Samuel's Tech Blog

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!

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).

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.

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

Databases

• Bio2RDF
• KEGG - Kyoto Encyclopedia of Genes and Genomes

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 http://wiki.bioclipse.net/index.php?title=Checking_out_Bioclipse_2.0, in Eclipses 3.5 and tried to run Bioclipse 2.2.

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

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.

http://heather.cs.ucdavis.edu/~matloff/UnixAndC/Editors/ViIntro.html 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


I found a git tutorial at http://git.or.cz/course/svn.html Looks useful for svn users, since it has the paired the corresponding git / svn commands. Another one is https://we.riseup.net/debian/git-development-howto as well.

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