Cytoscape: the network visualization tool for GenomeSpace workflows

TLDR

Modern genomic analysis relies on workflows that integrate multiple best‑of‑breed tools, and GenomeSpace is a web‑based visual workbench that combines such tools with data‑flow mechanisms, including the popular Cytoscape 3 application for graph‑oriented genomic network analysis and visualization. This paper presents the design and operation of the Cytoscape GenomeSpace app, which integrates Cytoscape into GenomeSpace to provide critical analysis and visualization functionality for users. The app was designed to bridge Cytoscape’s desktop environment with GenomeSpace’s web‑based platform, ensuring a seamless user experience and proper data flows. It has been downloaded over 850 times since its first release in September 2013.

Abstract

<ns4:p>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.</ns4:p>