The Galaxy Europe team at the ELIXIR All Hands Meeting 2025

The 11th ELIXIR All Hands meeting was held in Thessaloniki, Greece, from June 02 to 05, 2025. The Europen Galaxy team members from University of Freiburg attended this meeting, which aimed to bring together members of the ELIXIR community from across the ELIXIR Nodes, as well as collaborators from partner organisations, to review ELIXIR's achievements and activities and discuss future plans.

The mini-symposium on Research Software Quality, Resilience, Sustainability and Recognition: enabling reproducible analytics and infrastructure introduced the EVERSE framework for research software quality and ELIXIR-STEERS initiative for their best practices. Furthermore, challenges in maintaining software metadata across the platforms and an open software metadata commons were discussed. The meeting discussed testing services within the EOSC compute infrastructure through TES implementations, specifically highlighting the integration of the Galaxy platform.

Second day started with a workshop on Shared metrics, shared benefits: tool and workflow execution receipts to give credit to developers & compute infrastructures; inform funders; and enhance resource allocations The ELIXIR Compute WP5 session focused on collecting and sharing tool and workflow execution metrics to credit developers and infrastructure providers, including platforms like Galaxy. Galaxy was highlighted as an example where rich usage data—such as tool runs, parameters, and resource usage—can support metrics-driven decisions around funding, sustainability, and reproducibility. Participants discussed how platforms like Galaxy could help automate metric collection, track environmental impact, and contribute to a broader ecosystem of transparent, FAIR-aligned research infrastructure. The session encouraged institutional adoption and explored ways to align these efforts across ELIXIR.

In a parallel session, a workshop on Enhancing RDM resources: Strengthening synergies and advancing FAIR data practices focused on indentifying and addressing specific gaps in RDM resources. Our team participated in breakout room discussing on Data Management Plans (DMPs). During the meeting, participants discussed the varying quality of Data Management Plan (DMP) templates available through DMP online. Concerns were raised about poor-quality DMPs and the need for a unified checklist for both writers and evaluators to ensure compliance with funder requirements. It was suggested that the Research Data Management (RDM) community work together to collect, evaluate, and categorize existing DMP examples, making them accessible at a central location with public links.

In the later session, Anthony Bretaudeau and Bérénice Batut from the European Galaxy community led the workshop Evaluating and Enhancing Resources in Galaxy to Support Biodiversity Research focused on enhancing the Galaxy open-source analysis platform for biodiversity research. Participants evaluated existing resources and identified gaps in workflows and training. Led by facilitators from the ELIXIR Biodiversity, Microbiome, and Galaxy Communities, attendees engaged in collaborative discussions across four main activities: curating biodiversity tools and workflows, building a standardized Biodiversity Galaxy Lab, and defining effective learning pathways for researchers. The workshop concluded in a series of actionable outcomes, including a comprehensive list of essential workflows, a roadmap for resource curation, and strategies for developing educational content, thereby strengthening collaboration among the participating communities and enhancing Galaxy's capabilities in biodiversity research.

In the afternoon plenary discussion on Global Collaborations: Perspectives from Research Infrastructure started with flash talks on significant initiatives such as the International Staff Exchange Programme and ELIXIR's engagement with global projects like Euro-BioImaging, Instruct-ERIC and Galaxy showcasing global engagement. During the panel discussion Björn Grüning highlighted how international collaborations have been crucial for the success of Galaxy. This approach fosters a sense of shared ownership, enabling everyone to contribute to the project's development. Challenges such as funding and communication barriers were addressed, emphasizing the need for open access and effective dissemination of resources. The session concluded by identifying future opportunities for international partnerships and ways to enhance accessibility in scientific communication.

During the workshop on Working with sensitive research data in the cloud - services and perspectives from ELIXIR nodes and partners, participants examined the increasing importance of cloud technologies in life sciences, focusing on their impact on data-intensive fields like genomics and proteomics. Discussed the potential of the European Health Data Space (EHDS) to enhance translational research by providing secure access to clinical data. ELIXIR's role was highlighted, particularly through the EOSC-ENTRUST project, which collaborates with national cloud providers such as de.NBI, the German ELIXIR node. The de.NBI, using Galaxy and Trusted Research Environments (TREs), offers resources for processing sensitive data. The integration of Galaxy within de.NBI’s infrastructure, identifying gaps in current capabilities, and exploring future improvements to strengthen cloud-based solutions for life sciences research were discussed.

On the final day, the workshop of The highs and downs of federated analytical approaches for biomedical data centered on federated analysis methods, which allow sensitive data under GDPR to remain at its source while generating insights across institutions. The session brought together ELIXIR Communities to discuss issues such as data interoperability, infrastructure costs, and algorithmic trustworthiness, while gaining user perspectives. Björn Grüning presented Galaxy, highlighting its role in facilitating federated analysis within the ELIXIR framework. The workshop goal was to summarize insights gained and share via the RDMkit and the ELIXIR Federated Human Data community, ultimately strengthening the network around federated analysis and benefiting related projects.

In addition to participating in workshops and talks, our team also engaged in poster sessions, which provided insights into ongoing projects, and we had numerous opportunities to network with members of other ELIXIR nodes to strengthen collaborative efforts and foster synergies within the ELIXIR framework.