keiono edited this page Sep 30, 2014 · 5 revisions

System Requirements

  • Java 7
    • cyREST is NOT tested on Java 8. Please use latest version of Java 7 for now.
  • Cytoscape 3.1.1 and later
    • Some of the new features are available only to Cytoscape 3.2.0

REST Client

cyREST provides a platform-independent API to access Cytoscape. This means you can use any programming languages/tools to access the API. Here is a list of popular clients:

For Web Browsers

Command Line Tools

For Python

For R

For Node.js


From JAR File

From Cytoscape App Store

Once 0.9.0 release is available, cyREST can be installed directly from Cytoscape App Store.

From Source Code

git clone
cd cy-rest
mvn clean install

This creates new JAR file in target directory. Then, follow the instruction in From JAR File section of this document.

Test Your Installation

  1. Make sure you can see the App from App Manager:
  2. From your web browser, access the following URL:
  1. If you get the status message, you are ready to use cyREST!
    apiVersion: "v1"
    numberOfCores: 8
    -memoryStatus: {
        usedMemory: 532
        freeMemory: 1430
        totalMemory: 1963
        maxMemory: 28217