Geworkbench
 | |
| Developer(s) | Columbia University |
|---|---|
| Stable release | 2.6.0.2 / February 2015 |
| Development status | Active |
| Operating system | Windows, Linux, Mac OS X |
| Available in | English |
| License | See web site |
| Website |
www |
geWorkbench[1] (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[2] available, providing for the visualization and analysis of gene expression, sequence, and structure data.
geWorkbench is the Bioinformatics platform of MAGNet,[3] the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing[4] funded through the NIH Roadmap (NIH Common Fund[5]). 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[6] for Windows, Macintosh, and Linux.
References
- ↑ 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
- ↑ http://magnet.c2b2.columbia.edu
- ↑ http://www.ncbcs.org
- ↑ http://commonfund.nih.gov/researchteams
- ↑ http://wiki.c2b2.columbia.edu/workbench/index.php/Download_and_Installation
External links
- www.geworkbench.org - geWorkbench website, includes installation, tutorials, FAQs, known issues
- - geworkbench release downloads
- - geWorkbench plugins
- Genome Compiler