CytoscapeRPC install
From BioAssist
Install
- Download and install Cytoscape
- Install CytoscapeRPC, this can either be done via the plugin manager or by manually downloading the plugin:
- 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'.
- 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.
- After installation restart Cytoscape.
- Now install a XML-RPC client, some examples are listed below.
Clients
- 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.
Start
- Start Cytoscape.
- Go to Plugins -> CytoscapeRPC and choose 'Start CytoscapeRPC'.
Test
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:
import xmlrpclib
server = xmlrpclib.ServerProxy('http://localhost:9000')
server.Cytoscape.test()
The shell should now display 'It works!'