CytoscapeRPC install

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  1. Download and install Cytoscape
  2. Install CytoscapeRPC, this can either be done via the plugin manager or by manually downloading the plugin:
    1. Plugin manager: Start Cytoscape and go to Plugins -> Manage Plugins. Under 'Available for install' open 'Communication and Scripting'. Select the latest version of CytoscapeRPC and click 'Install'.
    2. Manual download: Go to the Cytoscape plugins site or NBIC Trac and download the latest version. Copy the downloaded jar file into the plugins directory of your Cytoscape folder.
  3. After installation restart Cytoscape.
  4. Now install a XML-RPC client, some examples are listed below.


  • RCytoscape: a R package which communicates with Cytoscape using CytoscapeRPC. You can also try this version, complete with installation instructions.
  • Python
  • Perl
  • Ruby

Installation instructions for all of these languages can be found on the web. Once installed you can try to connect using one of the examples in the tutorial.


  1. Start Cytoscape.
  2. Go to Plugins -> CytoscapeRPC and choose 'Start CytoscapeRPC'.


A method of testing Cytoscape using Python.

  • Open Cytoscape and activate the plug-in (Plugins->Cytoscape RPC->Activate CytoscapeRPC) keep the default port and click 'OK'.
  • Open a python shell
  • Type in the following commands:
  1. import xmlrpclib
  2. server = xmlrpclib.ServerProxy('http://localhost:9000')
  3. server.Cytoscape.test()

The shell should now display 'It works!'