Sometimes education can be a daunting process. It is quite obvious from the student side, we all have gone through exercises, corrections, learning what we did wrong on some of them, fixing and learning from those errors, rinse and repeat. That’s how it generally works.

On the teacher’s side, correcting assignments is easy and unbiased unless the number of students is considerably large. At
one of the sessions of our now official KTH course “DD3436 Scientific Programming in Python for Computational Biology” I was given the task to hold a session on software testing and continuous integration in Python… for around 50 students.

Continue reading →

I’ve just pushed a set of trivial modules system scripts that will hopefully ease your deployment of Cloudera Distribution for Hadoop 3 Beta 4 on your university cluster… partly, at least. This sad “partly” made me think about the current state of things on IT and HPC.

Over time I’ve learnt that there are several unexpected issues when deploying hadoop on custom clusters that you don’t own. Those are mainly related to software management policies, non-root access (being auto-deployment unfriendly), quotas and queueing or “batch” systems.

Ignoring most of these “fixable” issues, it becomes apparent that the most juicy problem for a sysadmin trying to get the most of hadoop-related tools is the batch system. Be it SGE, SLURM or other non-DRMAA compliant exotic batch system implementations, you’ll have to deal with annoying integration quirks at some point, granted.

Making it all work can be challenging to say the least… but the question is: does it have to be that hard ?

Continue reading →

Summarizing from their official page, iGEM is about:

Using standard biological parts to build biological systems and operate them in living cells.

I’ve been tracking them since before joining KTH’s Computational Biology Masters degree. Having a quick look at past editions is both surprising and enlightening to see what they archieve year after year.

Perhaps the most rewarding sensation is being able to incrementally be aware of what they are talking about on their projects as I progress on my studies. Indeed, before joining the Masters I could barely understand the general idea, and got absolutely lost in the biological details. Now I can follow it after stepping on some stones that the master provided me.

Last year, together with Hassan, we based our final Biomodelling presentation on one project that matched the models we were studying on the course: Reaction diffusion systems.

Just a few weeks ago, while learning again how to stand up on a snowboard table on Romme, I had the great opportunity to talk with one of last year’s Uppsala Team advisor, Daniel, who not only enjoyed the experience, but together with his team, managed to contribute back some biobrick.

Today I would even like to try (dare?) and join one of those groups, just for the fun of learning how this amazing world actually works and to struggle with a real world problem.

And you ? What are you doing this summer ?