Software Carpentry at SciLifeLab, Sweden

Software Carpentry at SciLifeLab, intermediate+ track

This has been my project of the past few months and of course I’m dying to share how it went.

This is how it all started. I got this email from Greg Wilson:

I hope you don’t mind mail out of the blue…[…]

I run a project for the Mozilla Foundation called Software Carpentry (, the goal of which is to teach basic computing skills to research scientists.  In the past eighteen months, we’ve run over 100 two-day bootcamps for almost 4000 scientists in a dozen countries; our instructors are volunteers, and overlap with groups like PyLadies, Ladies Learning Code, and others.  We’ve been to Norway, but never to Sweden — would you be interested in helping us put something together in Stockholm?

If this sounds good, let’s get it into the calendar and away we go!

So away we went… 🙂

I already knew about Software Carpentry and it’s efforts on making science reproducible and more efficient. And I thought it was amazing. So I became a local host. Greg put me in touch with their administrator and I started putting things together on my end.

I have now organised many events in the tech industry. It always goes like this:

  •  find the date that will fit as many people as possible
  •  find a room
  •  find funding

Now in academia “find funding” is always a tiny bit more challenging. Luckily, to bring Software Carpentry to your institution/conference you actually don’t need that much funding. Software Carpentry is backed by Mozilla Science Foundation. Instructor training, curriculum development, website, administrative costs are covered through donations. So first things first, it’s great if you can arrange a donation towards the central costs. $1500 is a good goal. Now here comes the problem that is slowing down Software Carpentry taking over Europe. It is close to impossible to arrange a donation from the University and any other grant based money to another non-profit. How would you motivate that? It would actually be easier if Software Carpentry required the money as a course fee. But that would kind of defeat the honourable goal of being a volunteer-based organisation, or would it? What do you think?

One cost that is absolutely required is the instructors’ travel costs. They’re volunteers, so they don’t need to be paid for their time, but it’s only common curtesy to compensate for plane tickets and a place stay.

Other costs to think about could be coffee/drinks and some food for participants to mingle around.

So, now, where can we get the money?  One option Software Carpentry suggest on their guide for the local hosts is to charge people for attendance. This lucrative option was quickly eliminated. Since 95% of our attendants are going to be PhD students, where do you think the money will come from in the end? Right, PI grants. Will that make it more difficult for everyone in the research group to sign-up? Will that limit the number of people who can participate? Quite possibly. Besides, charging money for something in academia is even worse than looking for funds. Which account to use? Who will be in charge of receipts? What to do with refunds? Anyways, just forget about it.

Luckily, I got tremendous level of support among my peers and senior colleagues. My supervisor professor Arne Elofsson and professor Lars Arvestad representing Swedish e-Science Research Center (SeRC)  thought it will fit nicely to our own local efforts of teaching Python and good programming practices to bioinformaticians at SciLifeLab and KTH.

National bioinformatics communities BILS and WABI supported us also.  In fact, I would like to thank both of the organisations for their financial support.

Next step is to find instructors for this particular bootcamp. Software Carpentry admin will help you with this! We got amazing ones I must say. Lots of positive feedback from the attendees and lots to learn for the local teachers.

Meet our heros:

Lex Nederbragt 

Husband, father of two, biologist, bioinformatician, researcher, Dutchman.

Research Fellow at the University of Oslo.


Karin Lagesen

Bioinformatician, python coder, science fiction conrunner, cat owner, synth music fan. Occational blogger at

Assistant professor at the University of Oslo.


Konrad Hinsen

Research scientist at the Centre de Biophysique Moléculaire in Orléans (France)

Associated scientist at the Synchrotron SOLEIL in Saint Aubin (France)


Nelle Varoquaux

PhD student at the Center for computational biology, which is part of the INSERM U900/Curis/Mines bioinformatics unit, currently working on inferring the 3D structure of the genome from Hi-C data.

Why were we lucky to get all 4 of them at once, you’d ask?

Well, Software Carpentry bootcamp at SciLifeLab had two tracks. One classical Software Carpentry workshop aimed at researchers with limited computing experience and the other one for more advanced programmers.

In the beginners track we covered the following topics:

  • Unix shell
  • Basics for Python programming
  • Git and GitHub
  • Data exploration and  testing with IPython

All materials are available on github:

Software Carpentry at SciLifeLab, beginners track
Software Carpentry at SciLifeLab, beginners track
Software Carpentry at SciLifeLab, beginners track
Software Carpentry at SciLifeLab, beginners track

 Intermediate+ track was focused on bringing the best practises and tricks of scientific computing to every day life of bioinformaticians and anyone involved in computational life sciences. The topics included:

  • Scientific computing in Python, Intro to NumPy/matplotlib
  • Collaborating using version control (git & github)
  • Object oriented programming in Python
  • Program design ( packaging and testing )

All materials are available on github:

Software Carpentry at SciLifeLab, intermediate+ track
Software Carpentry at SciLifeLab, intermediate+ track

All in all, two days of fun, learning and discussions of future collaborations!

45 people from SciLifeLab, KI and KTH attended and completed the training and 5 local volunteers were helping out. Our local team deserves a special mention. I’m hoping that highly skilled scientific computing community at SciLifeLab will only grow and here are the people at the frontier of it: Måns Magnusson, Jose Beltran, Robin Andeer Olav Vahtras and Radovan Bast. And yours truly, of course 😉

Thank you all for the amazing experience and for all the efforts of promoting reproducible research and open science in Sweden.

P.S: Little birdie told me that there soon will be an on-site instructor training in Europe, probably in the UK and if you got inspired by the event at SciLifeLab and would like to become an instructor yourself, just get in touch with me or Måns Magnusson and we’ll try to arrange it.


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