The year 2025 was marked by strong momentum around the training courses organized by the Institut Français de Bioinformatique (IFB) / ELIXIR France. Artificial intelligence, reproducible workflows, omics data analysis, and in various formats: BYOD tutoring, courses, workshops, etc. These initiatives have brought together a diverse scientific community in search of practical expertise and interdisciplinary exchange.
Artificial intelligence: a growing training offer
Three training courses dedicated to AI took place this year.
- Artificial Intelligence and Machine Learning in Life Sciences, May 19 to 23 in Aussois
This intensive training course brought together experts from four ELIXIR nodes (France, Belgium, Switzerland and Greece). The program covered the fundamentals of machine learning, deep learning, generative models and regulatory issues (DOME, European AI Act).
A “Bring Your Own Data” (BYOD) session enabled participants to apply these methods to their own datasets, enabling them to put them directly into practice in their own projects.
- Using generative AI, June 13 in Paris
In addition, a targeted training session on the uses of generative AI in the life sciences presented best practices, limitations, methodologies and concrete use cases in bioinformatics and data analysis.
- AlphaFold and beyond: 3D modeling of proteins, December 10-12 at Orsay
Organized with IDRIS and several IFB platforms, this new training course introduced participants to 3D modeling of proteins and complexes using the AlphaFold ecosystem. Two application cases were proposed for this first edition: protein interaction analysis and massive prediction sampling with MassiveFold. Participants were able to use Jean Zay’s GPU resources, interpret AlphaFold results and mobilize post-analysis tools, before a discussion session dedicated to individual problems.
IFB/ELIXIR-FR plans to continue these IA training courses in 2026.
EB3I levels 1 and 2: structuring training for omics data processing
Supported by Inserm, IFB and INRAE, the EB3I School of Bioinformatics has proposed two levels for 2025.
- EB3I Level 2, June 1-6 in Roscoff
Aimed at participants with beginner-level skills, this intermediate training course alternated theoretical sessions, practical workshops and group tutoring. Three thematic workshops were offered in parallel: RNA-seq, ChIP-seq and DNA-seq variants. Analysis was carried out on the IFB-core’s compute resources, using the command line and R.
This edition welcomed 17 participants in a studious and collaborative atmosphere.
- EB3I Level 1, November 17 to 21 in Roscoff
The beginners’ course took place at the Station Biologique de Roscoff. Over five days, participants were introduced to variant data processing, ChIP-seq, Bulk RNA-seq and Single-Cell RNA-seq, with an introduction to long-read technologies.
The format includes interactive workshops and a BYOD approach, enabling users to work on their own data through tutoring.
This edition welcomed 39 participants and 17 speakers.
FAIR-BIOINFO - Bioinformatics workflows: WF4bioinfo and ANF MERIT
The theme of workflows was also strongly represented this year.
- WF4Bioinfo 2025, September 29 to October 1 in Paris
This training course, organized in partnership with iPOP-UP (EDC), is aimed at bioinformaticians and bioanalysts wishing to master workflow languages for reproducible analyses.
Participants learn how to develop and run workflows on IFB resources, whether on a cluster or in the cloud.
- ANF MERIT – “Workflow and reproducibility”, November 25 to 27 in Paris
Advanced training to complement WF4Bioinfo, this National Training Action from the MERIT network, in partnership with IFB, takes a closer look at FAIR principles applied to workflows.
The program includes the drafting of a complete workflow (Nextflow, Snakemake), its execution and optimization using artificial intelligence.
As part of this training program, the IFB also made its digital infrastructure available.
FAIRomics: two training sessions for European doctoral students
The European FAIROmics project (2024-2028), coordinated by INRAE, aims to structure a network of PhD students around knowledge graphs applied to the study of fermented plant foods.
IFB/ELIXIR-FR actively contributes to the training program and organized two sessions in 2025:
- Data Management” training at Winter School (February 2025)
- FAIR principles applied to bioinformatics” course at the Paris Summer School (June 2025)
These training courses testify to the ongoing commitment of IFB/ELIXIR-FR and its partners to support the life sciences community in the rapid evolution of bioinformatics tools, from artificial intelligence to FAIR workflows. See you in 2026 for new training modules and new sessions of our annual training courses(IFB training agenda).
Metagenomics and Metatranscriptomics initiation
At the request of the Microbial Ecology laboratory in Lyon, the IFB Training team organized a two-day session on metagenomic and metatranscriptomic data analysis with Galaxy on June 17 and 18 in Lyon. Participants acquired theoretical and practical skills, carried out analyses on supplied data and initiated projects on their own datasets, with the support of the training team.