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.

Find me on:

Pondering over strategies for evaluating BLIPKIT vs Pellet for use with NMRShift data

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.

Testing out querying Prolog from Bioclipse

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".

Running Ubuntu Karmic Koala and sun-java-6

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.

Accessing BLIPKIT from command line Java or Eclipse Plug-in in Ubuntu

For my own documentation I went ahead and summarized all the steps I had to take

  1. In order to start blipkit from java commandline, and
  2. In order to start blipkit from an Eclipse plugin.

Got blipkit started from inside Eclipse

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

Finally got blipkit started from java via jpl :)

  • (Thanks to Andrew Koster on the SWIPL mailing list, who made me continue researching the LD_PRELOAD trick!)

In order to get the jpl java examples to work, LD_LIBRARY_PATH has to contain:

/usr/lib/jvm/java-1.5.0-sun-1.5.0.19/jre/lib/i386/client/:/usr/lib/jvm/java-1.5.0-sun-1.5.0.19/jre/lib/i386/

Furthermore, CLASSPATH has to be:
/usr/local/lib/pl-5.7.15/lib/jpl.jar:/home/samuel/install/swi-prolog/pl57/packages/jpl/examples/java/Test

Now firing up blipkit works, when calling Java from commandline!!!

Things learned today, 15/10 2009

  • Simply moving initialization statements from the blip startup script in /usr/local/bin/blip to /home/samuel/.plrc did not work.

SWI-Prolog JPL up running inside Bioclipse - Thinking about next steps

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.

"Refcards" for quickly getting into Bioclipse Plug-in development

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):

  • Eclipse Plug-in Development
  • Getting started with Equinox and OSGi
  • Spring Configuration
  • Spring Annotations

You will have to register at the site, and browse through the available ones in order to find them

Eclipse boot process, classloading, incorporation of native code etc.

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.

Tags: