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 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.

• 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 atGeWorkbench-web Tutorials.

• 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.

• Genome Compiler