Geworkbench
 | |
| 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[update], 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
[edit]- 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
[edit]- 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
[edit]References
[edit]- ^ 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.
- ^ "Plugins - Workbench".
- ^ MAGNet
- ^ "Home". ncbcs.org.
- ^ "NIH Roadmap - Research Teams of the Future". Archived from the original on 2013-06-21. Retrieved 2013-07-16.
- ^ "Download and Installation - Workbench".
External links
[edit]- Official website, includes installation, tutorials, FAQs, known issues
- - geworkbench release downloads
- - geWorkbench plugins