Docker and Singularity (Apptainer) for reproducible and automated data analysis
12 and 13 Oct
General context
The course will give an introduction to containers (Docker & Singularity) 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, Singularity will be highlighted as well.
- Learn the concept of and the difference between Docker & 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 a Singularity (Apptainer) image
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.
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
Building Singularity images
Practical info
12 October 2023 - 13 October 2023
Brussels - HOEK 38
Leuvenseweg 38
1000 Brussel
Belgium
12 October 2023 - 13 October 2023
Brussels - HOEK 38
No public transport information has been provided for this location.
12 October 2023 - 13 October 2023
Brussels - HOEK 38
12 October 2023 - 13 October 2023
Brussels - HOEK 38
No parking information has been provided for this location.
12 October 2023 - 13 October 2023
Brussels - HOEK 38
(+32) 251 291 10
hoek38@fwo.be