Cytoscape Automation Wiki

This wiki contains supporting documentation for Cytoscape Automation scripters and developers.

FAQ

Frequently Asked Questions about Cytoscape Automation -- a good place to start

Getting Started with Automation in R

Step-wise installation instructions leading to RCy3 vignettes.

Understanding Automation

How to easily experiment with Cytoscape Automation

Script Writers

Workflow Index

An index of links to useful Workflows in scripting languages such as R and Python

Sample Scripts

A collection of sample scripts that use Cytoscape Automation

App Developers

Adding Automation to Existing Apps

How to add Automation to an App you already maintain

Building CI Responses

How to build CI Responses for your Automation Functions.

Exercising Your App

How to access an app's automation features from clients, web browsers, and the Swagger UI

Using Scripting to Test Your App

How to write integration tests in a scripting language to test your App

Sample Apps

A collection of sample Apps that implement Cytoscape Automation

Best Practices

• Cytoscape Function Best Practices ... to follow when implementing Cytoscape Functions via JAX-RS
• Swagger Best Practices ... to follow when documenting automation functions
• Cytoscape Command Best Practices ... to follow when implementing Cytoscape Commands

Web developers

Adding Automation to Web Pages

How to add Automation to web page