On this page, you will find events and initiatives that I co-organised at the University of Amsterdam.

Software and Data Carpentry workshops

8-9 December 2022: Main organiser of a two-day Data Carpentry workshop on microbiome analysis using shotgun metagenomics in Utrecht. This workshop was kindly hosted by the group of Anita Schürch at the UMC Utrecht and several members from her group participated in teaching.

24-25 June 2021: I co-organised and taught at a two-day Software Carpentry workshop as part of the first Amsterdam Science Park Study Group Summer School website.

13-14 January 2019: I organised a two-day Software Carpentry workshop in Amsterdam to teach biologists basic skills in programming. This served as a “kickstart” for experimental life scientists that need to learn some programming in order to perform their research. Since 1998, the Software Carpentry foundation teaches researchers computing skills to speed up their research and embrace good practices.

March 13-14 March 2018: I participated to the Software Carpentry intructor training organised by Mateusz Kuzak on behalf of the eScience Center. Upon certification, this training allows one to self-organise its own Carpentry workshops. I am looking forward to that!

13-14 December 2017: I co-organised a two-day Data Carpentry workshop in Amsterdam to help biologists to find their way in genomics. I was lucky to be able to teach a small part of the workshop on day two (fastq file quality check). Thanks to Anita Schürch, Dennis Schmitz and Sam Nooij for this opportunity!

17-18 October 2016: I co-organised a two-day Software Carpentry workshop in Amsterdam to teach biologists basic skills in programming. This was the first Software Carpentry workshop in Amsterdam.

Specific events

June 21 - July 2, 2021: Summer School organised by the Science Park Study Group: together with Stacy Shinneman, I co-organised a series of training programming workshops for researchers at the beginner (week 1) or more advanced levels (week 2). The Summer School lasted two weeks, gathered around 60 participants and benefited from the participation of 15 instructors and helpers. The complete programm can be found on the Summer School website

June 25-27, 2019: Carpentry Connect 2019 I co-organised a workshop session entitled Building a local Carpentries institutional framework during the Carpentry Connect 2019 to gather issues and solutions on community building based on the Carpentries Foundation experience and philosophy. A blog post and a section in the Carpentries Handbook are in the making based on the outputs of this workshop.

December 15, 2017: Snakemake day: after the success of the first Snakemake day in Paris, the second Snakemake day took place in Amsterdam on December 15 2017. It brought together the creator of Snakemake Johannes Koster together with regular users of Snakemake at both the expert and beginner levels.

From the creator of Snakemake:

Snakemake is a workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable > execution environment, together with a clean and modern domain specific specification language (DSL) in python style.

A typical workshop scene
A typical workshop scene

The next Snakemake day event will be help in Essen (Germany) and organised by Johannes Koster.