100 Cre and other driver lines characterized in adult and several developmental time points by colorimetric in situ hybridization (CISH), fluorescence in situ hybridization (FISH) or other histological methods. ** Anatomic Reference: A collection of histology data and whole-brain neuroimaging data to better delineate cytoarchitectural details, including fiber tracts. * Key features ** Annotation of the injection sites for all tracer injected brains. ** Development of a new registration interface from perfused mouse brain and registration into the associated 3-D reference atlas. ** Signal detection, quantification or other informatics analyses of axonal projections. ** 2-D and 3-D interactive, relational database incorporating connectivity information from all brain regions and Cre mice. ** Search and visualization tools for exploring the connectivity data. Currently, the following data are available on the Allen Brain Atlas data portal: * Projection mapping from ~200 brain regions including images from more than 10 Cre driver lines. * BDA vs. rAAV comparison of more than 20 brain regions. * 5 series of histological reference datasets. * Characterization data from more than 100 Cre or other driver lines.

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    AmiGO

Cite this (AmiGO, RRID:SCR_002143)

URL: http://amigo.geneontology.org/

Resource Type: Resource, data analysis service, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resource

Official Web-based tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms. It can be accessed online at the main installation or deployed locally. The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. AmiGO can be used to:
* search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
* perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
* search for GO terms and view the genes or gene products they are annotated to
* browse the GO ontology and view terms
* the slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
* term enrichment tool is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
* GOOSE is for advanced users who want to run custom SQL queries against the GO database.

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Cite this (AMYL-PRED, RRID:SCR_006185)

URL: http://bioinformatics.biol.uoa.gr/AMYLPRED/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web tool using the consensus prediction method for identifying possible amyloidogenic regions in protein sequences. This tool uses an assortment of different methods that have been found or specifically developed to predict features related to the formation of amyloid fibrils. The consensus of these methods is defined as the the hit overlap of at least two out of five methods and it is the primary output of the program. However, the individual predictions of these methods are also made available in the form of a text file, maintained on the server for 1 (one) day. Consequently, the tool predicts probable amyloidogenic determinants for a given amino acid sequence of a peptide or protein.

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Cite this (APID: Agile Protein Interaction DataAnalyzer, RRID:SCR_008871)

URL: http://bioinfow.dep.usal.es/apid

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

An interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform known information about protein-protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore more than 40000 different proteins and close to 150000 different proven interactions. The website includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Parameters for the proteins are connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; for the interactions: number of methods, GO overlapping, Pfam domain-domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network. Platform: Online tool

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    AQUARIUM

Cite this (AQUARIUM, RRID:SCR_015760)

URL: http://klavinslab.org/aquarium.html

Resource Type: Resource, software resource, project portal, data or information resource, portal, programming language

Workflow software and methods language to improve the reproducibility of research results in the scientific community. The Aquarium Project aims to provide the means to specify, as precisely as possible, how to obtain a result using a combination of formal statements, informal descriptions, and photographs.

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    autoPROC

Cite this (autoPROC, RRID:SCR_015748)

URL: https://www.globalphasing.com/autoproc/

Resource Type: Resource, software resource, software application, data processing software, software toolkit

Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination.

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Cite this (Babelomics, RRID:SCR_002969)

URL: http://babelomics.bioinfo.cipf.es

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool

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Cite this (BARLEYMAP, RRID:SCR_015710)

URL: http://floresta.eead.csic.es/barleymap

Resource Type: Resource, data analysis software, data processing software, database, software application, sequence analysis software, web application, standalone software, software resource, data or information resource

Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map and the POPSEQ map. Its three main functions are finding markers, aligning sequences, and locating by position.

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    BaSiC

Cite this (BaSiC, RRID:SCR_016371)

URL: https://www.helmholtz-muenchen.de/icb/research/groups/quantitative-single-cell-dynamics/software/basic/index.html

Resource Type: Resource, software resource, software application, image processing software, data processing software

Software plugin for Fiji/ImageJ that performs retrospective image correction for optical microscopy. It is based on low rank and sparse decomposition, which corrects both shading in space and background bleaching in time.

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Cite this (Bioconductor, RRID:SCR_006442)

URL: http://www.bioconductor.org/

Resource Type: Resource, catalog, data or information resource, database

A catalog of tools and software packages for the analysis and comprehension of high-throughput genomic data that uses the R statistical programming language. Bioconductor has a development version to which new features and packages are added prior to incorporation in the release. A large number of meta-data packages provide pathway, organism, microarray and other annotations. The broad goals of the Bioconductor project are: to provide widespread access to a broad range of powerful statistical and graphical methods for the analysis of genomic data; to facilitate the inclusion of biological metadata in the analysis of genomic data; to provide a common software platform that enables the rapid development and deployment of extensible, scalable, and interoperable software; and to train researchers on computational and statistical methods for the analysis of genomic data.

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Cite this (BioSolveIT, RRID:SCR_003949)

URL: http://www.biosolveit.de/

Resource Type: Resource, software resource, commercial organization

Commercial provider of software solutions for drug discovery applications offering tools, services, and research collaborations. The software portfolio ranges from design, over screening, to the visualization of ligand libraries, for hit identification, optimization, and scaffold hopping. With a stellar scientific advisory board and founders from academia who intensely collaborate with pharma, BioSolveIT catalyzes products off of university research successes with proven pharmaceutical industry application. They provide software products within the areas of ligand and structure-based drug design and is the pioneer of computational fragment-based ligand design. BioSolveIT innovate break-throughs in drug discovery by supplying smooth, user-centered designed tools bringing different researchers together for efficient multidisciplinary drug design.

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    Blast2GO

Cite this (Blast2GO, RRID:SCR_005828)

URL: http://www.blast2go.com/b2ghome

Resource Type: Resource, software resource, software application

An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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Cite this (Brede Toolbox, RRID:SCR_006204)

URL: http://neuro.imm.dtu.dk/software/brede/

Resource Type: Resource, software resource, software application, image processing software, data processing software, image analysis software

A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions.

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Cite this (CandiSNPer, RRID:SCR_005173)

URL: http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer/

Resource Type: Resource, software resource, source code, service resource

A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region.

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Cite this (CateGOrizer, RRID:SCR_005737)

URL: http://www.animalgenome.org/bioinfo/tools/catego/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

CateGOrizer takes batch input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, or a self-defined classification list, find its parental branch and performs an accumulative classification count, and returns the results in a sorted table of counts, percentages, and a pie chart (if it takes longer than standard time out period, it will email the user with a URL link to the results). This tool is comprised with a set of perl CGI programs coupled with a MySQL DBMS that stores the GO terms DAG data. Platform: Online tool

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Cite this (CGAP-Align, RRID:SCR_000350)

URL: http://sourceforge.net/projects/cgap-align/

Resource Type: Resource, software resource

A time efficient read alignment tool built on the top of BWA.

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