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Bioinformatics software
Geworkbench
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    Geworkbench

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    geWorkbench
    Developer(s) Columbia University,
    First Genetic Trust
    National Cancer Institute
    Initial release 2004 (2004)
    Stable release
    2.6.0.3 / December 21, 2016 (2016-12-21)
    Operating system Windows, Linux, Mac OS X
    Platform x86
    Available in English
    Type Genome data analysis
    License BSD-like
    Website www.geworkbench.org

    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.

    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.

    See also

    External links


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