Codefest 2015

I had the great pleasure of attending the Codefest 2015 in Dublin. Not only did I get to meet some really nice people but I also got some work done. Below are the projects that I worked on and some general notes.


In the first day I joined Mirjam Rehr and Maciej Pajak in working on a Shiny app to visualize targeted sequencing data in an interactive way. Not only was this a nice opportunity to shape up on on R and Shiny, but I was also introduced to something new and interesting.

I’d never seen the R-package Packrat before – it’s used to create a set of local dependencies for a R project. Thus making sure that updating a dependency in one project does not break other projects that you might have that uses a older version of the same library. It also bootstraps all the dependencies into the project when you load it, which is just an added benefit.


I’ve been wanting to try out ADAM for some time now, but I haven’t found the time for it. It felt like the Codefest was a excellent opportunity to get into something new, so that’s what I did day two. After a short brainstorming session, me and Roman Valls Guimerà decided to see if we could port (and possibly improve upon) then idea used in FACS of using bloom filters to find contamination in short read data.

We got off to a good start and got a lot of fun hacking done. We even got some remote help, both with pull requests and advice from Michael L Heuer and Christian Pérez-Llamas, which was awesome!

Not only did I learn a lot in this day, but it also got me excited to keep working on this and see if we could actually make a real product out of this. We’ll see how that goes, but regardless getting it started in the Codefest was super exciting.

Other things of note

A large part of Codefest 2015 was dedicated to the Common Workflow Language – and it seems that there was some progress made in the hackaton. I think it’s going to be very interesting to see where this project is going in the future. If it keeps getting traction in the community I think that it could actually be the solution to the N + 1 pipeline system in bioinformatics. Wouldn’t what be awesome?

Finally, if you’re in any way interested in open source coding for bioinformatics I’d absolutely recommend going to the Codefest. Hope to see you there in the future!

P.S.  Robin Ander also did a write up of the Codefest here, check it out! (even later edit): Here Guillermo Carrasco also wrote about the Codefest here.