Programmatic Access to Cytoscape Features

In this section, you will learn how to use programmatic access features for advanced Cytoscape users.



Cytoscape has intuitive graphical user interface for interactive network data integration, analysis, and visualization. It is a great way to exploratory analyze your data sets, but what happens if you have hundreds of data files? It is virtually impossible to apply same operations to hundreds of networks manually with GUI.

More importantly, although you can save your results as session files, you cannot save your workflows if your analysis is based on point-and-click GUI operation. Recording workflows is the key feature for reproducible data analysis, but it was a missing feature in past versions for Cytoscape. Latest version of Cytoscape has several options to script and automate your workflows.


There are two ways to access Cytoscape programmatically: Commands and RESTful API.


Commands is the built-in Cytoscape feature to automate your workflow as a simple script.

Sample Scripts



In some cases, you may need to use fully featured programming languages, such as Python, R, Ruby, or JavaScript,

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

MoinMoin Appliance - Powered by TurnKey Linux