Samuel Lampa's blog

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.

Learning abbreviations

Reading the paper on the Bio2RDF database.

It contains something that I need, an overview of different techniques, databases and formats that are common in the semantic web community, but of which I know to few still.

Some useful abbreviations just learned (some I knew somewhat, but was not sure):

Formats / Languages

  • RDF - Resource Description Framework
  • OWL - Web Ontology Language
  • LSID - Life Sciences ID
  • Dublin core


  • Bio2RDF
  • KEGG - Kyoto Encyclopedia of Genes and Genomes

Upgrading to Eclipse 3.5 / Bioclipse 2.2

Bioclipse now runs on Eclipse 3.5, so time to grab it. I grabbed Eclipse "classic".

I then just opened the workspace that I had prepared earlier by following the instructions at, in Eclipses 3.5 and tried to run Bioclipse 2.2.

It "almost" started... Errors are documented in the attached log file and screenshot.

Had to learn some basic vim

I just realized that git is using vim as text editor (hope it is possible to change to nano or equivalent). Anyway, as for now I guess I better just learn som basic vim commands. saved me.

The most important commands to remember are:

i - enter "insert mode"
a - enter "append mode"
ESC - leave "insert" or "append mode"
x - delete one character
dd - delete one line (and store it in clipboard)
ZZ - Save and close
ZQ - Close w/o saving


Looking into git

I found a git tutorial at Looks useful for svn users, since it has the paired the corresponding git / svn commands. Another one is as well.


First blog entry

My first blog entry here! Congrats to me! =)