Bioinformatician / Developer at UPPMAX HPC Center, Uppsala University. Interested in Semantic Web, Bioinformatics and Computational Systems Biology, Java, Python, Go, Prolog, Domain Driven Design, Model Driven Development, MediaWiki and Drupal.
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As a subproject, I'm now focusing on doing some comparison between reasoning in Prolog and Pellet, using example data from NMRShiftDB.org. Below I'm documenting my planning, + any new findings while I'm digging in to this subpeoject.
My project has been more or less on hold for around a week because of exams and other stuff. Looking forward to getting some concrete things done now. While still reading up a bit on OWL, I've started taken the first steps of the prolog/blipkit integration with a simple method for querying a prolog on the form "subject, a predicate, and an object".
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.
For my own documentation I went ahead and summarized all the steps I had to take
I now also managed to start blipkit from inside Eclipse.
The trick was to start the whole eclipse (The eclipse using for building Bioclipse) preceded with LD_PRELOAD=...the path to libjpl.so , and before that adding the paths to where libjava.so and libjvm.so are located.
Finally got blipkit started from java via jpl :)
In order to get the jpl java examples to work, LD_LIBRARY_PATH has to contain:
Now firing up blipkit works, when calling Java from commandline!!!
So, today I finally got the jpl (Java / Prolog API) up running inside Bioclipse, succeeding with compiling a simple test prolog program (The "test 0" in the "Test" example supplied with SWI-Prolog). Only talking to swi-prolog so far though, not blipkit. Starting blipkit includes loading prolog files etc. as specified in the blipkit startup script, so will have to study that in more detail.
A link by Arvid led me to Dzone, where I found their "refcards": http://refcardz.dzone.com/ and after 15 minutes of reading, a lot of things, like file structure of Eclipse plug-in projects, had became much clearer.
For anyone new to Bioclipse plugin development, I think the following ones are the most relevant (especially the first two):
You will have to register at the site, and browse through the available ones in order to find them
This was a very good article on classloading and booting etc. in Bioclipse, with indispensable hints for how to best incorporate native code in eclipse plugins.