Visualizing Complex Networks using New Cytoscape v3
On April 22, 2013, computational biologists and computer scientists at UC San Diego released version 3 of Cytoscape for general availability. Cytoscape is the leading open source visualization software platform supporting systems biology; it enables researchers to visualize molecular interaction networks and biological pathways and integrate them with annotations, gene expression profiles and other state and process data.
Cytoscape was developed in the early 2000s to meet the need for an analytical tool that would allow researchers to organize, view and interpret large-scale biological data in a unified conceptual framework.
Approximately 1,600 scientific papers have cited the software to date, with approximately 300-400 new papers each year.
The Cytoscape-generated image below is a visualization of a data set composed of molecular and genetic interactions within cells in the human body.
Although it was originally designed for biological research, Cytoscape is now a general platform for complex network analysis and visualization, with additional applications in software engineering and the study of social networks.
Features new in Cytoscape v3 include edge bending and bundling visualizations (see image below), network annotations, advanced searching, node grouping and associated tutorials.
Cytoscape v3 also incorporates a new App Store, which enables Cytoscape users to access and use a large and growing pool of community-published visualization and analytics modules, thereby driving and enabling Cytoscape’s use both in biology and in diverse research environments.
The Cytoscape core application is open source and is distributed under a Library GNU Public License; each app carries an independent software license. Cytoscape’s open application programmer interface is based on Java™ technology.
Cytoscape project principal investigator Trey Ideker, PhD (left), said, “Cytoscape v3 is an important milestone in the support of systems biology, enabling deep insights into complex biologic relationships and processes.
“From a biological perspective, it will enable multiscale, dynamic, and ontological studies. From a systems perspective, it will enable collaborative workflows and better, more intensive use of existing and future computing resources.”
Ideker is professor of bioengineering and professor and chief of the Division of Medical Genetics in the Department of Medicine.
The Ideker laboratory offers Cytoscape and a number of other software packages and tools for download. (http://idekerlab.ucsd.edu/software).
There are approximately 6,000 Cytoscape downloads each month, Ideker said.
Lead Cytoscape software architect Barry Demchak, PhD, pictured above right, said Cytoscape v3 represents a major redesign to boost the program’s performance, improve the user interface, and make the software more extensible and stable.
New feature in Cytoscape 3: Automatic edge bundling consolidates multiple edges to de-clutter dense network views.
Cytoscape v3 is the culmination of two years’ work conducted by the National Institutes of Health-funded Cytoscape Consortium, which includes collaborators at UC San Diego, UC San Francisco, the University of Toronto, the Pasteur Institute, the Broad Institute, the Memorial Sloan-Kettering Cancer Center, and the Institute for Systems Biology.
Cytoscape is available for free download at http://cytoscape.org.
User support, education and new initiatives for Cytoscape are supported by the National Resource for Network Biology under award numbers P41 RR031228 and GM103504. | Watch Trey Ideker’s video introduction to NRNB
For further information, contact Barry Demchak (firstname.lastname@example.org or 858-452-8700) at UC San Diego.
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