Upgraded to Ubuntu Karmic Koala, and took the occasion to swith to sun-java-6 (Had problems with OpenJDK before).
Bioclipse with blipkit plugin still works like a charm. Just had to modify the Eclipse startup script, since the path's to my java libraries changed.
Content of my start-eclipse-for-blipkit.sh script:
export LD_LIBRARY_PATH="/usr/lib/jvm/java-6-sun-22.214.171.124/jre/lib/i386/client:/usr/lib/jvm/java-6-sun-126.96.36.199/jre/lib/i386" LD_PRELOAD=/usr/local/lib/pl-5.7.15/lib/i686-linux/libjpl.so /home/samuel/program/eclipse/eclipse &