Geworkbench
 | |
| Developer(s) |
Columbia University, First Genetic Trust National Cancer Institute |
|---|---|
| Initial release | 2004 |
| Stable release |
2.6.0.2
/ February 20, 2015 |
| Development status | Active |
| 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 at http://wiki.c2b2.columbia.edu/workbench/index.php/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.
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. PMC 2894520
. PMID 20511363. - ↑ http://wiki.c2b2.columbia.edu/workbench/index.php/Plugins
- ↑ MAGNet
- ↑ http://www.ncbcs.org
- ↑ http://commonfund.nih.gov/researchteams
- ↑ http://wiki.c2b2.columbia.edu/workbench/index.php/Download_and_Installation
See also
External links
- Official website, includes installation, tutorials, FAQs, known issues
- - geworkbench release downloads
- - geWorkbench plugins