IDEKER LAB
University of California,San Diego
OVERVIEW: Mapping the DNA Damage Response Application to the Study of Pathogens and Disease Galactose Utilization as a Model System |
| Cytoscape and Community Software |
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The Lab is involved in a collaborative open-source software project called Cytoscape (http://www.cytoscape.org). Originally designed by Dr. Ideker in 1999, Cytoscape has become a core community bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. It is central to all of the Lab’s research activities. Corporate involvement is important to an open-source software project because it establishes support outside of federal sources. Corporate sponsors include Unilever PLC, as well as Agilent Labs, a corporate contributor of open-source Java code. Beyond these contributions, a half dozen laboratories, none of them affiliated with the Cytoscape project, have chosen to extend the Cytoscape environment through so-called Java plug-ins (see http://www.cytoscape.org/plugins2.php/). A number of pathway, protein interaction, and genome databases now allow users to launch Cytoscape to visualize data, including Reactome (EMBL), BIND, and in the near future Saccharomyces Genome Database. The number of user downloads of Cytoscape has also skyrocketed recently and is currently in the range of 2,000 per month.
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