Singularity & Containers

Duration: 4 hours / 1 days

Date: 27th of March

Time: 9:30 - 14:00 (30 min break)

Level: Basic level with intermediate programming skills required

Format: Presential

ROOM: Dr. Aiguader 80, Barcelona. 61.212

Registration opening date: 27 of February

Deadline for registration: 13 of March

Course Description

In this course we will explore what containerization is and why it can be useful. We will also explore different container engine technologies and we will focus on Singularity. 

Why should you attend the course?

You will learn the basic concepts and commands to start building your own containers. In addition, you will have the opportunity to think about reproducibility, portability…

Prerequisites

Course content and hands-ons will be easier to fully understand and fulfill with intermediate programming skills and basic knowledge of bash. 

You should bring your own laptop with Singularity installed. To install Singularity you can follow this documentation: 

https://docs.sylabs.io/guides/latest/user-guide/

Schedule

The main topics covered during this course are: 

• Introduction to containerization

• Definition and conceptualization

  • Reasons to use containers

  • Applications

  • Differences with virtualization

  • Container engine technologies

• Singularity

  • Build and use containers

  • Use Docker with Singularity

  • Main command line arguments

• Hands-on

Class Pace 

We encourage the participants to do as many questions as needed during the whole course. The hands-on practical session aims to enhance dynamic learning.  

References

https://docs.sylabs.io/guides/3.5/user-guide/index.html

Short biography 

Marta Sanvicente is a PhD candidate in the Translational Synthetic Biology laboratory at Universitat Pompeu Fabra. Previously, she did the Master in Bioinformatics for Health Sciences at Universitat Pompeu Fabra (2017-2019) and Bachelor’s degree in Genetics at Universitat Autònoma de Barcelona (2013-2017). Her research interests include Next Generation Sequencing data analysis, nextflow pipelines development, and analysis, simulation and prediction of genome editing and gene writing outcomes. For her nextflow and web applications she has used Docker and Singularity containers.