Topic outline
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This training session in part of the FAIROmics project Summer School (2-13th June 2025, Paris)Pedagogical objectives
This training provides an introduction to the main tools for making bioinformatics more FAIR (Findable, Accessible, Interoperable, Reusable). Through both theoretical and practical sessions, participants will explore key concepts and learn how to use essential tools to enhance data management, sharing, and reuse in bioinformatics. The goal is to provide a comprehensive understanding of best practices while applying these tools to real-world scenarios.
Useful links
- OnDemand : https://login.cluster.france-bioinformatique.fr/dex/auth/ldap/login?back=&state=cvu4hnkrcaneklxjioymvcl3p
- Interactive tutorials on Unix basic commands for bioinformatics: https://sandboxbio.france-bioinformatique.fr/
Trainers
- Thomas Denecker - CNRS / IFB - https://orcid.org/0000-0003-1421-7641
- Imane Messak - CNRS / IFB - https://orcid.org/0000-0002-1654-6652
- Baptiste Rousseau - CNRS / IFB - https://orcid.org/0009-0002-1723-2732
- Julien Seiler - CNRS / IFB - https://orcid.org/0000-0002-4549-5188
Program
Thursday, June the 5th pm
Title
Duration
Trainers
Documents
[Theory] FAIR principles applied to bioinformatics
1h
Imane Messak
FAIR principles applied to bioinformatics [Theory + Workshop] Introduction to Git
1h
Julien Seiler / Baptiste Rousseau
Introduction to Git Break (15 min.)
[Theory + Workshop] Introduction to Git
1h
Julien Seiler / Baptiste Rousseau
Friday, June the 6th am
Title
Duration
Trainers
Documents
[Theory/Workshop] Introduction to notebooks (Jupyter/Quarto)
1h
Thomas Denecker
Notebook.pdf [Theory] Overview of workflow systems
45 min
Baptiste Rousseau Worklflow.pdf Break (15 min.)
[Theory] Introduction to controlled environments
45 min
Julien Seiler
Introduction to Conda, Docker and Apptainer [Theory] Code sharing
30 min.
Thomas Denecker
CodeSharing.pdf
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Forum
- OnDemand : https://login.cluster.france-bioinformatique.fr/dex/auth/ldap/login?back=&state=cvu4hnkrcaneklxjioymvcl3p