🎉 W4E2025 Workshop Review – Empowering Metabolomics Researchers with W4M

The Workflow4Experimenters (W4E2025) workshop successfully took place in April and May 2025, bringing together a vibrant international community of scientists passionate about LC-MS, GC-MS, and NMR data analysis. Hosted in Rouen, France, with preliminary webinars conducted online, this hybrid-format event helped researchers unlock the full potential of the Workflow4Metabolomics (W4M) platform via the Galaxy interface.

📚 Workshop Format Recap

This year’s edition introduced a redesigned format to help participants better prepare and take full advantage of their on-site time.

🖥️ April 28–30, 2025: Online Theoretical Webinars

Over the course of three days, participants attended a series of online webinars that introduced them to:

• The Galaxy platform and its role in metabolomics analysis.
• Core tools in the W4M infrastructure, including preprocessing, normalization, and statistical modules.
• Practical guidance on preparing datasets for analysis.
• Walkthroughs of real-case scenarios using public data.

These sessions offered a deep dive into theoretical foundations and essential workflow strategies, allowing participants to familiarize themselves with the environment before the in-person training. Attendees were also encouraged to complete optional exercises in advance to reinforce learning and prepare their own datasets.

🧑‍🏫 May 12–16, 2025: In-Person Training in Rouen

Hosted at the PBS Laboratory in Rouen, the on-site training week focused on the application of theory to participants' own data. Each day was structured around:

• Small-group tutoring sessions, where attendees received personalized support from experienced instructors.
• Hands-on use of the W4M workflows for data processing, multivariate statistics, and molecular annotation.
• Peer discussions and troubleshooting in a collaborative, supportive setting.
• Opportunities to ask specific questions relevant to each participant’s research.

The in-person week also featured three invited talks:

• Hélène Lavanant (COBRA, Univ Rouen, France): Ultra-High Resolution Mass Spectrometry in Metabolomics
• Isabelle Schmitz (PBS, CNRS Rouen, France): Advanced Analytical Strategies for Molecular Profiling¨
• Téo Hebra (IOCB, Prague, Czech Republic): Molecular networking

These talks provided additional insights into cutting-edge research and applications in metabolomics, enriching the learning experience.

🔬 Scientific Program Highlights

Participants benefited from:

• Expert-led sessions on data preprocessing, feature extraction, statistical analysis, and annotation.
• Deep dives into Galaxy workflows for LC-MS, GC-MS, and NMR data.
• Real-time problem solving with experts across multiple disciplines.

🗣 Survey Feedback Snapshot

Participants overwhelmingly expressed strong satisfaction with W4E2025. Most reported that the workshop fully met their expectations, particularly appreciating the quality of the tutoring sessions and the supportive, knowledgeable team of instructors. The Galaxy initiation and data processing sessions were especially well-received, while several attendees suggested that more time and depth could be dedicated to annotation and molecular network analysis in future editions.

The hybrid format—webinars followed by on-site tutoring—was seen as effective, with many valuing the ability to work on their own datasets. Several participants also recommended improvements for future workshops, including more hands-on tips, clearer workflow diagrams, extended Q\&A time after webinars, and the option for more structured follow-up support.

Overall, the feedback highlighted a successful and well-organized event, with thoughtful suggestions to make future editions even more impactful and tailored to participants’ needs.

💬 Voices from the Community

“Everything was really well thought out and done in a great spirit. We need more initiatives like this!”
— Anonymous participant

“I feel I now know how to use Galaxy! I’d just love more support on annotation.”
— NMR participant

“The hybrid format was really effective. The small-group tutoring made all the difference.”
— GC-MS researcher

🧑‍🔬 Organizers & Acknowledgements

The success of W4E2025 was made possible by the dedicated scientific committee and tutors from institutions across Europe, including ULB, INRAE, CNRS, IRBA, and more. Special thanks to our keynote speakers and the MetaboHUB and ELIXIR and EIRENE infrastructures for their ongoing support. We extend our gratitude to all participants for their enthusiasm and engagement, which made this workshop a truly collaborative and enriching experience. We also acknowledge the contributions of our organizing team, including:

C. Delporte (ULB, Bruxelles), C. Dalle (U.DAB IRBA, Brétigny-sur-Orge), Y. Guitton & J. Saint Vanne (Laberca INRAE, Nantes), C. Joly & M. Pétéra (PFEM INRAE, Clermont-Ferrand), G. Le Corguillé (Abims, Roscoff), B. Diémé (PFEM Université Clermont Auvergne), F. Souard (ULB, Bruxelles & Université de Grenoble), C. Canlet, M. Tremblay-Franco (Toxalim INRAE, Toulouse), I. Schmitz (PBS, CNRS, Rouen), S. Chéreau (INRAE, Rennes), H. Hecht (Masaryk University, Brno), R.Weber (University of Birmingham), S. Dechaumet (CEA, Saclay)

📣 Looking Ahead

Plans are already underway to improve future editions of W4E with:

• Extended sessions on annotation and network analysis.
• More customization based on analytical platforms.
• Continued focus on using your own data during training.

We sincerely thank all participants for their enthusiasm, feedback, and collaborative spirit.

Stay connected with the W4M community and join us again in the future for another empowering edition of Workflow4Experimenters!

📧 Contact: workflow4metabolomics@proton.me

🌐 Website: https://workflow4metabolomics.org

About the Author

Helge Hecht is a researcher specializing in computational mass spectrometry applications in exposome studies. He is affiliated with RECETOX, a research center at Masaryk University, Brno, Czech Republic, focusing on environmental health and exposomics. Helge is also involved with the EIRENE-CZ research infrastructure and ELIXIR-CZ, both of which are dedicated to advancing bioinformatics and exposome research in the Czech Republic and across Europe.

RECETOX is part of Masaryk University and serves as a national node for both ELIXIR-CZ and EIRENE-CZ, supporting collaborative research and the development of open, FAIR tools for the life sciences community.