Cytoscape 3.5.0

A visualization application for molecular interaction networks

Cytoscape is a comprehensive bioinformatics software platform designed for visualizing biological pathways and molecular interaction networks.

The application can also integrate 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 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.

You can export networks as publishiable-quality images. Supports PDF, EPS, SVG, PNG, JPEG, and BMP files.