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F1000Res DOI:10.12688/f1000research.4492.2

Cytoscape: the network visualization tool for GenomeSpace workflows.

Publication TypeJournal Article
Year of Publication2014
AuthorsDemchak, B, Hull, T, Reich, M, Liefeld, T, Smoot, M, Ideker, T, Mesirov, JP
Date Published2014

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.


Alternate JournalF1000Res
PubMed ID25165537
PubMed Central IDPMC4133763
Grant ListU41 HG007517 / HG / NHGRI NIH HHS / United States