Cytoscape is a free, open source visualization tool for modeling complex networks and integrating network points with attribute data. Cytoscape can create visualizations of a variety of different types of networks, including molecular and genetic, social networks, and semantic Web. Adding free plugins to Cytoscape also provides functionality including literature mining, network inference, topological clustering, and network comparison.
A variety of apps extend Cytoscape's basic functionality by adding support for automatic data import, pathway analysis, and more. For a list of free apps, visit the Cytoscape App Store. Cytoscape can read delimited text files, Excel files (.XLS and .XLSX), and network/pathway files in many common standard formats. Several free apps also allow users to automatically download and import data from online sources like KEGG, WikiPathways, BioPAX L3. To download network import apps, visit the Cytoscape App Store.