The lab is involved in a collaborative software project called Cytoscape (http://www.cytoscape.org). Cytoscape is a free, Open Source bioinformatics environment for integration, visualization, and query of biological networks. Cytoscape's core software component provides basic functionality for network import and export, integrating arbitrary data on a network, network and integrated data visualization, and network filtering and query tools. The Cytoscape core is extended through a straightforward plugin architecture, allowing rapid prototyping and development of advanced computational analyses and features. Dozens of Cytoscape plugins have been developed and released by a variety of research groups and are available at http://www.cytoscape.org/plugins/index.php. The Cytoscape source code is developed in Java and distributed under a permissive open source license (the GNU LGPL or Library General Public License). This promotes both non-profit and commercial use and ensures that the bioinformatic resources developed for the Cytoscape project will remain publicly available.

Cytoscape usage has increased at a rate of approximately 50% per year (25,000 downloads during 2007), and Cytoscape has been featured in hundreds of recent publications. Popular databases link to Cytoscape for network visualization, including Reactome, MiMI, BIND, SGD, and IntAct. We believe that this success comes from cultivating a vibrant Cytoscape user and developer community which, in large part, is due to our commitment to an Open Source policy. It is this aspect that we consider to be the most significant feature of Cytoscape—its role not as a “one-off” analysis tool but as a platform for new tool development, much like R and Matlab provide for the statistics and engineering communities.

Cytoscape development in the lab is funded by grant GM070743.