Geworkbench

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geWorkbench
GeWorkbench logo file.png
Developer(s) Columbia University
Stable release 2.5.1 / November 2013
Development status Active
Operating system Windows, Linux, Mac OS X
Available in English
License See web site
Website www.geworkbench.org

geWorkbench[1] (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the Java programming language. geWorkbench uses a component architecture. At present, there are more than 70 plug-ins[2] available, providing for the visualization and analysis of gene expression, sequence, and structure data.

geWorkbench is the Bioinformatics platform of MAGNet,[3] the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing[4] funded through the NIH Roadmap (NIH Common Fund[5]). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins.

Features[edit]

  • 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[edit]

  • 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[6] for Windows, Macintosh, and Linux.

References[edit]

External links[edit]