Samuel's Project Blog

I needed a Bioclipse manager method that could take an arbitrary number of arguments, (for a general purpose prolog method mapper). Through a useful discussion with jonalv, we figured out that there exists at least one working way of doing this, while there are a number of ways that do not work across both the Rhino/JavaScript though they work in Java alone.

A strategy for how to work with the Bioclipse/JPL/Prolog/Blipkit combination I'm setting up, is becoming clear.

The main idea with Bioclipse, as well as with having a prolog engine available in it, is for flexible and "interactive" knitting together of knowledge. One of the main questions regarding how to use a Bioclipse/JPL/Prolog/Blipkit combination, has been where to put the bulk of knowledge integration/reasoning code? There would in principle be three options for that:

1. Bioclipse (Javascript environment)
2. The Blipkit-Prolog/Bioclipse integration plugin (Java code, a.k.a. "Manager methods")
3. The prolog engine (As a prolog file)

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".

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.

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):

• 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

I switched laptop recently, so I needed to set up my development environment for Bioclipse 2.2 plugin development from scratch. Since the instructions for how to do this are spread over a couple of blogs and the wiki, I used the occasion to create an integrated howto, for my own documentation as well as for anyone interested.

After installation problems with DR-PROLOG, and after looking closer to Blipkit/BioProlog (Biomedical Logic Programming Knowledge Integration Kit), after a suggestion by Claes Andersson, I now aim to integrate it instead of DR-PROLOG.

So, one week has passed, or almost one, since my official (degree-)project start this monday.

Will start off with a short presentation of what I'm doing (or going to). My suggested project title is "Integration of DR-PROLOG for semantic reasoning in Bioclipse".

Will now start the work of creating a Bioclipse manager for the integration of DR-PROLOG into Bioclipse.

Egon pointed me to a blog post about a feature they've made in order to make it easier for us who are new to Bioclipse development to get started. Nice, det tackar vi för!