Who We Are: Willem Ligtenberg,A Member

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.


Willem Ligtenberg


Backport spyder 2.3 to Ubuntu 14.04 LTS

News from Ghislain Vaillant:

The recently released Spyder version 2.3 introduced the much awaited Python 3 support. Debian already has a working package in testing/unstable for both Python 2 (spyder) and Python 3 (spyder3). I have proposed a backport of this version of Spyder to the current LTS in the following bug report: https://bugs.launchpad.net/ubuntu/+source/spyder/+bug/1347487 For those who are interested, please back this proposal up by adding any additional comments up in the bug report or simply marking yourself as affected.

UPDATE: https://bugs.launchpad.net/trusty-backports/+bug/1351131 is where the action is happening now. Please come on in and join in for testing if you’d like this backport to happen soon.

August 4, 2014 UPDATE: Spyder 2.3 is now available via the trusty-backports channel. A big thank you to Stephen Michael Kellat for working on the backport and Scott Kitterman for the upload and communication with Debian.

Who We Are: Svetlana Belkin, Admin/Founder

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.

Team Wiki Pages Update: June 19, 2014

Today, Svetlana Belkin (belkinsa), done work on the team wiki pages, mainly the home page.  The home page now has a cleaner look where the basics, such as the introduction about the team all the way to how to contact the team and how to join the team.  Svetlana also removed some of the excess “tabs” on the menu bar and added a “Site Map” tab, where users can see what other pages are there.

There is still work to be done on a homepage, mainly with menu and a lot of work on those team wiki pages, as stated here and in the UOS session.  Hopefully, the team’s wiki pages will be finished by the end of July 2014 in order for a clearer understanding for newcomers.


Introducting the “Ubuntu Scientists Blog”!

In the last UOS, the founder (belkinsa, Svetlana Belkin) of Ubuntu Scientists decided to create a blog where the team will post news, interviews of the members, and stories of members to help other scientists to get a feeling of who we are, how to help us, and how to use FOSS in the science fields.  Another team also have done this in the past.

Other posts are HERE