I recently created a proof-of-principle for a deeper integration of jupyter notebooks with nextflow and started implementing my first modules in the new Nextflow DSL2. While doing so, I learned a lot about Groovy, and Nextflow itself.

Science is facing a reproducibility crisis. Poorly designed or implemented scientific software represent a major limitation in making packages reusable and analyses reproducible. In this article, I’ll break down good software engineering practices to six hallmarks. These hallmarks guide researchers through improving their code quality, maximizing the utility and impact of the software, and in the long run improve the perspective of replication in science.

Over the last months, posts about Zettelkästen tended to show up quite frequently on Hacker News and caught my attention.

I used to be a big fan of projects like Versioneer or get_version because they make releasing a new version of a package as easy as

In this post, I will describe a data-analysis workflow I developed to address the challenges I face as a computational biologist:

Here, I present ipymd, a plugin for jupyter that allows to read and write R Notebook format. The package is freely available from github.

As a Bioinformatician, I am mainly confronted with two programming languages in my everyday tasks: R and python.

In an earlier blog post I described GEOS, the Google Earth Overlay Server. The python-tool allows to display web maps (such as Google Maps or open streetmaps) as an overlay in Google Earth.

There’s a plethora of maps freely available out there, offered by different companies or states. Just to name a few:

To share the stories of my Erasmus exchange in Tondheim, Norway, I created the outdoor and travel blog ⟨ ut ⟩. “ut” stands for out, outside in Norwegian.

“Write a game that has something to do with Bioinformatics”. That was everything they said to us. They – that’s the rostlab. Us – that’s me and Sebastian Wilzbach, one of my fellow students. So we went to tackle this incredibly specific task and well, this is what we ended up with:

Pupils are likely to know the problem: Somewhere in the school building there is a printed copy of the so-called “subsitution schedule” where you can look up which lessons will be off the next day. The hardcopy comes with several limitations:

The Crossmedia-Festival is a multimedia contest for Bavarian pupils. The contest is an initiative to promote the students’ “digital creativity”. Every november, all participants are intived to the headquarter of the “Landesbausparkasse” in Munich. There, a great variety of amazing contributions from the field of graphic design, music design, literature, web design, games, 3D-Animations and short movies is presented.