How one can create Cytoscape plugins using Jython?

I (MarcioSilva) found at Cytoscape CVS the following file:


from Dan Tenenbaum, explaining how to run Jython plugins using Java Web Start.

I tried to follow the directions from the document above, but then I have the following files:

My question is: what should I do with this .jar files?

I tried to put all of them in the plugins/ folder of cytoscape, but then I have this error:

Exception in thread "main" java.lang.NoClassDefFoundError:
       at java.lang.ClassLoader.defineClass0(Native Method)
       at java.lang.ClassLoader.defineClass(
       at Method)
       at java.lang.ClassLoader.loadClass(
       at java.lang.ClassLoader.loadClass(
       at cytoscape.CytoscapeInit.isClassPlugin(
       at cytoscape.CytoscapeInit.loadPlugins(
       at cytoscape.CytoscapeInit.init(
       at cytoscape.CyMain.<init>(
       at cytoscape.CyMain.main(

This seems to happen when Cytoscape tries to load jython.jar (because I removed PyConsolePlugin.jar from there and the same error happened -- when I removed jython.jar Cytoscape loaded normally).

Another question: in that document Dan mentions a file called:


Where can I get it? And how to add it to the jython.jar (It is ok just do a jar xf add the file and jar cf again?).

I just want to make some plugins for Cytoscape using Jython. The reason is that I want to use some Python tools like NetworkX

Anyone with experience in this topic?

PluginsWithJython (last edited 2009-02-12 01:03:29 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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