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Name

geWorkbench

Byline

Center for Computational Biology and Bioinformatics, Columbia University

Description

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 30 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include:

1. loading data from local or remote data sources.
2. visualizing gene expression and sequence data in a variety of ways.
3. providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
4. validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.

geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks (one of the 7 National Centers for Biomedial Computing funded through the NIH Roadmap Initiative).

NIfTI-1 support

Creator

Center for Computational Biology and Bioinformatics, Columbia University

Contact

WWW

http://www.geworkbench.org/workbench

Availability

Free (see web site for license details).

How to get

Download from web site.

Current version

1.0.1

Current version release date

2/28/06

Open source

Yes

License

See Web site for full license details.

Available free of charge

Yes

Requirements

Sun Java J2SE 5.0 or higher. Memory of 512MB or higher recommended. For large datasets (hunders of microarrays) more memory will be necessary for acceptable perormance.

Technical publications

Applications publications

Other information

Keywords

Classification, Clustering, Gene expression data analysis, Genomic sequence analysis, Integrated genomics, MAGNet (NCBC), Regulatory networks, statistical, visualization

Platforms

Linux, MacOS, UNIX, Windows

IATR listing last updated

14 Mar 2006

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