Docker and Singularity (Apptainer) for reproducible and automated data analysis

advanced bioinformatics
research data management
programming
ELIXIR
live training

Docker and Singularity (Apptainer) for reproducible and automated data analysis

Target Audience:
All VIB staff
Location:

Brussels - HOEK 38

Duration:

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. 

Learning outcomes
  • 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
Event intended for

Bioinformaticians with no or little knowledge of containers. 

Required skills

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
VIB Training & Conferences / ELIXIR, BE

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'.

Contact Alexander Botzki :
Bruna Piereck
VIB Training & Conferences - Trainer picture - Bruna Piereck
VIB Training & Conferences / ELIXIR, BE

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.

Contact Bruna Piereck :

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

Location & Venue

12 October 2023 - 13 October 2023

Brussels - HOEK 38

Leuvenseweg 38
1000 Brussel
Belgium

Public transport

12 October 2023 - 13 October 2023

Brussels - HOEK 38
Public transport

No public transport information has been provided for this location.

Bike

12 October 2023 - 13 October 2023

Brussels - HOEK 38
Route description

12 October 2023 - 13 October 2023

Brussels - HOEK 38
Parking

No parking information has been provided for this location.

Venue contact

12 October 2023 - 13 October 2023

Brussels - HOEK 38
Location contact

(+32) 251 291 10
hoek38@fwo.be