Cytoscape

Cytoscape is the open-source platform for visualizing complex networks (e.g., molecular, social) and integrating them with attribute data.

Cytoscape is an open-source, Java-based desktop platform (Cytoscape 3) engineered for large-scale network visualization and analysis. While initially designed for systems biology—mapping molecular interaction networks and integrating them with high-throughput data like gene expression profiles—its utility now spans fields like social science and semantic web analysis. The core distribution handles basic data integration and visualization; its true power lies in the App Store, which offers hundreds of community-developed Apps for advanced functions, including specialized layouts, network statistics (e.g., degree distribution), and database connections. This architecture ensures high extensibility and robust handling of complex, attribute-rich network data.

https://www.cytoscape.org