Table 1. Existing Cytoscape apps to control Cytoscape from scripts.

Application Name	Description	Supported Version
Command 5	A domain specific language to automate simple tasks in Cytoscape	3.x and 2.x
Cyrface 6	An interface to call R packages from Cytoscape	3.x
ScriptingEngine 8	Exposes Cytoscape API to scripting engines for JVM (JavaScript, Jython, JRuby, etc.)	2.x
CytoscapeRPC 15	Plugin to call low-level Cytoscape API through XML-RPC	2.x
RCytoscape 17	Bioconductor package to call Cytoscape from R using CytoscapeRPC	2.x