2025/05/01 by Keiichiro Ono, Dylan Fong, Chengzhan Gao +14 · 1 voice · 1 citation
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #Gene expression and cancer classification #Genetics, Bioinformatics, and Biomedical Research
paper · pdf · doi:10.1093/nar/gkaf365
openalex publication_date 2025/05/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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.