Cytoscape

If you’re a biology student, biology researcher or a general biology enthusiast that wants to dig deeper and broaden your your knowledge, then Cytoscape is the tool for you. With it you can visualize molecular interaction networks and biological pathways, all while integrating them with annotations and state data.

The interface of the application is very well structured and requires a couple of minutes to understand its layout and functions and a few finished projects to really get the handle of it. It offers you a network management panel, a network viewing window and an attribute browser from where you can quickly and easily change various attributes.

You are able to load multiple networks at a time, analyze and modify them as you wish. But there are some cases in which you are not able to view them. This is because some of these networks are simply too large and take a long time to display. The application helps you figure out which ones have and which don’t have views by displaying them with black and red highlights.

In the case of large networks that are viewable, you can study their structure using a bird’s eye view. This way, you can simply pan around the network to view its nodes and zoom in and for a detailed or ensemble view.

Cytoscape offers you support in system biology, genomics and proteomics. With it you can load protein-protein interaction data sets in Graph Markup Language, SBML, BioPAX, GraphML and Excel Workbook formats. The use of Cytoscape isn’t limited to biology as it is very well capable of processing and analyzing large social networks with interpersonal relationships as well as visualizing Resource Description Framework data.

Cytoscape is a complex application designed to handle both simple and complex data when it comes to visualizing and analyzing interaction networks from both biology and social science fields.