GeWorkbench

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^[update], there are more than 70 plug-ins^[3] available, providing for the visualization and analysis of gene expression, sequence, and structure data.

geWorkbench

Developer(s)	Columbia University, First Genetic Trust National Cancer Institute
Initial release	2004; 21 years ago (2004)
Stable release	2.6.0.3 / December 21, 2016; 8 years ago (2016-12-21)
Operating system	Windows, Linux, Mac OS X
Platform	x86
Available in	English
Type	Genome data analysis
License	BSD-like[1]
Website	www.geworkbench.org

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 GeWorkbench-web Tutorials.^[7]

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^[8] for Windows, Macintosh, and Linux.