(Starting to summarize how to solve those frustrating Eclipse problems, that come up over and over again ...)
If you get error messages like various ClassNotFoundException or:
"The activator net.bioclipse.ui.Activator for bundle net.bioclipse.ui is invalid"
... then, Click the little validator icon in the product file (right left to the question mark icon). Add the mission plugins/features in the corresponding tabs (plugins/features) in the product file editor (the tabs are at the bottom of the editor).
So, the things you have to know how to do, sometimes over and over again:
Also, when importing jar files into the build path of a plug-in, you have to include the jar file itself, it does not work with just the folder that contains it.