Cytoscape: A Modeling Platform for Biomolecular Networks

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CYTOSCAPE: A MODELING PLATFORM FOR BIOMOLECULAR NETWORKS Administrative supplement request to extend R01 HG009979 for a period of one year (7/1/21 to 6/30/22) PI: Trey Ideker (University of California San Diego) Project Summary Cytoscape is an open source software platform for biological network analysis, visualization and modeling. It is a critical bioinformatics resource in academia and industry, with 300,000+ downloads per year and 25,000+ citations. Cytoscape has been widely adopted due mainly to its utility in diverse biological analyses, its sustainable open development model, and its extensible architecture, which enables anyone to add algorithmic functionality and has attracted hundreds of third-party developers. Access to network analysis tools is particularly important now, at a time when network knowledge and concepts are increasingly central to genomics research. Cytoscape addresses this need and serves as a hub for knowledge-based genome analysis. Here in this administrative supplement application, we are requesting additional funds to permit a one-year extension to the budget period of the current grant (R01 HG009979). These bridge funds will enable continued maintenance and dissemination of the Cytoscape ecosystem of tools while our U24 Genomic Community Resource application is still under review (U24 HG012107, resubmission May 25, 2021). The requested $586K in total costs is a reduction from the current award and the base amount required to maintain, support and incrementally update the widely used Cytoscape platform during the intervening period. These funds will also serve to retain our highly specialized Cytoscape development team. With this one-year supplemental funding request, we propose to: 1. Continue our longtime commitment to maintain, update and distribute the Cytoscape ecosystem of tools. 2. Further develop a web- and cloud-based version of Cytoscape, Cytoscape Explore, and release v1.0 with basic Cytoscape Desktop functionality. 3. Continue our rich set of Cytoscape outreach and training programs.