User:Kncsmith/Sandbox

geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the Java programming language.

Using a component architecture, geWorkbench allows individually developed plug-ins to be configured into complex bioinformatic applications. At present, there are more than 70 available plug-ins supporting the visualization and analysis of gene expression, sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing funded through the NIH Roadmap (NIH Common Fund ). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins.

Features

 * Access to client- and server-side computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory nework reconstruction, BLAST searches, pattern/motif discovery, protein structure prediction, structure-based protein annotation, etc.
 * Advanced visualization of gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
 * Validating computational hypothesis through the 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: expression datasets, interaction networks, sample and marker (gene) sets, sequences.
 * Dataset History tracking - complete record of data sets used and input settings.
 * Seamless integration with 3rd party tools such as Genepattern, Cytoscape, Genomespace and the Multi-Experiment Viewer.

Availabililty

 * geWorkbench is available as open-source software that can be downloaded and installed locally.
 * Prepackaged installer versions are available for Windows, Macintosh, and Linux. A zip file of the released version Java source is also available.