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:

Ghent - VIB-UGent FSVM II

Duration:

15 and 16 April 2024

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

9h30 - Introduction to Docker containers

Advantages of using containers & Typical use cases

Using existing images

16h00 - Docker recipes: build your own image (part 1)

9h30 - Docker recipes: build your own image (part 2)

Introduction to Singularity

Run and execute Singularity images

16h00 - Building Singularity images

Practical info

Location & Venue

15 April 2024 - 16 April 2024

Ghent - VIB/UGent FSVM II

Technologiepark 75
9052 Zwijnaarde
Belgium

Public transport

15 April 2024 - 16 April 2024

Ghent - VIB/UGent FSVM II
Public transport

From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.

Bike

15 April 2024 - 16 April 2024

Ghent - VIB/UGent FSVM II
Bike

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.

Route description

15 April 2024 - 16 April 2024

Ghent - VIB/UGent FSVM II
Parking

Route description

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.

Venue contact

15 April 2024 - 16 April 2024

Ghent - VIB/UGent FSVM II
Extra information

Room: L4 on the fourth floor