Revision as of 17:31, 29 July 2011

Quick Start

Please see the Quick Start guide to geWorkbench to see how to get started using geWorkbench right away. We are continuing to develop new material for this guide.

Overview

Welcome to geWorkbench. The current version is 2.2.1, released July 29th, 2011.

See the list of the most important fixes, changes and enhancements. This release was entirely devoted to improvements of existing components. More than 90 issues were addressed. The most important are summarized below.

The latest Release Notes and downloads can be obtained from https://gforge.nci.nih.gov/frs/?group_id=78. Installation instructions can be found on the Download and Installation page of this Wiki.

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 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include:

• loading data from local or remote data sources.
• visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
• 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.
• 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). Additionally, geWorkbench is supported by caBIG^®, NCI's cancer Biomedical Informatics Grid initiative.

End-user and developer support for geWorkbench is provided through the caBIG^® Molecular Analysis Tools Knowledge Center, a component of the caBIG^® Enterprise Support Network.

Graphical User Interface

The figure above shows the full geWorkbench graphical user interface. The Cellular Network Knowledge Base B-cell interactome was queried for interactions of two master regulator genes, and the result displayed in Cytoscape.

Brief Overview of Changes in geWorkbench 2.2.1

geWorkbench 2.2.1 provides a number of improvements, especially as related to network import, display and export, sequence retrieval, and pattern discovery. If a network is generated or loaded that may be to large to view in Cytocape, it can now instead by viewed as a text file. The new "Fold Change" analysis component is included, which was to be released in version 2.2.0 but was omitted. A new feature to overlay a t-test result onto a Cytoscape network, which was inadvertantly disabled in release 2.2.0, now works again. The Gene Ontology analysis component now supports uses of alternate ontology files (e.g. from the GO website). Sequence retrieval for DNA sequences is now done using the UCSC refGene table, and is available for all organisms with genomes supported by UCSC.

Previous Releases

See the Previous Releases page for full details.