After a few days of discussion on the cytoscape-discuss google group, I’ve finally managed to run a simple plugin in Eclipse (from a separate project) that will work with the other Cytoscape source code (Special Thanks to Piet Molenaar for the patience and assistance!). Now I can also debug plugins in Eclipse!
Now that I’ve got my programming environment correctly set up (hopefully), the next step will be to start on Subproject 1. For details on this subproject, please visit the About page.
Congrats!