Cytoscape is an open-source software platform that allows for the visualization and analysis of complex networks. With Cytoscape, users can integrate various types of attribute data, enabling the comprehensive analysis of networks in fields such as bioinformatics, social network analysis, and semantic web. The platform provides a wide range of apps to address diverse problem domains, making it a versatile tool for researchers and scientists.

In the field of biology, Cytoscape supports molecular and systems biology, genomics, and proteomics. Users can load and integrate global datasets, establish visual mappings, and perform advanced analysis using Cytoscape Apps. Additionally, Cytoscape allows for the visualization and analysis of curated pathway datasets like WikiPathways, Reactome, and KEGG.

Social scientists can utilize Cytoscape to visualize and analyze large social networks, assemble networks from tables and forms, and gather social interactions from the web. The platform also enables the calculation of network statistics and integration with other tools like R and NetworkX for more advanced analysis. Cytoscape is not limited to specific domains and serves as a powerful tool for complex network analysis in general.

Users can calculate network statistics, find shortest paths, and identify clusters using various algorithms. Additionally, Cytoscape allows for the import of networks from tools like igraph, Pajek, and GraphViz. The platform boasts a vibrant app developer community, making it expandable and extensible.

Cytoscape is supported by the National Resource for Network Biology and the National Institute of General Medical Sciences of the National Institutes of Health. To sustain its federal funding, Cytoscape encourages users to cite the original Cytoscape paper when utilizing the platform. 0