Agenda

We welcome everyone to the ELIXIR All Hands 2026 in Lyon, France. This session will provide an overview of the event’s themes and programme, logistics and messages about the running of the event, introductions to ELIXIR in 2026 and the ELIXIR French Node, followed by an opening keynote. 

Full agenda here

Harmonised and empirical service evaluation is a growing challenge across ELIXIR. Several initiatives, including Germany’s NFDIs, the UK’s BioFAIR, and Australia’s ARDC, aim to build federated digital research infrastructures offering computing and analysis resources, databases, training, and tools to research communities. Across these initiatives, Key Performance Indicators (KPIs) are widely used to capture service usage, quality, sustainability, and impact, yet their selection and implementation vary considerably across countries and domains. This fragmentation makes coherent reporting, comparison, and strategic decision-making at the ELIXIR level difficult.
This workshop provides an opportunity for the ELIXIR community to collaboratively address this challenge. It aligns with the Nodes and People Tier of the ELIXIR Programme 2024–2028, supporting service sustainability, evidence‑based decision‑making, and interoperability across the ELIXIR ecosystem. The workshop targets ELIXIR Platforms, Communities, and Commissioned Services that contribute to or depend on consistent service monitoring and impact assessment. The workshop builds on results from the METRICS project, initiated at BioHackathon Europe 2025, which brought together experts from several ELIXIR nodes to identify, harmonise, and semantically model KPIs that capture service quality, usage, sustainability, and impact [https://doi.org/10.37044/osf.io/2jgk4_v1]. METRICS started developing an ontology‑driven framework to enable interoperable KPI monitoring and support transparent, FAIR-aligned evaluation practices.
The session will open with an overview of the METRICS results, establishing a shared understanding of the emerging ontology‑driven approach for KPI harmonisation. We will highlight how a consistent KPI framework can help Platforms, Communities and Nodes articulate their contributions, align reporting with programme objectives, and support decisions on service enhancement and long-term sustainability. Participants will then engage in an interactive World Café discussion focusing on KPI selection, semantic alignment, monitoring practices, and integration into ELIXIR’s operational and governance structures. This collaborative format will aggregate diverse perspectives across ELIXIR Platforms and Communities to identify practical needs, gaps, and opportunities for coordination, and to explore how harmonised KPIs can strengthen a FAIR research infrastructure landscape and improve impact assessment.
The workshop will conclude by synthesising insights on KPI selection, interoperability, and monitoring practices, and by outlining concrete next steps for coordinated implementation of KPI practices across ELIXIR. Participants will be invited to contribute to a forthcoming White Paper, which will consolidate METRICS findings, workshop outcomes, and community input. It will provide recommendations for implementing consistent, transparent, and interoperable KPI practices across ELIXIR.
 

This workshop will test the ELIXIR Data Stewardship Handbook (currently a Minimal Viable Product from the RDM Community’s DATAREX Implementation Study: https://elixir-europe.github.io/ds-handbook/) across ELIXIR Nodes, Platforms and Communities. The Data Stewardship Handbook is a community-driven and practice-oriented resource supporting data stewards in developing and operating RDM services across ELIXIR.
Participants will collaboratively apply Handbook sections to real-world data steward scenarios to assess clarity and usability, and then translate findings into concrete improvements that strengthen the Handbook.
Key objectives
•       Test selected sections of the ELIXIR Data Stewardship Handbook against real Node- level use cases and daily data steward tasks
•       Identify strengths, gaps and ambiguities in the Handbook through expert review
•       Deliver practical outcomes such as page updates and community examples for the Data Stewardship Handbook
Audience
The workshop is open to:
•       Data stewards/managers from ELIXIR Nodes who (plan to) work with the Data Stewardship Handbook
•       Node coordinators involved in coordinating or sustaining data stewardship activities
•       Members of ELIXIR Platforms, Communities, and Focus Groups relying on data stewardship guidance and can help align the Handbook content with broader ELIXIR initiatives.
Both current contributors and newcomers are encouraged to participate, to ensure a diversity of perspectives and familiarity with the Handbook.
Alignment with ELIXIR’s strategic tiers
This workshop supports the People tier by strengthening the skills and professional practice of data stewards. By testing and refining the Data Stewardship Handbook with Node representatives, the workshop supports exchange, shared problem solving and retaining practical expertise in ELIXIR’s distributed infrastructure. It brings together participants across ELIXIR to improve a shared resource supporting sustainable data stewardship services and consistent implementation of ELIXIR’s research data management efforts.
Format and structure
This workshop is structured to maximise active participation and practical testing:
•       15 min - Introduction to the Data Stewardship Handbook and testing approach
•       60 min - Group sessions where participants apply selected Handbook sections to real-world problems and identify improvements
•       15 min - Next steps and alignment with ongoing Handbook development within the ELIXIR RDM Community
Engagement and interaction
Participants will actively engage through:
•       Hands-on use of the Data Stewardship Handbook, peer discussion, and shared problem-solving in small groups
•       Collaborative testing, ensuring that insights are grounded in real practice based on the exchange of experiences and discussion
•       Dynamic hybrid participation, ensuring engagement of online and in-person attendees through breakout rooms and shared documentation
Shared notes will be taken for follow-up and future refinements of the Handbook.
 

