Ono Keiichiro, Fong Dylan, Gao Chengzhan, Churas Christopher, Pillich Rudolf, Lenkiewicz Joanna, Pratt Dexter, Pico Alexander R, Hanspers Kristina, Xin Yihang, Morris John, Kucera Mike, Franz Max, Lopes Christian, Bader Gary, Ideker Trey, Chen Jing
Department of Medicine, University of California, San Diego, CA 92093, United States.
Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, United States.
Nucleic Acids Res. 2025 Jul 7;53(W1):W203-W212. doi: 10.1093/nar/gkaf365.
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.
自2003年推出以来，Cytoscape一直是可视化和分析生物网络的事实上的标准。我们现在推出Cytoscape Web（https://web.cytoscape.org），这是一个在线实现，它捕捉了桌面版的界面和关键可视化功能，同时提供与网络工具和数据库的集成。Cytoscape Web提高了可访问性，通过在线数据共享简化了协作。它通过CX2网络交换格式与Cytoscape桌面版集成，并与网络数据交换集成以存储和共享网络。该平台通过用于用户界面组件的应用框架和用于算法集成的服务应用支持可扩展性，促进了社区驱动的新分析工具开发。总体而言，Cytoscape Web通过提供一个通用、可访问且协作的在线平台来增强网络生物学，该平台适应不断演变的计算挑战，为社区未来纳入先进的网络分析能力奠定了基础。
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