Last month I had that opportunity to visit the University of Concepción, and teach a course at the Austral Summer Institute – “Physiological response of marine organisms to environmental change from a genomic perspective”.

This is a five day course with AM lectures and hands-on bioinformatics modules in the afternoon. The learning objectives of this course include
1) Understanding of fundamental physiological processes
2) Acquisition of core computing skills
3) Hands-on experience with genomic datasets

  • via course website aka GitHub wiki


    Mornings were physiology lectures with most of the day in the computer lab. We were very lucky to have Mac minis with the instructor’s computer a wall-mounted 50 in HDTV. The lab started with the Unix Shell thanks to Software Carpentry lessons. I trimmed the lesson a bit but think this was a good way to start as it gave the students something real text to reference. In the first day we made it through blast at the commandline and SQLShare. I used the command-line some so they could follow along but had prepared modules in IPython. The students were exposed to IPython by day three using SageMathCloud, though they did not use it regularly during the course. Day two was a carry-over from day one with an emphasis on gitting familar with the shell and transcriptome annotation. We went on to RNA-seq with everyone also setting up their own GitHub repository and learning how to operate with GitHub for Mac. We did not get much more genomics done though I did show them a little SNP and CpG prediction workflows. In the end It seems like everyone got at least something out of the course. As might be expected many students appreciated the web services that help make pretty pictures including DAVID, Revigo, and SQLShare.


If I were to do something like this again (which I hope I will be able to) a few things I might do is get more post-it note feedack and make an effort to get content to students ahead of time, so the have the opportunity to play with some of the tools.

Austral Summer Institute Course Wrap-up