Geworkbench

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geWorkbench
Developer(s)Columbia University,
First Genetic Trust
National Cancer Institute
Initial release2004; 20 years ago (2004)
Stable release
2.6.0.2 / February 20, 2015; 9 years ago (2015-02-20)
Operating systemWindows, Linux, Mac OS X
Platformx86
Available inEnglish
TypeGenome data analysis
LicenseBSD-like[1]
Websitewww.geworkbench.org

geWorkbench[2] (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins[3] available, providing for the visualization and analysis of gene expression, sequence, and structure data.

geWorkbench is the Bioinformatics platform of MAGNet,[4] the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing[5] funded through the NIH Roadmap (NIH Common Fund[6]). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins.

Features

  • Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc.
  • Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence and protein structure data (e.g., MarkUs).
  • Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
  • Component integration through platform management of inputs and outputs. Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences.
  • Dataset history tracking - complete record of data sets used and input settings.
  • Integration with 3rd party tools such as Genepattern, Cytoscape, and Genomespace.

Demonstrations of each feature described can be found at http://wiki.c2b2.columbia.edu/workbench/index.php/Tutorials.

Versions

  • geWorkbench is open-source software that can be downloaded and installed locally. A zip file of the released version Java source is also available.
  • Prepackaged installer versions also exist[7] for Windows, Macintosh, and Linux.

References

  1. ^ geWorkbench license
  2. ^ Floratos, A.; Smith, K.; Ji, Z.; Watkinson, J.; Califano, A. (2010). "GeWorkbench: An open source platform for integrative genomics". Bioinformatics. 26 (14): 1779–1780. doi:10.1093/bioinformatics/btq282. PMC 2894520. PMID 20511363.
  3. ^ http://wiki.c2b2.columbia.edu/workbench/index.php/Plugins
  4. ^ MAGNet
  5. ^ http://www.ncbcs.org
  6. ^ http://commonfund.nih.gov/researchteams
  7. ^ http://wiki.c2b2.columbia.edu/workbench/index.php/Download_and_Installation

See also

External links

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