Cytoscape Web: bringing network biology to the browser
Keiichiro Ono, Dylan Fong, Chengzhan Gao, Christopher Churas, Rudolf Pillich, Joanna Lenkiewicz, Dexter Pratt, Alexander R. Pico, Kristina Hanspers, Yang Xin, John H. Morris, Mike Kucera, Max Franz, Christian Lopes, Gary D. Bader, Trey Ideker, Jing Chen
Abstract
Since its introduction in 2003, Cytoscape has been a de facto standard for visualizing and analyzing biological networks. We now introduce Cytoscape Web (https://web.cytoscape.org), an online implementation that captures the interface and key visualization functionality of the desktop while providing integration with web tools and databases. Cytoscape Web enhances accessibility, simplifying collaboration through online data sharing. It integrates with Cytoscape desktop via the CX2 network exchange format and with the Network Data Exchange for storing and sharing networks. The platform supports extensibility through an App framework for UI components and Service Apps for algorithm integration, fostering community-driven development of new analysis tools. Overall, Cytoscape Web enhances network biology by providing a versatile, accessible, and collaborative online platform that adapts to evolving computational challenges, laying a foundation for future incorporation of advanced network analysis capabilities by the community.