title: Cytoscape: the network visualization tool for GenomeSpace workflows.
abstract: Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.
authors.affiliation: Department of Medicine, University of California, San Diego, La Jolla, 92093-0688, USA.
authors.forename: Barry
authors.initials: B
authors.lastname: Demchak
authors.affiliation: Department of Medicine, University of California, San Diego, La Jolla, 92093-0688, USA.
authors.forename: Tim
authors.initials: T
authors.lastname: Hull
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Reich
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, USA.
authors.forename: Ted
authors.initials: T
authors.lastname: Liefeld
authors.affiliation: Qualcomm, Inc, San Diego, 92121, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Smoot
authors.affiliation: Department of Medicine, University of California, San Diego, La Jolla, 92093-0688, USA.
authors.forename: Trey
authors.initials: T
authors.lastname: Ideker
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, USA.
authors.forename: Jill P
authors.initials: JP
authors.lastname: Mesirov