From June 2nd to 5th, the ELIXIR-FR team was in Thessaloniki (Greece) to participate in the ELIXIR 2025 All Hands Meeting, the general assembly of the European ELIXIR infrastructure. This 11th edition brought together representatives from the various ELIXIR nodes, institutional and scientific partners. The French node, faithful to the meeting, was represented by a well-mobilized team, including our “Triangle Coordinators” accompanied by our co-Head of Node, who took part in the strategic highlights. Four days of discussions, workshops, presentations and meetings to take stock of current projects… and imagine those of tomorrow.
Workshops, mini-symposiums, posters… many French contributions
Among the French node delegation present, several spoke during well-attended workshops and thematic sessions, but also during the major traditional events such as poster sessions.
- In terms of biodiversity and microbiome, we will note:
- a workshop on Galaxy resources for biodiversity research, led by Bérénice Batut and Anthony Bretaudeau.
The “Evaluating and Enhancing Resources in Galaxy to Support Biodiversity Research” workshop brought together experts to improve the Galaxy Codex, a tailored collection of biodiversity tools, workflows, and tutorials. Four groups worked on the tools, tutorials, workflows, and interface for a future dedicated Galaxy Lab. Results include the addition of a metagenomic category, the updating of 30 tutorials, the evaluation of 38 workflows, and concrete steps toward an expanded Codex, available soon.
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- And another on the mobilization of microbial data, presented by Erik Hjerde (ELIXIR-NR) and Bérénice Batut.
The “Mobilizing Microbial Data” workshop, led by Bérénice Batut and Erik Hjerde, brought together ELIXIR experts to improve microbial data sharing. Discussions focused on harmonizing annotation practices, ontologies, and metadata standards. Use cases, strategies, and recommendations were discussed, and a report will be published on F1000 to preserve a lasting record.
- On the AI and ontology side, Claire Rioualen (ELIXIR-FR) co-presented with Maria Doyle (Bioconductor / ELIXIR-IR) at a mini-symposium on methodologies for bringing together data, ontologies, and software. Claire Rioualen also spoke at a workshop on the use of ontologies in ELIXIR communities.
Bioconductor is a global open source project providing over 2,000 packages for bioinformatics, but its metadata structure (biocViews) limits interoperability with other tools. This project aims to enrich this metadata using the EDAM ontology, a key standard for making ELIXIR resources more FAIR, and to automate the integration of Bioconductor packages into the bio.tools registry. Initiated during the ELIXIR BioHackathon 2024, this work has established a mapping between biocViews and EDAM, developed an automatic EDAM term suggestion tool, and strengthened the links between Bioconductor and the ELIXIR ecosystem.
- Regarding the essential bioinformatics resources section, Hervé Ménager presented a poster on the Bio.tools catalog.
The bio.tools registry has become an essential resource for documenting and retrieving life sciences software, with over 30,000 tools referenced by 12,000 contributors. A new user interface, an improved function editor, and better integration with the EDAM ontology now facilitate tool annotation. Connected to the ELIXIR software ecosystem (RSEc), bio.tools benefits from increased interoperability, and future enhancements will aim to refine metadata quality through automatic checks, synonym management, and the integration of generative AI capabilities for assisted curation.
- On the issues of food security, biodiversity and pathogens, Bérénice Batut presented the FAIRyMAGs project during a mini-symposium.
Talk “FAIRyMAGS – Optimizing Metagenomics Assembled Genomes building: workflow finalization, training material development, real data evaluation, and resource allocation tool creation” – Biodiversity Food Security and Pathogens MiniSymposium – Slides
At the Biodiversity, Food Security and Pathogens (BFSP) mini-symposium, an update on the FAIRyMAGs project was presented. Bérénice discussed progress in developing and sharing the Galaxy workflow for constructing metagenomics-based assembled genomes (MAGs). Next steps include a hackathon, the creation of training materials, real-world evaluation, and the development of a resource allocation tool.
- In terms of training, Olivier Sand participated in a talk on the Training Metrics Database, a joint initiative with the Swedish and Slovenian nodes.
During the plenary session “ELIXIR Nodes, Services and Connections” (June 4 afternoon), Nina Norgren of ELIXIR-SE presented the multi-node service of the “Training Metrics Database”, a system for tracking, analyzing and reporting metrics associated with training within ELIXIR. ELIXIR-SE is responsible for maintaining the code, ELIXIR-FR for user support and ELIXIR-SI for hosting the database. The advantages and challenges of a distributed service across multiple nodes were highlighted.
- Another poster, presented by Bérénice Batut, highlighted French involvement in the Galaxy Training Network.
Poster “Contributing to the ELIXIR Training Life-Cycle from the GTN perspective” – F1000
The Galaxy Training Network (GTN) is a comprehensive bioinformatics training platform, complementary to that of ELIXIR. The poster presents how GTN fits into the ELIXIR training lifecycle, comparing its practices with Splash recommendations and ELIXIR tools/services. With 34 themes, 464 tutorials and innovative features, GTN positions itself as an essential resource for the community.
- On strategic issues, Anne-Françoise Adam-Blondom, head of node ELIXIR France, co-presented a poster on reflections relating to the evolution of ELIXIR communities.
The ELIXIR Communities Future Focus Group was created to rethink the long-term role of ELIXIR Communities, taking into account their growth, the emergence of new initiatives and budgetary constraints. This group brings together key stakeholders to propose a sustainable strategic framework to guide the Communities’ mission and vision. This poster presents their work and invites everyone to share their ideas for improving the support, organization and impact of Communities within ELIXIR.
All IFB/ELIXIR-FR presentations can be found in the IFB-core HAL collection.
An enriching event and… an announcement for 2026!
Between the scientific sessions and the more informal moments, this 2025 edition made it possible to strengthen links with other nodes and to bring out new avenues of collaboration.
To crown and close this edition, Anne-Françoise Adam-Blondon, co-head of node ELIXIR France and deputy director of the IFB, had the honor of announcing the future destination of the All-Hands Meeting 2026, which will take place…. in France (more precisely in Lyon)!! A great prospect for the teams of the French node!
