Cytoscape is an open source program platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

An open source bioinformatics program platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration and visualization. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. Plugins may be developed by anyone using the Cytoscape open API based on Java technology and plugin community development is encouraged. Most of the plugins are freely available.

Cytoscape supports a lot of standard network and annotation file formats including: SIF (Simple Interaction Format), GML, XGMML, BioPAX, PSI-MI, SBML, OBO, and Gene Association. Delimited text files and MS Excel Workbook are also supported and you can import data files, such as expression profiles or GO annotations, generated by other applications or spreadsheet programs. Using this feature, you can load and save arbitrary attributes on nodes, edges, and networks. For example, input a set of custom annotation terms for your proteins, create a set of confidence values for your protein-protein interactions.

Why are there no biological semantics in the core, given that Cytoscape is targeted to biologists?
Biological semantics are poorly defined, so any model we build that assumes a given biological model will be wrong and will change frequently over time. By keeping the core of Cytoscape generic and free of bio semantics, we can add bio semantics as plugins as we need them and multiple people can add their own semantics without creating conflicts. Keeping biology out of the core helps us think a bit more generally about the functionality of the software.

Cytoscape Features:
1. Filter the network to select subsets of nodes and/or interactions based on the current data.
2. Find active subnetworks/pathway modules.
3. Zoom in/out and pan for browsing the network.
4. Image Export
5. Customize network data display using strong Visual Styles.
6. Layout networks in two dimensions
7. Since Cytoscape supports import/export standard file formats, you can easily put Cytoscape into your workflow.

The license of this software is Free, you can free download and free use this graphing software.