I have a new blog!

Problems getting DR-PROLOG up running

Trying to get DR-PROLOG up running, following the instructions found here.

I have installed SWI Prolog and XSB Prolog. In order to compile SWI-Prolog, I had to install the following packages in Ubuntu (9.04), as mentioned in the README.debian file:

libxext-dev libice-dev libjpeg62-dev libxinerama-dev libxft-dev libxpm-dev libxt-dev pkg-config

It is now possible to start the DR-PROLOG Java application, but not to start the DR-PROLOG engine (from the DR-PROLOG menu in the Java application) .

Status: Git on windows

Since I'm originally a windows user and still using it sometimes, I'm keeping an eye on the status of git on windows.

Seems like there's more to do, but some things are happening: MSysGit Seems to be the currently best solution, while GitSharp looks promising. For MSysGit there's a guide on getting started with Git and GitHub on Windows.


Must-have git how tos

Realized I would need to go through a git tutorial containing the basics.

I liked this one. Very concise, and has sections for the typical roles you might have as a git user. I liked this one too. A good complement to the other.

Empty plugin / Bioclipse manager up running, showing up in Bioclipse JS console

After som hard work by Egon (finally resulting in this commit), which includes (in addition to the plugin file structure created with the Bioclipse SDK) an eclipse product file which means Bioclipse can now be started with the (empty) drprolog plugin enabled, and available in the JavaScript console inside Bioclipse.

How to check out a specific branch from github

I ran into troubles trying to check out a specific branch from github.

I asked about it at #git on FreeNode IRC channel. I'll summarize how to do it:

First run:
git clone git://github.com/...[path to your project]...git

Then go:
git branch -a
...to see what branches you have.


First week of my degree project passed

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".

Even more abbreviations...

Reading up on Life Science databases et.c... which continues to generate "abbreviations" that are useful to know well.


  • DBPedia - RDF version of Wikipedia
  • LODD - Linking Open Drug Data (contains an overview of the included databases)
  • PubChem

Formats et.c.

  • InChI - IUPAC International Chemical Identifier

Starting work on creating a Bioclipse manager

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!

Up and running on Eclipse 3.5 (Bioclipse 2.2)

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:

 git pull

Then i had to refresh all the projects in Eclipse, one by one, (select projects and click F5, one at a time).

Blipkit, A Biomedical Logic Programming Integration Kit

A collegue of Mats Gustafsson mentioned about Blipkit today. Seems worth checking up.

The thought struck me for a second that it could be even more interesting to integrate, than DR-PROLOG, since it is biomedically oriented. Maybe not, but worth thinking of I guess.

EDIT: Checked up with Egon, who pointed out that it doesn't seem to have a good interface for integration to Java, which would complicate things. Seems like a good point.