Workshop Cluster Computing for Life Sciences

Learn during the workshop how the supercomputer can help you in your daily work. You get started with the Unix-Shell tool and we tell you more about the use of Python in high-performance computer environments to automate data analysis pipelines with Snakemake.

Verschillende iconen met focus op icoon workshop
01 — 02 Jul 2019
9 am to 5 pm
SURF-office, Utrecht

Combine existing programs

The Unix shell has been around for longer than most users. It has been preserved for so long because it is a powerful tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them to combine existing programs in new ways and to automate repetitive tasks so that they do not always type the same things.

For whom?

This workshop is relevant for students and / or researchers, in particular from the life sciences.


Day 1

The morning focuses on the base of the Unix shell. The use of the shell is fundamental to the use of a wide range of other powerful tools and computer resources (including super-computers with high-performance computing). These lessons will help you on your way to using these resources effectively. In the afternoon you put those skills into practice. You learn about calculation clusters, how you can use them for your calculations and what the best methods are.

Day 2

The second day focuses on the use of Python in high-performance computing environments to automate data analysis pipelines with Snakemake (for a detailed discussion of why we learn Snakemake, see the discussion page of this lesson). We start with the basics and handle everything you need to get started. Some elements of writing performance-based code are covered, but it is not the main focus. There is no required knowledge for this tutorial, although having some experience with the command line or a compute cluster will be very useful.


Please bring your own laptop, with a Mac, Linux or Windows operating system (no tablet, Chromebook, etc.).

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