Cytoscape is a free and open source application designed to help you visualize molecular interaction networks and biological pathways, as well as for integrating the networks with gene expression profiles, annotations and relevant stare data.

Primarily created for biological research, Cytoscape expanded its reach and became a general platform for complex network analysis and visualization.

Cytoscape’s core distribution comes with basic set of features specially designed for data analysis, integration and visualization.

You can expand the feature set with Apps, formerly known as Plugins, which are available for network and molecular profiling analyses, new layouts, extended file format support, scripting and connection with databases.

Most Apps are freely available on the Cytoscape App Store, but you can take advantage of the Cytoscape open API based on Java technology and develop new ones.

Cytoscape features a modular architecture and it is aimed for long-term maintainability with support for a wide variety of standard network and annotation file formats, including SIF, XGMML, GML, BioPAX, PSI-MI, KGML, GraphML, OBO, SBML and Gene Association.

On top of that, Cytoscape offers support for delimited text files, MS Excel Workbook and you can even import data files like expression profiles and GO annotations generated by third-party apps or spreadsheet apps.

Moreover, Cytoscape can be used as a web service client and connect it to external public databases in order to import network and annotation data.

Your work, all your data files, settings and visualizations can be quickly saved within a session file and you can export networks as PDF, PS, SVG, JPEG, PNG and BMP files with the click of a mouse button.

In conclusion, the Cytoscape utility is a comprehensive and, at the same time, easily expandable OS X application that makes it easy for you to integrate and visualize complex networks with various types of attribute data using a Mac.