Events

Johannes will talk about Generic Solutions for Specific Problems in Genomics: Snakemake, Datavzrd, and Varlociraptor in 2025

Abstract
At the example of the successful open source projects Snakemake, Datavzrd, and Varlociraptor, I outline the development of continuously maintained, tested, and improved software solutions that arose from the necessity to solve at first sight rather specific and narrowly scoped bioinformatics problems. I describe the generalization steps and demonstrate how this approach enhanced their sustainability, leading to their current feature sets and ongoing advancements.

About the speaker
Johannes Köster is professor for Bioinformatics and Computational Oncology at the Institute for AI in Medicine (IKIM), University Medicine Essen, University of Duisburg-­Essen with a focus on algorithm engineering and data analysis. Johannes studied computer science at the University of Dortmund. Johannes' research is focused on reproducibility in three ways. First, he is the author of the popular workflow management system Snakemake and the founder of the Bioconda project for sustainably distributing bioinformatics software as easily installable packages. Second, Johannes is the author of the Rust-­Bio library, enabling the use of the Rust programming language for bioinformatics by providing standard bioinformatics algorithms and data structures. Third, Johannes is working in the field of Bayesian statistics (e.g., for variant calling and single cell transcriptomics) in order to provide algorithms for analysis of high­throughput data while capturing and quantifying all known sources of uncertainty, thereby providing more reproducible predictions.

Contact: Laura Godfrey (+49 221 478 51455, laura.godfrey@iccb-­cologne.org), Stefanie Fleer (+49 221 478 15104, stefanie.fleer@iccb­-cologne.org)