Software:Geworkbench
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| Developer(s) | Columbia University, First Genetic Trust National Cancer Institute |
|---|---|
| Initial release | 2004 |
| Stable release | 2.6.0.3
/ December 21, 2016 |
| Operating system | Windows, Linux, Mac OS X |
| Platform | x86 |
| Available in | English |
| Type | Genome data analysis |
| License | BSD-like[1] |
| Website | www |
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), 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
References
- ↑ geWorkbench license
- ↑ 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. PMID 20511363.
- ↑ "Plugins - Workbench". http://wiki.c2b2.columbia.edu/workbench/index.php/Plugins.
- ↑ MAGNet
- ↑ "Home". http://www.ncbcs.org/.
- ↑ "NIH Roadmap - Research Teams of the Future". http://commonfund.nih.gov/researchteams.
- ↑ "Download and Installation - Workbench". http://wiki.c2b2.columbia.edu/workbench/index.php/Download_and_Installation.
External links
- , includes installation, tutorials, FAQs, known issues
- - geworkbench release downloads
- - geWorkbench plugins
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