Genomespace

GenomeSpace
DeveloperBroad Institute
Stable release
beta 5.0 / April 2012; 14 years ago (2012-04)
Operating systemCross-platform
PlatformWeb browser
Available inEnglish
LicenseLGPL 2.1
Websitewww.genomespace.org

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

  1. ^ "Home". cytoscape.org.
  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). 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.
  4. ^ "Home". genepattern.org.
  5. ^ "Segal Lab: Genomica". Archived from the original on 2012-02-02. Retrieved 2012-04-24.
  6. ^ "Home". geworkbench.org. Archived from the original on 2008-08-27. Retrieved 2022-08-07.
  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.
  8. ^ "Home | Integrative Genomics Viewer".
  9. ^ http://hgwdev-gs.cse.ucsc.edu/cgi-bin/hgTables[permanent dead link]

Official website

Content Disclaimer

Informasi ini disarikan dari Wikipedia dan disajikan kembali untuk tujuan edukasi. Konten tersedia di bawah lisensi CC BY-SA 3.0. Kami tidak bertanggung jawab atas ketidakakuratan data yang bersumber dari kontribusi publik tersebut.

  1. The information displayed on this website is sourced in part or in whole from Wikipedia and has been adapted for the purpose of restating it. We strive to provide accurate and relevant information, however:
  2. There is no guarantee of absolute accuracy. Wikipedia is an open, collaborative project that can be edited by anyone, so information is subject to change.
  3. It is not intended to constitute professional advice. The content displayed is for informational and educational purposes only. For important decisions (e.g., medical, legal, or financial), please consult a professional.
  4. Content copyright. Wikipedia is licensed under the Creative Commons Attribution-ShareAlike License (CC BY-SA). This means that content may be reused with appropriate attribution and shared under a similar license.
  5. Responsible use. Any risk arising from the use of information from this website is entirely the responsibility of the user.