Category Archives: talks

The one where I went to Sweden

I spent some days two weeks ago in Stockholm, Sweden. Lex Nederbragt and I were invited by SciLifeLab to teach a Software Carpentry workshop there. This coincided with the very first PyCon Sweden Conference, and as the organizers would have it, I got to present a talk.

The workshop

The workshop went very well. Lex and I taught the by-now fairly well known novice workshop (if you want one at your institution, let them know!). Oxana Sachenkova, the local organizer, had also set up an intermediate workshop. The teachers in that one were Konrad Hinsen and Nelle Varoquaux, both flying in from Paris. Their workshop focused more on object oriented programming and intermediate git use. It was great meeting them, the only sad thing is that I could not sit in on their workshop

The division of labor between Lex and I have until now been that he teaches shell and unit testing, while I teach git and python. This time I taught both these parts from the new lesson material that has been developed. I had taught the git lesson earlier once before, so that material was well known to me. I think this lesson is reasonably easy to teach, the real challenge is to convey to the students why version control is useful at all. At this stage I am leaning towards most people not really understanding the need for version control before they have either messed up their work pretty badly, or have become involved in a joint development project.

I had not taught the python lessons before. These now take place entirely in the iPython Notebook. The first time I went through them, I actually wondered if I should return to the old lesson material, if nothing else because on the printout I had somewhere around 50 pages to go through. On the second run through, however, I realized that the notebook is a game changer. With the notebook, I could have the students editing and copy-paste code from earlier in the lesson, which would reduce the typing time and hence the teaching time dramatically. There were still things that I cut from this lesson – I did for example not go through he python call stack, simply because I still think this is too complicated for novices. Instead, I teach them the basic tenant “What happens in a function, stays in a function”, and that does seem to stick.

The conference and my talk

Due to teaching I only got to attend the last day of the conference. The programme looked really nice, and I got to see some really great talks. The morning of the last day opened with Laurens Van Houtven speaking about cryptography, and Jackie Kazil speaking about how she started using programming in her journalism and how that lead her to new pastures. After lunch there were several other talks, most of which were pretty technical. Such talks can be really good, but to me they lose their value when they don’t even have a 3 minute “subject of my talk for dummies” intro. 

My talk was at the end of the day, and was entitled “Python and Biology: a shotgun wedding” (pardon the pun, when the title appeared in my head, resistance was futile). The background for the talk was that I have several times during the last couple of years helped people – primarily biologists – start programming. Naturally, as opinionated as I am, I have ended up with some do’s and don’ts on where to start. I also included a bit of background on why life scientists have had to get into this game, and also showed some examples. I have included the slides below.

The talk seemed to be fairly well received – it was however aimed at novices, and there did not seem to be too many of those in attendance. I did however see some people nodding vigorously in the front, and got some really nice questions at the end, so all in all I think it went over well.