Cluster Computing for Life Sciences

from 23 APR 2019 until 24 APR 2019 

This workshop focusses on the basics of the Unix shell and on using Python in high-performance computing environments to automate data analysis pipelines with Snakemake. Specifically for the Life Sciences.

23 Apr 2019
SURF Utrecht
Prior knowledge needed?
Meeting type

Combine excisting programs

The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks, so they aren’t typing the same things over and over again. 


Day 1      

The morning will focus on the basics of the Unix shell. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). These lessons will start you on a path towards using these resources effectively. In the afternoon you will put those skills into practice. You will learn about compute clusters, how to use them for your computations and what are the best practices for it.
Day 2 Second day will focus on using Python in high-performance computing environments to automate data analysis pipelines with Snakemake (for a detailed discussion for why we are teaching Snakemake, see this lesson’s discussion page). We’ll start with the basics and cover everything you need to get started. Some elements of writing performance-oriented code will be covered, but it is not the main focus. There is no prerequisite knowlege for this tutorial, although having some prior experience with the command-line or a compute cluster will be very helpful.


For who?

The course is aimed at graduate students and other researchers, particularly from life sciences, who would like to know how a supercomputer can help to accomplish their everyday work.


Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.).

Latest modifications 18 Mar 2019