From June 2 to 5, the ELIXIR-FR team was in Thessaloniki, Greece, to attend the ELIXIR All Hands Meeting 2025—the annual general assembly of the European ELIXIR infrastructure. This 11th edition brought together representatives from across the ELIXIR nodes, as well as institutional and scientific partners. As in previous years, the French node was actively represented, including our ‘Coordinators Triangle’ accompanied by our co-Head of Node who participated in key strategic sessions. Over four days, participants engaged in workshops, presentations, and networking opportunities to review ongoing projects and explore future initiatives.
Among the French delegation, several members presented during thematic workshops and sessions, as well as at the traditional poster sessions.
Bérénice Batut and Anthony Bretaudeau led the workshop “Evaluating and Enhancing Resources in Galaxy to Support Biodiversity Research.” Experts collaborated to improve the Galaxy Codex—a curated set of tools, workflows, and training materials tailored for biodiversity. Four working groups focused on tools, tutorials, workflows, and the interface of a future dedicated Galaxy Lab. Key outcomes included the addition of a metagenomics category, updates to 30 tutorials, evaluation of 38 workflows, and concrete progress toward a richer Galaxy Codex to be released soon.
Bérénice Batut and Erik Hjerde (ELIXIR-NR) co-led the workshop “Mobilizing Microbial Data,” which convened ELIXIR experts to improve microbial data sharing. Discussions focused on harmonizing annotation practices, ontologies, and metadata standards. Use cases, strategies, and recommendations were shared. A summary report will be published on F1000 to ensure long-term visibility.
Claire Rioualen (ELIXIR-FR) co-presented with Maria Doyle (Bioconductor / ELIXIR-IR) in a mini-symposium focused on integrating data, ontologies, and software tools. Claire also contributed to a workshop on ontology usage across ELIXIR communities.
Bioconductor, an open-source global project with over 2,000 bioinformatics packages, currently uses a metadata structure (biocViews) with limited interoperability. The initiative aims to enhance this by incorporating the EDAM ontology—key for making ELIXIR resources more FAIR—and to automate the integration of Bioconductor packages into the bio.tools registry. Initiated at the ELIXIR 2024 BioHackathon, this project has already delivered a mapping between biocViews and EDAM, an EDAM term suggestion tool, and stronger links between Bioconductor and the ELIXIR ecosystem.
Hervé Ménager presented a poster on bio.tools, the ELIXIR registry documenting over 30,000 life science tools contributed by 12,000 users. A redesigned user interface, enhanced function editor, and improved EDAM integration now simplify tool annotation. Integrated within ELIXIR’s software ecosystem (RSEc), the registry is set to improve further with enhanced metadata quality checks, synonym handling, and the use of generative AI to support assisted curation.
Bérénice Batut presented the talk “FAIRyMAGs - Optimising Metagenomics Assembled Genomes building…” during the Biodiversity, Food Security and Pathogens mini-symposium. The session covered updates on the development and dissemination of the FAIRyMAGs Galaxy workflow for building metagenome-assembled genomes (MAGs). Upcoming steps include a hackathon, training material development, real data testing, and a tool to allocate computational resources.
Training and Metrics :
During the plenary session “ELIXIR Nodes, Services and Connections” (June 4), Nina Norgren (ELIXIR-SE) presented the multi-node Training Metrics Database service (https://tmd.elixir-europe.org/), which tracks and analyzes ELIXIR training metrics. ELIXIR-SE maintains the codebase, ELIXIR-FR provides user support, and ELIXIR-SI hosts the database. The talk highlighted the advantages and challenges of maintaining such a distributed service.
Bérénice Batut presented a poster titled “Contributing to the ELIXIR Training Life-Cycle from the GTN perspective” (F1000 link). The Galaxy Training Network (GTN) is a comprehensive, community-driven platform that complements ELIXIR’s training efforts. The poster showcased GTN’s alignment with ELIXIR’s Splash recommendations and services. With 34 topics, 464 tutorials, and innovative features, GTN continues to be a cornerstone training resource for the community.
ELIXIR Communities Strategy
Anne-Françoise Adam-Blondon, Head of Node for ELIXIR France, co-presented a poster on the ELIXIR Communities Future Focus Group. This working group was established to rethink the long-term role of ELIXIR Communities in light of their growth, emerging initiatives, and funding constraints. The poster detailed strategic planning efforts and invited feedback to improve the organization, support, and impact of ELIXIR Communities.
All IFB/ELIXIR-FR contributions can be accessed in the IFB-core HAL collection.
Beyond the scientific sessions and informal networking, the 2025 edition fostered stronger connections among ELIXIR nodes and sparked new collaboration opportunities.
To close the event, Anne-Françoise Adam-Blondon—Co-Head of Node for ELIXIR France and Deputy Director of the IFB—had the honor of announcing the location of the next All Hands Meeting in 2026: France, more precisely Lyon! A promising outlook for the French node teams.
Collection HAL IFB-core
