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Summary: Cytoscape Web is a web-based network visualization tool–modeled after Cytoscape–which is open source, interactive, customizable and easily integrated into web sites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF.
Supplementary information: Supplementary data are available at Bioinformatics online.
Increasing amounts of high-throughput data are being collected, stored, shared and analyzed on the web, highlighting the need for effective web-based data visualization. Network visualization components are especially valuable to help researchers interpret their data as part of data analysis tools. However, current web-based network visualization components lack many useful features of their desktop counterparts. Medusa (Hooper and Bork, 2005) is a Java applet originally used in the STRING database (Jensen et al., 2009) and by many other web sites for network visualization, but lacks advanced features, such as detailed customization of the network view. jSquid (Klammer et al., 2008) expands Medusa's functionality, but does not provide an easy way for the client web site to change and interact with the network view after it has been rendered. TouchGraph (http://www.touchgraph.com/navigator.html) is another Java applet for network visualization, but provides only one mode of network interaction designed for exploration and is not easily customizable. yFiles Flex (http://www.yworks.com/en/products_yfilesflex_about.html) is a rich Internet application with a feature-rich user interface, an architecture that balances client/server work and supports efficient data communication. This commercial software is customizable within the bounds of the code already written, but is not open source. Cytoscape (http://www.cytoscape.org/) is an open source Java network visualization and analysis tool that provides a large array of useful features (Shannon et al., 2003), but is not specifically designed for use on the web except via Java WebStart or as a library to generate static network images for web display. The field of network visualization is lacking an interactive, easily customizable, open source, web-based visualization component.
Cytoscape Web is an interactive, web-based network visualization tool, modeled after the popular Cytoscape software (Fig. 1). Using basic programming skills, Cytoscape Web can be customized and incorporated into any web site. Cytoscape Web is not intended as a replacement for the Cytoscape desktop application, for example, it contains none of the plugin architecture functionality of Cytoscape; instead it is intended as a low overhead tool to add network visualization to a web application.
Cytoscape Web works best with small- to medium-sized networks, generally with up to a few hundred nodes and edges. Larger networks can be visualized, but the user interaction can become sluggish around 2000 elements (nodes or edges)—800 nodes and 1200 edges, for example (tested on an Apple laptop computer with 2 GHz dual core CPU and 4 GB RAM). Use of the force-directed layout is the major bottleneck in the initial rendering of a typical network. However, faster layouts are available and overall performance is dependent upon the client web site implementation and the end user configuration. Additional performance statistics for Cytoscape Web are available in the Supplementary Material.
Cytoscape Web is actively developed as an open source project and is freely available at http://cytoscapeweb.cytoscape.org/. This web site includes a tutorial, with ready to use sample code, the API documentation and a showcase of major Cytoscape Web features. The online examples can be freely used as a template for building web sites containing Cytoscape Web.
Future plans include the implementation of custom graphics for nodes and edges, additional network layouts and support for importing and closer integration with Cytoscape [e.g. importing/exporting networks in Cytoscape (.cys) file format].
Cytoscape is developed through an ongoing collaboration between the University of California at San Diego, the Institute for Systems Biology, Memorial Sloan-Kettering Cancer Center, Institut Pasteur, Agilent Technologies, Unilever, the University of Michigan, the University of California at San Francisco and the University of Toronto. We gratefully acknowledge the contributions of many Cytoscape developers who developed software that Cytoscape Web was based on. We thank the entire GeneMANIA team for support during the development of Cytoscape Web.
Funding: Genome Canada through the Ontario Genomics Institute (grant number 2007-OGI-TD-05); the U.S. National Institute of General Medical Sciences of the National Institutes of Health (grant number 2R01GM070743-06).
Conflict of Interest: none declared.