Cytoscape Web: bringing network biology to the browser
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.
Authors
- Christopher Churas (ORCID: https://orcid.org/0000-0001-9998-705X)
- Gary D. Bader (ORCID: https://orcid.org/0000-0003-0185-8861)
- Christian Lopes
- Joanna Lenkiewicz (ORCID: https://orcid.org/0000-0001-7252-8638)
- Mike Kucera
- Dexter Pratt (ORCID: https://orcid.org/0000-0002-1471-9513)
- John H. Morris (ORCID: https://orcid.org/0000-0003-0290-7979)
- Keiichiro Ono (ORCID: https://orcid.org/0000-0003-4042-3748)
- Kristina Hanspers (ORCID: https://orcid.org/0000-0001-5410-599X)
- Alexander R. Pico (ORCID: https://orcid.org/0000-0001-5706-2163)
- Max Franz (ORCID: https://orcid.org/0000-0003-0169-0480)
- Dylan Fong
- Yang Xin (ORCID: https://orcid.org/0000-0002-9706-3950)
- Rudolf Pillich (ORCID: https://orcid.org/0000-0001-8682-0568)
- Jing Chen (ORCID: https://orcid.org/0000-0002-9291-7507)
- Chengzhan Gao
- Trey Ideker
Institutions
- Gladstone Institutes (US)
- University of California, San Francisco (US)
- University of Toronto (CA)
- University of California San Diego (US)
- Biocom (US)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-05-01
- DOI
- https://doi.org/10.1093/nar/gkaf365
- Citations
- 59
- Primary Topic
- Bioinformatics and Genomic Networks
- Type
- article
- Field-Weighted Citation Impact
- 45.94
Funders
- National Institutes of Health
- National Human Genome Research Institute
- National Cancer Institute
- National Institute of General Medical Sciences