Current research infrastructures excel at handling quantitative data but often fail to capture the user need and context essential for impactful science. This creates a "context gap" where user experiences, and societal insights (usually presented as qualitative data) are systematically lost.
FAIRMIX4EOSC exists to close this gap, FAIRMIX4EOSC is a European consortium bringing together 15 partners from across Europe, spanning ELIXIR nodes, clinical research infrastructures, data stewardship experts, AI and semantic technology, and social science specialists. The consortium addresses challenge of how to support user-centred and context-aware research infrastructures by applying FAIR principles to mixed-methods research?
This topic connects to ELIXIR’s Data, tools, Interoperability Platform, and the Research Data Management Community because it advances FAIR, open, and interoperable practices for mixed methods research and we are interested in bringing it in both to broaden ELIXIR’s perspective on data reuse and integration beyond purely quantitative life science data and to obtain structured feedback from the community on how ELIXIR tools and services can better support mixed-methods research workflows.
Expected outcomes:
1. Define User-Centred and context-awareness Requirements for infrastructures to make mixed-methods data FAIR
2. Identify where and how user centredness and context and qualitative evidence are currently lost or excluded in research workflows and infrastructures.
3.  Critically evaluate existing ELIXIR tools for their potential to support context-aware, mixed-methods research.
4. Co-Design a Strategic Path: Establish a shared, practical direction for both the FAIRMIX4EOSC project and ELIXIR communities to advance support for user-centred and context-aware research infrastructures.
Structure
Our workshop includes three sessions allowing collaboration and brainstorming:
Session 1: Include talks to introduce the problem, current solutions and challenges
Session 2 and 3 are mini-hackathons, using interactive tools, discussing the following:
- Are we identifying the right problem for the context-awareness and user-centredness?
•       How do you ensure user-centredness and context awareness in your research? When has a user's centredness fundamentally contradicted your data model/infrastructure?
•       Where do qualitative data already appear in your ELIXIR-supported workflows (e.g. phenotyping notes, cohort metadata, clinical annotations, lab protocols, free text)? and What challenges have you experienced in integrating them?
•       Frameworks that exist to support user-centredness and context awareness
- AI, Tools, and Resources for context-aware, user-centred research.
•       What are the current ELIXIR resources/tools that enables context-aware, user-centred research?
•       Which AI, semantic technologies and ontologies methods are best suited to capturing context and user perspectives?
•       What standards or infrastructures are missing for scaling mixed data reuse across disciplines?
 

