Supriya Ghosh (Editor)

Geworkbench

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Development status
  
Active

Platform
  
x86

Developer(s)
  
Columbia University,First Genetic TrustNational Cancer Institute

Initial release
  
2004; 13 years ago (2004)

Stable release
  
2.6.0.3 / December 21, 2016; 2 months ago (2016-12-21)

Operating system
  
Windows, Linux, Mac OS X

geWorkbench (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 available, providing for the visualization and analysis of gene expression, sequence, and structure data.

Contents

geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing funded through the NIH Roadmap (NIH Common Fund). 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 for Windows, Macintosh, and Linux.

    • References

    Geworkbench Wikipedia
    (Text) CC BY-SA


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