Bioclipse on Classpath
Classpath is a GPL library of java.* classes, and is used by many open source virtual machines (e.g. gcj, kaffe, sablevm) as library to run Java program, like Bioclipse.
Bioclipse can be run with Classpath, just like Eclipse does. There are a few problems though, which sometime origin from incompatible code in the Eclipse RCP.
The Swing-in-SWT problem
Running Swing applications with Classpath is often no problem, but Eclipse' way of embedding Swing code in SWT widgets uses proprietary Sun classes, for which no free alternative is available. This is a known Eclipse bug, and being worked on. Alternatively, one may better not use Swing classes, and use SWT widgets directly, but thus often requires considerable refactoring.