Blue Waters Webinars

Reproducible data analysis with Snakemake

Photograph of Johannes Köster
Johannes Köster

Computer Scientist
Group leader
Algorithms for reproducible bioinformatics
Institute of Human Genetics
University of Duisburg-Essen


Bio
Johannes Köster is a computer scientist with a focus on algorithm engineering and data analysis in bioinformatics. Johannes studied computer science at the University of Dortmund (diploma thesis 2010, with Max Planck Institute of Molecular Physiology Dortmund). Then, he did his PhD in the group of Prof. Sven Rahmann (TU Dortmund, 2015). Afterwards, Johannes was a postdoc in the groups of Prof. Shirley Liu and Prof. Myles Brown at Dana Farber Cancer Institute and Harvard University (2015-2016). In 2016, Johannes moved to the lab of Prof. Alexander Schönhuth for a brief second postdoc at Centrum Wiskunde & Informatica Amsterdam, Netherlands (CWI), where he quickly received a VENI grant for an independent position. In 2017, Johannes became the head of the Algorithms for reproducible bioinformatics group at the University of Duisburg-Essen in Germany.

Abstract

The webinar will present a live demo of the popular workflow management system Snakemake, https://snakemake.readthedocs.io. Using an example from bioinformatics, we will show how Snakemake can be used to perform data analyses in a reproducible, scalable and portable way. Thereby, we will highlight typical design patterns and best practices.


Session details
When: 10:00 CDT, March 20, 2019
Length of session: 1 hour
Prerequisites: The webinar requires basic knowledge of the Python programming language. It is helpful, but not necessary, to have some background in bioinformatics.

Webinar video

URL: https://youtu.be/hPrXcUUp70Y
Slides: Link (slides.com)
Survey: Link (Google Forms)