geWorkbench: an open source platform for integrative genomics.

SUMMARY: geWorkbench (genomics Workbench) is an open source Java desktop application that provides access to an integrated suite of tools for the analysis and visualization of data from a wide range of genomics domains (gene expression, sequence, protein structure and systems biology). More than 70 distinct plug-in modules are currently available implementing both classical analyses (several variants of clustering, classification, homology detection, etc.) as well as state of the art algorithms for the reverse engineering of regulatory networks and for protein structure prediction, among many others. geWorkbench leverages standards-based middleware technologies to provide seamless access to remote data, annotation and computational servers, thus, enabling researchers with limited local resources to benefit from available public infrastructure. AVAILABILITY: The project site (http://www.geworkbench.org) includes links to self-extracting installers for most operating system (OS) platforms as well as instructions for building the application from scratch using the source code [which is freely available from the project's SVN (subversion) repository]. geWorkbench support is available through the end-user and developer forums of the caBIG Molecular Analysis Tools Knowledge Center, https://cabig-kc.nci.nih.gov/Molecular/forums/