Health data standards are a cornerstone of reproducible, scalable, and trustworthy health data research. Yet across Europe, health data remains fragmented, heterogeneous, and difficult to reuse both within and across countries. While genomics and molecular data have benefited from mature, widely adopted standards thanks to the efforts of ELIXIR and the Global Alliance for Genomics and Health (GA4GH), the application of standards for health and clinical data has lagged behind due to the complexity of data and a sparsity of implementation examples.
This workshop aims to bring together ELIXIR nodes to align efforts around health data standards, such as the OMOP Common Data Model, and implementing GA4GH standards such as Beacon, TES/WES, Phenopackets and Passports/AAI, for clinical and health data research use cases. The workshop will provide an interactive forum to share progress, challenges, and lessons learned in adopting OMOP, GA4GH, and related health data standards.
The workshop is structured around three complementary pillars:
1. Current State (Experience Sharing):
Participants from multiple ELIXIR Nodes will provide short, focused updates on the adoption, roll‑out, training, and operational use of OMOP, GA4GH, and related clinical data standards. This will include governance, ethical considerations, tooling, training, and interoperability with existing national and European infrastructures.
2. Current Value (Use Cases):
Real‑world examples will be explored, which go beyond success stories and surface real implementation challenges, to demonstrate the value of standardised health data, such as HDR UK’s Cohort Discovery tool.
3. Future Steps (Co‑creation and Alignment):
Through facilitated breakout discussions, participants will identify shared gaps, priorities, and opportunities for collaboration across ELIXIR. We will discuss how OMOP‑based infrastructures can be connected to GA4GH standards to enable integrated genotype‑to‑phenotype research workflows. Topics will include training needs, technical interoperability, sustainability, alignment with European Health Data Space (EHDS) efforts, and opportunities for joint activities or service development.
This workshop will be relevant across Platforms (as Data access, Tool development, and Interoperability are critical components of standard roll-out) and Communities such as Federated Human Data, Cancer and Rare Disease.
Format
•       Context setting
•       Lightning updates from Nodes
•       Use cases
•       Breakout discussions
•       Plenary synthesis & next steps
Outcomes
•       Shared understanding of how OMOP and health data standards are being used across ELIXIR Nodes
•       Identify collaborative actions to support health data standards adoption across ELIXIR communities
A summary report will be prepared after the workshop signposting state-of-the-art health data standards implementations across ELIXIR.
 

Artificial Intelligence (AI) is increasingly central to data-driven life science research, supporting tasks such as omics analysis, imaging, text mining and clinical data interpretation. ELIXIR already provides a strong foundation with high-quality data resources, interoperability standards, software development practices, access to computational capabilities through its national nodes, and a complete programme around training, including capacity-building aspects. Interaction with ELIXIR Communities has enabled the organisation of community-oriented scientific benchmarking activities. In this context, one of the key activities that ELIXIR has the expertise and capacity to advance is AI model evaluation, arguably a key element of a much-needed open and sustainable AI ecosystem in the Life Sciences. Indeed, AI model evaluation can serve to i) define how AI can be integrated into ELIXIR's infrastructure and services, ii) facilitate and promote interactions across Nodes to create capacities where needed, and iii) drive specific actions to interconnect ELIXIR with stakeholders in this area, from AI Factories to efforts in EOSC and other European research infrastructures, to communities specialised in AI development and evaluation well beyond the life sciences.
This 90-minute hybrid workshop builds on this opportunity by bringing together a diverse audience from ELIXIR Platforms, Communities, Focus Groups, EU-funded Projects and Nodes. Leveraging the hybrid format, we will actively engage external AI experts beyond our ecosystem. While ELIXIR as a whole is not an AI community of practitioners, it is uniquely positioned to act as a gateway, facilitating access to and use of constantly evolving AI technologies for the Life Sciences. Indeed, AI activities are channelled through the dedicated AI Ecosystem Focus Group, which is central to this workshop.
The workshop will combine short introductory talks (3x5 min each) with interactive breakout discussions (30 min in total). Participants will be divided into two breakouts: (1) map existing ELIXIR data resources, standards and services that could support AI model evaluation from the users/developers perspective; and (2) identify high-priority AI tasks where past experience with community-driven benchmarks would bring the most value. The final session (30 min) would capture feedback from the breakouts and collectively outline practical requirements and next steps for an ELIXIR-wide approach to AI model evaluation.
The expected outcome is a short, actionable roadmap and follow-up activities that contribute directly to the ELIXIR Scientific Programme, strengthen connections across the ELIXIR ecosystem, and position ELIXIR as a gateway for reliable and transparent AI in the life sciences.
 

