Samuel's Tech Blog

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

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.

As a side-note, this looks interesting (Googled up by Egon), a Prolog Eclipse Plugin:

• http://eclipse.ime.usp.br/projetos/grad/plugin-prolog/index.html#Screenshots

Could be interesting to combine that, in the future, with the results of my current project. Worth thinking about at least.

EDIT: Se solution at the bottom of the page

I'm trying to set the java.library.path system setting for my Bioclipse manager/Eclipse plugin.

Normally, if running java from command line, this variable should be set like so (According to what I've googled up):

java -Djava.library.path=/usr/local/lib/pl-5.7.15/lib/i686-linux/JavaClassName

so I have tried to add the line

-Djava.library.path="/usr/local/lib/pl-5.7.15/lib/i686-linux/"

Being completely new to development for Bioclipse, I'm trying to dig into the developer-centric information available, primarily on the Bioclipse Wiki. Thinking that the feedback from a newcomer might be of some value, I'll below share my reflections and ideas for the wiki.

MediaWiki as platform

I think it has been a wise choice to use MediaWiki as a backend. since it is today becoming a de facto standard, both for huge community-driven knowledge bases with millions of users, as well as in the industry.

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.

When trying to build swi-prolog packages from source, the xpce package complains:

I ran into the trouble that I needed to clean up some software built from source, that did not have the "make uninstall" option, what a mess!

Just found a solution though: paco. Paco keeps track of installed files if you run "make install" through it. Later you can easily remove the installed packages.

Egon pointed me to an interesting blog post on RIF and OWL. The post highlights a situation very relevant for my project: The apparent existence of two main approaches in the field of "knowledge representation and reasoning" (maybe it should be called simply handling?) on the Semantic Web.