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:
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):
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.
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! =)