I am Willem Ligtenberg.
I have studied Biomedical Engineering and later specialized myself in bioinformatics, which is also
known as computational biology. More specifically, I specialized myself in biomodeling and bioinformatics.
During my PhD thesis I investigated the use of graph theoretic approaches in biology.
I used graph algorithms in combination with machine learning algorithms to reverse engineer gene regulatory networks. If you are interested you can have a
read here: http://www.biomedcentral.com/1471-2105/13/281
During this I used a lot of Python and a bit of R for the statistics. I also took a course on
biostatistics for PhD students and although the course was given using Statgraphics, I did using R.
Which the tutors thought was fine, but it was not their expertise. However, they did give me the
e-mail address of a collegue of theirs who used R as well.
Fast-forward a couple of years, and currently I am working as a consultant for Open Analytics
(http://www.openanalytics.eu), which is a company that helps with the data analysis from start to finish. As the name suggests
the company believes in openness and therefore focusses on the use of (fibre/libre) open source software (FLOSS).
The FLOSS aspect of the company was a big plus for me, since I have been using Ubuntu since Warty (2004).
For the data analysis part we mainly use R, but we will use other languages if they are more
appropriate. So I still get to use Python now and then.
I have written and contributed to a few R packages that are on Bioconductor: (reactome.db,
the a4 packages and MLP). I am currenty working on an Object Relational Mapper in R, which
I hope to publish soon. Feel free to reach out to me if you want to know more about data analysis
using open source software, specifically bioinformatics and databases.
Welcome all to the first of many “Who We Are” posts. These posts will introduce you to many of our members of the team. We will start with Svetlana Belkin, the founder and admin of the team:
I am Svetlana Belkin (A.K.A. belkinsa everywhere in Ubuntu community and
Mechafish on the Ubuntu Forums), and I am getting my BS in biology with
molecular sciences as my focus at University of Cincinnati. I used
Ubuntu since 2009, but the only “scientific” program that I used was
Ugene. But hopefully, I will get to use more in my field.