Bioclipse has outgrown its original design. We have therefore decided to start the design of Bioclipse2, which will be a complete rewrite of the core API and extension points to overcome the many deficiencies of the current design/implementation. I have established a wiki page for this. If you'd like to participate in the redesign, please add your name in the members section. The discussion will be carried out in IRC (irc.freenode.net, #bioclipse) and on the mailing list bioclipse-devel.