Samuel Lampa's blog

Switching to Blipkit/BioProlog

After installation problems with DR-PROLOG, and after looking closer to Blipkit/BioProlog (Biomedical Logic Programming Knowledge Integration Kit), after a suggestion by Claes Andersson, I now aim to integrate it instead of DR-PROLOG.

Installing gPapers in Ubuntu Jaunty (9.04)

I discovered Mendeley today. Except for it's citation organization features, for which it is not unique (there are CiteUlike, JabRef and more) it works as a desktop app that indexes all your local PDF documents, and has an internal PDF viewer that lets you annotate the documents. These two are killer features that I've been looking for since a long time.

It's a pity though that it is proprietary. It would naturally feel better to put your work in the hands of an open system.

Blipkit/BioProlog quotes

I just read a paper on BlipKit/BioProlog, (July 2009). This is interesting stuff!

I'll collect some quotes from the paper, that give some key info about the system's capabilities:

  • "Logic programming can provide a means of both performing integrative queries and rule-based inference to accound for implicit knowledge"
    • These are key concepts.

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://[path to your project]...git

Then go:
git branch -a 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