Docker and Apptainer (Singularity) for reproducible and automated data analysis
Docker and Apptainer (Singularity) for reproducible and automated data analysis
31 March 2025, 9h30-17h00
1 April 2025, 9h30-17h00
General context
The container workshop will give an introduction to Docker & Apptainer which are great components to achieve portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, the Apptainer application, previously Singularity, and its use in the HPC will be highlighted as well.
This course is part of a micro-credential track; a micro-credential has the added value of being like a mini-diploma. When following the full track, you will be able to improve the reproducibility of your research. Check this opportunity: Reproducible Data Analysis: an Essential Capability in Modern Science (registration for micro-credential closes 20/2/2025)
- Learn the concept of and the difference between Docker & Apptainer (Singularity) containers
- Write a Docker recipe, build and run a Docker image and containers
- Pull and push Docker container to/ from Docker hub
- Docker files and layers; Docker cashing
- Working with volumes
- Pull Docker containers as an Apptainer (Singularity) image
- Use Apptainer on HPC
Bioinformaticians with no or little knowledge of containers.
You're familiar with doing bioinformatics on the command-line.
If you have no experience with command line, you can follow the Linux initiation training first.
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.
Tatiana Woller
Tatiana Woller is a data expert at the BioImaging Core Leuven and the VIB Data Core.
Her task focuses on exploring and finding solutions for data management of biological images.
Program
Introduction to Docker containers
Advantages of using containers & Typical use cases
Using existing images
Docker recipes: build your own image (part 1)
Docker recipes: build your own image (part 2)
Introduction to Singularity
Run and execute Singularity images on HPC
Building Singularity images
Practical info
31 March 2025 - 01 April 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
31 March 2025 - 01 April 2025
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
31 March 2025 - 01 April 2025
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.
31 March 2025 - 01 April 2025
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.
31 March 2025 - 01 April 2025
Ghent - VIB/UGent FSVM II
FSVM II, room L4 on the 4th floor