Teaching the “Linux for Scientists” course in Rotterdam

Next week, I will be back at the Erasmus Medical Centre in Rotterdam to teach the EL016 Linux for Scientists course, which is part of the NIHES MSc programme in genetic epidemiology.

Running for two full days, the course aims to teach students with a background in the life sciences to work on a (remote) Linux server. No previous Linux or scripting knowledge is required, as I start from scratch: a bit of history and then “how to log in”. Over the course of the two days, we cover topics that include basic tools and utilities like ls, cp, mkdir and cd, moving on to grep, awk, etc. towards writing simple Bash script to help automate analyses and make them more reproducible.

The course consists of a combination of lectures in which I give some background and demonstrate how to use the various tools, and a series of practicals from which the students will learn the most: hands-on learning by doing. The book I wrote over the years can be found at thea DOI 10.5281/zenodo.1412441.

This will be the 13th year I’ll be teaching this course, something I didn’t expect when I started it back in 2010 (the two missing years were due to the COVID pandemic in 2020/2021). Every one of those years has been great fun. I love the interactions with the students, which are generally enthusiastic, open and ask lots of questions. A great attitude!