Genomespace

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GenomeSpace
Developer(s) Broad Institute
Stable release beta 5.0 / April 2012
Operating system any
License LGPL 2.1
Website http://www.genomespace.org
GenomeSpace Logo.png

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. sand facilitates the transfer of data between tools via automatic format conversion. Analyses can use local data as well as from cloud-based data stores.

GenomeSpace consists of a web-based UI for users and both a RESTful API and a Java-based client development kit (CDK) for developers integrating their applications with GenomeSpace.

GenomeSpace Tools[edit]

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, and next-generation sequence analysis, as well as genomic datasets. Developers of other genomics software can use the GenomeSpace API to add their tools.

Collaborators[edit]

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[edit]

  1. ^ [1]
  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.  edit
  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". "Current Protocols in Molecular Biology". Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] Chapter 19: Unit Un19.10.Un19–21. doi:10.1002/0471142727.mb1910s89. ISBN 0471142727. PMID 20069535.  edit
  4. ^ [2]
  5. ^ [3]
  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.  edit
  8. ^ [4]
  9. ^ [5]