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. 2014 Jul 1:3:151.
doi: 10.12688/f1000research.4492.2. eCollection 2014.

Cytoscape: the network visualization tool for GenomeSpace workflows

Barry Demchak  1 , Tim Hull  1 , Michael Reich  2 , Ted Liefeld  2 , Michael Smoot  3 , Trey Ideker  1 , Jill P Mesirov  2
Affiliations

Cytoscape: the network visualization tool for GenomeSpace workflows

Barry Demchak et al. F1000Res. .

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.

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Conflict of interest statement

Competing interests: No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Launching Cytoscape from GenomeSpace.
Figure 2.
Figure 2.. Template H. sapiens before gene expression data.
Figure 3.
Figure 3.. Template H. sapiens after gene expression data.
See this image and copyright information in PMC

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