Docker (and Singularity) for reproducible and automated data analysis

advanced bioinformatics
research data management
programming
ELIXIR
live training

Docker (and Singularity) for reproducible and automated data analysis

Target Audience:
All VIB staff
Location:

Ghent

Building 75 (CMB building),
4th floor - room: L4

Duration: 24th and 26th of October

Duration:

2 days

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. 

Objectives
  • 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 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

Alexander Botzki is heading the Technology training unit at VIB, the Flemish Institute of Biotechnology, Belgium. The main mission of this unit is 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 / ELIXIR-BE

Bruna Piereck is a bioinformatics trainer coordinator working at VIB Technology Training and ELIXIR Belgium. She obtained a PhD in Molecular Genetics, with a focus on Bioinformatics from the Federal University of Pernambuco, Brazil, in September 2019. During her PhD, she had the chance to collaborate with the university of Luxembourg and McGill university in Quebec for a short time. Ever since she has been involved with teaching  and Since March 2022, she joined the Technology Training team at VIB.

Contact Bruna Piereck :

Program

9:30 - 10:00 Introduction to containers

10:00 - 15:00 Docker containers

15:00 - 17:00 Singularity containers

Exercises

Practical info

Location & Venue

24 October 2022 - 26 October 2022

Ghent - VIB/UGent FSVM II

Technologiepark 75
9052 Zwijnaarde
Belgium

Public transport

24 October 2022 - 26 October 2022

Ghent - VIB/UGent FSVM II
Public transport

From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.

Route description

24 October 2022 - 26 October 2022

Ghent - VIB/UGent FSVM II
Parking

Route description

There is only one entrance to Technologiepark. At the entrance, please take a ticket and have it validated at the reception desk of the FSVM building. Parking will only be allowed in regular parking spots (for instance in front of the building) and in the new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited and after initial warnings, fines will be issued (€ 50).

Venue contact

24 October 2022 - 26 October 2022

Ghent - VIB/UGent FSVM II
Extra information

Info for trainer
Elixir code: 7469