Cytoscape is a versatile program for Windows that gives you the means to visualize molecular interaction networks and biological pathways. There are also functions for integration with annotations as well as real time data.

Overview

The utility comes with a well organized graphical interface which requires a few minutes to understand its layout and features. It provides a network management panel, a viewing window, and a browser. The latter component enables you to easily change various attributes.

Please note that the software offers support for systems biology, genomics, and proteomics. Using it, you can load protein interaction datasets in formats such as GraphML, SBML, BioPAX, and Excel. Alternatively, you may try an application called BioLayout Express 3D.

Visualize and explore networks

You can load multiple networks simultaneously. This gives you the freedom to analyze and make alterations as needed. However, there are instances where viewing them may not be possible due to their size. To address this, the tool identifies entries with available views by highlighting them in black and red.

For large networks that are viewable, you can explore their structure from an aerial perspective. This allows you to easily navigate through the network and observe its nodes. You can also zoom in for a detailed or ensemble view.

Features

free to download and use;
compatible with modern Windows versions;
allows you to visualize molecular interaction networks;
you can load datasets in a wide range of file formats;
there is an option to quickly change attributes.