Cytoscape is a free, open source Java program, originally designed for highly specialised use in bioinformatics. But if you’re glazing over, stick with me here: Through all the versions leading up to 2.7, its present release, it has developed into a general purpose analysis and visualisation tool for complex networks. It has just been added to Mind-Mapping.Org.
The core distribution provides a basic set of features for data integration and visualization. Plugins are available, most of them free, to extend the functionality to network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. Anyone can develop plugins using the Cytoscape open API.
Quite an eye-full, huh?
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