The new Cytoscape 3 is based on OSGI, which I barely know anything about. Even though Cytoscape 3 is still in beta, manuals, wikies and tutorials have been flowing around in the web, which could be overwhelming if you want to create a new C3 compatible bundle app. Today I tried to set up an Cytoscape 3 bundle App (aka Plugin in the Cytoscape 2.x world) development environment in Eclipse. To my surprise, it is without any hassle by following a tutorial and a wiki page.

First, by following this tutorial: Create a Bundle App Using IDE , it’s really straightforward to create the app with Maven and Eclipse (M2Eclipse is required). After everything is set up, I made sure that the app was installed by running “mvn install” (either in the app directory from command line or within eclipse) and checked my local maven repository ~/.m2/repository/groupid/architectid (yes I am using Linux).

Then I followed this wiki page: Interactive Shell , and deployed the app and tested it.

First download cytoscape 3:

> wget http://chianti.ucsd.edu/cytoscape-3.0.0-M4/cytoscape-unix-3.0.0-M4.tar.gz
> tar xzf cytoscape-unix-3.0.0-M4.tar.gz
> cd cytoscape-unix-3.0.0-M4
> ./cytoscape.sh # this will start cytoscape shell and the GUI
Cytoscape 3.0.0-M4> install mvn:groupid/artifactid
Bundle ID: 162
Cytoscape 3.0.0-M4> start 162

Now go to the Cytoscape GUI, and open Apps menu, and there it is: “Hello World!”

cytoscape hello world plugin after deployment

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