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on page 1 showing 20 out of 108 results from 1 sources

    3DSwap

Cite this (3DSwap, RRID:SCR_004133)

URL: http://caps.ncbs.res.in/3dswap/index.html

Resource Type: Resource, data or information resource, database

Curated knowledegbase of protein structures that are reported to be involved in 3-dimensional domain swapping. 3DSwap provides literature curated information and structure related information about 3D domain swapping in proteins. Information about swapping, hinge region, swapped region, extent of swapping, etc. are extracted from original research publications after extensive literature curation.

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Cite this (ACT: Artemis Comparison Tool, RRID:SCR_004507)

URL: http://www.sanger.ac.uk/resources/software/act/

Resource Type: Resource, software resource

A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

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Cite this (Africa Centre for Health and Population Studies, RRID:SCR_008964)

URL: http://www.africacentre.ac.za/Default.aspx?tabid=69

Resource Type: Resource, data set, data or information resource

Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present.

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Cite this (Alien-hunter, RRID:SCR_015967)

URL: http://www.sanger.ac.uk/science/tools/alien-hunter

Resource Type: Resource, software resource, software application

Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer.

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    ALSPAC

Cite this (ALSPAC, RRID:SCR_007260)

URL: http://www.alspac.bris.ac.uk

Resource Type: Resource, project portal, portal, data or information resource

A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.

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    Ariba

Cite this (Ariba, RRID:SCR_015976)

URL: https://github.com/sanger-pathogens/ariba

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

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

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    ARNIE

Cite this (ARNIE, RRID:SCR_000514)

URL: http://www.sanger.ac.uk/cgi-bin/teams/team30/arnie

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

Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.

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Cite this (Artemis: Genome Browser and Annotation Tool, RRID:SCR_004267)

URL: http://www.sanger.ac.uk/resources/software/artemis/

Resource Type: Resource, software resource

A free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

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Cite this (Bio-eagle, RRID:SCR_015991)

URL: https://data.broadinstitute.org/alkesgroup/Eagle/

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

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

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Cite this (Bio-Formats, RRID:SCR_000450)

URL: https://www.openmicroscopy.org/site/products/bio-formats

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

A 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)

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Cite this (BioLexicon, RRID:SCR_000589)

URL: http://www.nactem.ac.uk/biolexicon/

Resource Type: Resource, data or information resource, database

A large-scale English terminological database that contains over 2.2.M lexical entries (3.3M semantic relations), terminological variants and rich linguistic information (subcategorization frames) which supports text mining systems. It is primarily intended to support text mining and information retrieval in the biomedical domain. The BioLexicon provides specific information to help determine the relevant facts to be extracted. BioLexicon is available in a relational database format (MySQL dump format) and it adheres to the EAGLES/ISO standards for lexical resources.

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Cite this (BioMart MartView, RRID:SCR_010714)

URL: http://www.biomart.org/biomart/martview/ddb9ce1ad275cde372c968d13fa11f5f

Resource Type: Resource, data set, web service, software resource, data access protocol, data or information resource

A web server interface of BioMart software and provides a unified view over disparate data sources that enable bioscientists to retrieve data from one or multiple sources in a simple and efficient way. This MartView web server features seamless data federation making cross querying of data sources in a user friendly and unified way. Data sources include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase, etc. The web server not only provides access through a web interface, it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services.

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Cite this (BioMart Project, RRID:SCR_002987)

URL: http://www.biomart.org

Resource Type: Resource, software resource, web service, data access protocol

A query-oriented data management system that can be used with any type of data and is particularly suited for providing "data mining" like searches of complex descriptive data. BioMart comes with an "out of the box" website that can be installed, configured and customized according to user requirements. Further access is provided by graphical and text based applications or programmatically using web services or API written in Perl and Java. BioMart has built-in support for query optimization and data federation and in addition can be configured to work as a DAS 1.5 Annotation server. The process of converting a data source into BioMart format is fully automated by the tools included in the package. Currently supported RDBMS platforms are MySQL, Oracle and Postgres.

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Cite this (Bio-tradis, RRID:SCR_015993)

URL: https://github.com/sanger-pathogens/Bio-Tradis

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

Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.

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    BoxPlotR

Cite this (BoxPlotR, RRID:SCR_015629)

URL: http://shiny.chemgrid.org/boxplotr/

Resource Type: Resource, data visualization software, software application, web application, data processing software, software resource

Web application that allows users to generate customized box plots in a number of variants based on their data. It creates basic box plots based on the data and can be modified to include additional information.

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Cite this (Burroughs Wellcome Fund, RRID:SCR_005772)

URL: http://www.bwfund.org/

Resource Type: Resource, funding resource

The Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation.

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Cite this (CellML Model Repository, RRID:SCR_008113)

URL: http://www.cellml.org/models

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.

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    CellML

Cite this (CellML, RRID:SCR_008061)

URL: http://www.cellml.org/

Resource Type: Resource, narrative resource, interchange format, markup language, standard specification, data or information resource

The CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org.

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    ChEMBL

Cite this (ChEMBL, RRID:SCR_014042)

URL: https://www.ebi.ac.uk/chembl/

Resource Type: Resource, data or information resource, database

A database of bioactive drug-like small molecules that contains 2D structures, calculated properties (logP, molecular weight, etc.), and abstracted bioactivities (binding constants, ADMET data, etc.). The database attempts to normalize the bioactivities into a uniform set of end-points and units when possible. Links between a molecular target and a published assay (with a set of varying confidence levels) are tagged.Clinical progress of new compounds is continuously integrated into the database. Users can search target data by keyword, protein sequence search, or by navigating the target classification hierarchy. Compound data can be searched via keyword, SMILES strings, compound identifiers, or chemical structure. Assay data can be searched by keyword.

  • From Current Category

Cite this (Clonalframe, RRID:SCR_016060)

URL: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

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

Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

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