Containerise data analysis with Docker & Apptainer
Containerise data analysis with Docker & Apptainer
11 May 2026, 9h30-17h00
12 May 2026, 9h30-17h00
General context
In this workshop, you will dive into container technologies - Docker and Apptainer - that enhance the portability and reproducibility of analysis workflows. You'll learn how to create containers from scratch, share them with others, and reuse or adapt existing ones. After an in-depth introduction to Docker, we will also explore Apptainer (formerly Singularity) and its application in High Performance Computing (HPC) environments.
- Run Docker containers using volumes and ports
- Write and build Docker recipes and images
- Explain key differences between Docker and Apptainer
- Convert and use Docker images as Apptainer images
- Run Apptainer containers in an HPC environment
This course is part of a micro-credential track that helps you strengthen the reproducibility of your research. By completing the full track, you earn a mini-diploma that validates your skills in this essential area of modern science.
Check this opportunity: Reproducible Data Analysis: an essential capability in modern science
This course is intended for researchers with little or no prior experience with containers who want to improve their reproducibility workflows.
Participants should:
- Have basic command-line skills for bioinformatics workflows
- Have completed an HPC course if they do not have prior experience with High Performance Computing
If you lack command-line experience, you can prepare by following the e-learning Linux command, Linux initiation training, or this tutorial before enrolling.
This course is part of the learning path Reproducible data analysis.
Trainers
Alexander Botzki
Alexander Botzki at the Flemish Institute of Biotechnology, Belgium has with his group the mission of providing technology training in domains of VIB Technologies, Bioinformatics & AI, Software Development, and Research Data Management. Between 2014 and 2022, he was head of the VIB Bioinformatics Core. From September 2009 to July 2014, he was responsible for the roll-out of E-Notebook (electronic lab notebook) to VIB's researchers within 75 research groups.
Before joining VIB, Alexander worked on various computational biology projects for Algonomics (bought by Lonza, 2008-2009) and DevGen (now Syngenta, from 2006-2008). During Alexander's PostDoc at Sanofi Aventis in Strasbourg, he executed various virtual screening campaigns on the compound selection of the merged enterprise. He received his doctoral degree with the group of Prof. Dr. Armin Buschauer (University of Regensburg, Germany) on 'Structure-based design of hyaluronidase inhibitors'.
Bruna Piereck
Bruna Piereck is a bioinformatics trainer at VIB and ELIXIR-BE training coordinator deputy. She obtained a Master and PhD degree in Molecular Genetics, with a focus on Bioinformatics from the Federal University of Pernambuco, Brazil, in 2019. During her PhD, she had the chance to collaborate with the university of Luxembourg and the McGill university in Quebec Canada for a short time. Ever since she has been involved with teaching and research and Since March 2022, she joined VIB with the mission of teaching and assist other trainers in a variety of topics.
Program
Introduction to Containers
Introduction to Docker as virtualisation environment
Advantages of using containers & Typical use cases
Using existing images
Docker recipes: build your own image (part 2)
Docker recipes: build your own image (part 2)
Introduction to Singularity
Run and execute Singularity images on HPC
Building Singularity images
Practical info
11 May 2026 - 12 May 2026
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
11 May 2026 - 12 May 2026
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
11 May 2026 - 12 May 2026
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
11 May 2026 - 12 May 2026
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.