Geworkbench Explained

geWorkbench
Logo Size:	250px
Developer:	Columbia University, First Genetic Trust National Cancer Institute
Latest Release Version:	2.6.0.3
Operating System:	Windows, Linux, Mac OS X
Platform:	x86
Language:	English
Genre:	Genome data analysis
License:	BSD-like^[1]

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., 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.

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 atGeWorkbench-web 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^[7] for Windows, Macintosh, and Linux.

See also

• Genome Compiler

External links

• , includes installation, tutorials, FAQs, known issues
• - geworkbench release downloads
• - geWorkbench plugins

Notes and References

1. http://wiki.c2b2.columbia.edu/workbench/index.php/GeWorkbench_License geWorkbench license
2. Floratos . A. . Smith . K. . Ji . Z. . Watkinson . J. . Califano . A. . GeWorkbench: An open source platform for integrative genomics . 10.1093/bioinformatics/btq282 . Bioinformatics . 26 . 14 . 1779–1780 . 2010 . 20511363 . 2894520 .
3. Web site: Plugins - Workbench.
4. http://magnet.c2b2.columbia.edu/ MAGNet
5. Web site: Home . ncbcs.org.
6. Web site: NIH Roadmap - Research Teams of the Future . 2013-07-16 . https://web.archive.org/web/20130621191343/https://commonfund.nih.gov/researchteams/ . 2013-06-21 . dead .
7. Web site: Download and Installation - Workbench.