|Stable release||2.5.1 / November 2013|
|Operating system||Windows, Linux, Mac OS X|
|License||See web site|
geWorkbench (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 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.
- 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.
- 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.
- Floratos, A.; Smith, K.; Ji, Z.; Watkinson, J.; Califano, A. (2010). "GeWorkbench: An open source platform for integrative genomics". Bioinformatics 26 (14): 1779–1780. doi:10.1093/bioinformatics/btq282. PMC 2894520. PMID 20511363.