The Eclipse dialogs had changed location and structure a little, so for my documentation, I included a screenshot of the dialog under "Run > Debug configurations" below.
I just had my 3rd, and last project update presentation (before the final presenation on April 28th), presenting results from comparing the performance of the integrated SWI-Prolog against Jena and Pellet, for a spectrum similarity search query. Find the sldes below.
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:
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".
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.
As a side-note, this looks interesting (Googled up by Egon), a Prolog Eclipse Plugin:
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):
so I have tried to add the line
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.
I now got up and running Bioclipse (2.2) on Eclipse 3.5 :)
I had problems first when just copying the old worspace (Bioclipse 2.0 for Eclipse 3.4), but it was just because I had forgot to upgrade the Bioclipse code base. So I did it, with the command: