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 | |
| Developer(s) | Broad Institute |
|---|---|
| Stable release | beta 5.0
/ April 2012 |
| Operating system | Cross-platform |
| Platform | Web browser |
| Available in | English |
| License | LGPL 2.1 |
| Website |
www |
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 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
- ^ "Home". cytoscape.org.
- ^ 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.
-
^ Blankenberg, D.; Kuster, G. V.; Coraor, N.; Ananda, G.; Lazarus, R.; Mangan, M.; Nekrutenko, A.; Taylor, J. (2010). Frederick M. Ausubel (ed.). Galaxy: A Web-Based Genome Analysis Tool for Experimentalists. Vol. Chapter 19. pp. Unit Un19.10.Un19–21.
doi:
10.1002/0471142727.mb1910s89.
ISBN
978-0471142720.
PMC
4264107.
PMID
20069535.
{{ cite book}}:|journal=ignored ( help) - ^ "Home". genepattern.org.
- ^ "Segal Lab: Genomica". Archived from the original on 2012-02-02. Retrieved 2012-04-24.
- ^ "Home". geworkbench.org.
- ^ 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.
- ^ "Home | Integrative Genomics Viewer".
- ^ http://hgwdev-gs.cse.ucsc.edu/cgi-bin/hgTables
External links
| This article has multiple issues. Please help
improve it or discuss these issues on the
talk page. (
Learn how and when to remove these template messages)
|
|
| |
| Developer(s) | Broad Institute |
|---|---|
| Stable release | beta 5.0
/ April 2012 |
| Operating system | Cross-platform |
| Platform | Web browser |
| Available in | English |
| License | LGPL 2.1 |
| Website |
www |
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 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
- ^ "Home". cytoscape.org.
- ^ 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.
-
^ Blankenberg, D.; Kuster, G. V.; Coraor, N.; Ananda, G.; Lazarus, R.; Mangan, M.; Nekrutenko, A.; Taylor, J. (2010). Frederick M. Ausubel (ed.). Galaxy: A Web-Based Genome Analysis Tool for Experimentalists. Vol. Chapter 19. pp. Unit Un19.10.Un19–21.
doi:
10.1002/0471142727.mb1910s89.
ISBN
978-0471142720.
PMC
4264107.
PMID
20069535.
{{ cite book}}:|journal=ignored ( help) - ^ "Home". genepattern.org.
- ^ "Segal Lab: Genomica". Archived from the original on 2012-02-02. Retrieved 2012-04-24.
- ^ "Home". geworkbench.org.
- ^ 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.
- ^ "Home | Integrative Genomics Viewer".
- ^ http://hgwdev-gs.cse.ucsc.edu/cgi-bin/hgTables