The methods, models, and data produced by the Center's research activities are made available though geworkbench, an interoperable, grid-enabled, state-of-the-art bioinformatics platform that allows them to be:
In addition to MAGNet tools, geWorkbench provides access to a rich collection of components supporting the analysis and visualization of many genomic data types (gene expression, sequence, structure, gene networks, etc). Some of these components have been developed de novo while others wrap popular 3rd party software such as Cytoscape, the Multi Experiment Viewer (MEV) and GenePattern. Over 70 geWorkbench modules are available, including:
geWorkbench is also supported through the cancer Biomedical Informatics Grid (caBIG®) initiative and leverages many of the caBIG® technologies. For example, computationally intensive analyses are wrapped and deployed as grid services using caGrid, the grid middleware layer of caBIG®. Similarly, caGrid as well as the cancer Bioinformatics Infrastructure Objects (caBIO) programmatic interface are used in order to provide seamless access to remote data and annotations sources. For instance, geWorkbench offers an integrated interface to the caArray genomic data repository and it also allows the retrieval of gene, pathway and disease information from the Cancer Genome Anatomy Project (CGAP), the NCI-Nature Pathway Interaction Database, and the Cancer Gene Index (CGI), to name a just a few.
geWorkbench is an open source Java-based platform and contributions by members of the community are welcome and encouraged. Access to the geWorkbench source code repository and to the latest production code releases is available through the project's gForge page. Additional technical documentation, including code samples, can be found in the "Developers" section of the geWorkbench web site. Finally, support for both developers and end users of geWorkbench is offered through the caBIG® Molecular Analysis Tools Knowledge Center which provides access to documentation, FAQs, Knowledge base entries and user forums for community and expert support.