Genomespace

GenomeSpace is an environment for genomics software tools and applications. It helps users manage their analysis workflows involving multiple diverse tools, including web applications and desktop tools and facilitates the transfer of data between tools via automatic format conversion. Analyses can use data from local or cloud-based stores.

GenomeSpace
Developer(s)Broad Institute
Stable release
beta 5.0 / April 2012 (2012-04)
Operating systemCross-platform
PlatformWeb browser
Available inEnglish
LicenseLGPL 2.1
Websitewww.genomespace.org

GenomeSpace consists of a web-based user interface (UI) for users, and both a representational state transfer (RESTful) application programming interface (API) and a Java-based client development kit (CDK) for developers integrating their applications with GenomeSpace.

GenomeSpace tools

GenomeSpace is linked with several tools and data sources for genomics analysis: Cytoscape,[1] Galaxy,[2][3] GenePattern,[4] Genomica,[5] geWorkbench,[6] InSilico DB ,[7] the Integrative Genomics Viewer (IGV),[8] and the [9] UCSC Genome Browser. These programs provide a wide variety of genomic analyses, including network analysis and visualization, sequence analysis, whole-genome analysis, general statistical methods, gene expression analysis, proteomics, flow cytometry, next-generation sequence analysis, and genomic datasets. Developers of other genomics software can use the GenomeSpace API to add their tools.

Collaborators

The GenomeSpace project is a collaboration of the Mesirov and Regev laboratories at the Broad Institute; the Chang laboratory at Stanford University; the Ideker laboratory at the University of California, San Diego; the Nekrutenko laboratory at Pennsylvania State University; the Segal laboratory at the Weizmann Institute of Science; and the Haussler and Kent laboratories at the University of California, Santa Cruz. GenomeSpace is funded by the National Human Genome Research Institute of the National Institutes of Health.

References
  2. Goecks, J.; Nekrutenko, A.; Taylor, J.; Galaxy Team, T. (2010). "Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences". Genome Biology. 11 (8): R86. doi:10.1186/gb-2010-11-8-r86. PMC 2945788. PMID 20738864.
  3. Blankenberg, D.; Kuster, G. V.; Coraor, N.; Ananda, G.; Lazarus, R.; Mangan, M.; Nekrutenko, A.; Taylor, J. (2010). "Galaxy: A Web-Based Genome Analysis Tool for Experimentalists". In Frederick M. Ausubel (ed.). Current Protocols in Molecular Biology. pp. Unit Un19.10.Un19–21. doi:10.1002/0471142727.mb1910s89. ISBN 0471142727. PMID 20069535.
  6. http://www.geworkbench.org
  7. Coletta, A.; Molter, C.; Duqué, R.; Steenhoff, D.; Taminau, J.; De Schaetzen, V.; Meganck, S.; Lazar, C.; Venet, D.; Detours, V.; Nowé, A.; Bersini, H.; Weiss Solís, D. Y. (2012). "InSilico DB genomic datasets hub: An efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor". Genome Biology. 13 (11): R104. doi:10.1186/gb-2012-13-11-r104. PMC 3580496. PMID 23158523.

Official website

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