ELIXIR’s 2024-28 Scientific Programme brings together national data services to enable scientists to discover, access and analyse life science data across borders, communities, and domains. This session will focus on the Science Tier priority areas and how their activities translate into concrete benefits for users via the data resources, interoperable services and workflows. Three short talks (one per priority area) will present current achievements and future directions, illustrated by real scientific use cases. These examples will demonstrate how coordinated improvements in data quality, metadata, standards, interoperability, and data reuse across distributed resources can directly support better, faster, and more reproducible research. A concluding panel will reflect on infrastructure delivery, outlining current strengths, remaining challenges, and ELIXIR’s vision for turning scientific advances developed within Nodes into robust, dependable services and data resources that sustain and accelerate discovery across the priority areas for the benefit of the wider community. 
 

The ELIXIR Compute Platform has given considerable attention to providing compute services in a federated setting in order to serve a range of use cases across Nodes. There is a renewed focus to these activities for life sciences researchers in the context of the emerging EOSC Federation, EuroHPC and the new AI Factories. In this session we will seek to position key developments including deploying ELIXIR On Cloud services in national and thematic settings and seek to address new use cases from ELIXIR’s Communities. 

ELIXIR’s people-centred activities are critical to building sustainable, collaborative research infrastructures. This MiniSymposium showcases the outcomes and impact of two flagship capacity-building programmes within the ELIXIR People Tier: ELEAD and Train the Trainer (TtT). Through programme overviews, impact stories, and panel discussions, the session will illustrate how both initiatives strengthen leadership, mentoring, and training capabilities across Nodes, institutions, and communities. Beyond presenting results, the MiniSymposium will focus on the broader value these programmes deliver at national and international levels, including cultural change, skills development, and community resilience. Participants will hear concrete examples of how ELEAD and TtT have influenced individual careers, institutional practices, and Node-level activities, as well as reflections on challenges such as sustainability, funding, and scaling impact. The session will conclude with a forward-looking discussion on how leadership development and mentoring can be sustained and embedded across ELIXIR and beyond, including opportunities for collaboration with other research infrastructures.

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The workshop offers a practical introduction to ELIXIR's structure, operations, strategy and mission. It is particularly suitable for people who have been part of ELIXIR for less than two years but is open to all, including those outside ELIXIR. Participants will leave with answers to their questions about how ELIXIR works and an understanding of where to find further information and how to actively engage.
The session will be tailored to the audience and designed to encourage the exchange of knowledge and experience. Remote participation will be supported. The aim is to help connect people who are relatively new to ELIXIR with the many opportunities of the community and with each other.
The workshop will start with a presentation to address common queries and guide participants through the available ELIXIR information sources. It will be followed by the opportunity to ask questions to a panel composed of members of the ELIXIR Hub and Nodes. By the end of the session, attendees should have a clearer picture of how they fit into ELIXIR and how best to apply their knowledge and skills to maximise their impact.
 

Equity, diversity and inclusion (EDI) are fundamental to cultivating a collaborative, innovative and sustainable research environment within ELIXIR. Building on previous work on this topic by ELIXIR STEERS, ELEAD and other initiatives, we aim to establish a structured platform for dialogue and exchange, identifying the priorities of the ELIXIR network. The workshop seeks to raise awareness of important EDI topics and encourage coordinated action that could be implemented within ELIXIR.

It is intended as an opportunity for individuals interested in EDI within ELIXIR to meet and discuss the topic. The main objective is to listen to and better understand the perspectives of the community, identify common challenges and determine areas in which ELIXIR could take collective action in future. By facilitating dialogue and exchange, the workshop will raise awareness of significant past EDI-related work and lay the groundwork for an EDI focus group within ELIXIR. Particular attention will be given to the accessibility and inclusivity of ELIXIR's digital resources, services and working practices across platforms, as well as sustainable tools and recommendations that promote inclusive participation within ELIXIR. By identifying and addressing existing accessibility barriers — including those experienced by disabled people — future initiatives can help ensure that ELIXIR’s websites, databases and digital tools are inclusive and accessible to all users.
The workshop wants to develop these ideas in the following agenda:
1. Introduction to the past, present and future EDI work within ELIXIR
2. Interactive World Cafe to analyse the perspectives of the ELIXIR network
3. Outcomes and key ideas related to an EDI focus group
The overall aim of the workshop is the strengthening of connections between people, Nodes and platforms, and the continuation of ELIXIR's current efforts to promote a diverse, inclusive and equitable environment. The outcomes of this workshop, based on shared expertise, open and honest dialogue, and collective reflection, will shape further ongoing EDI work within ELIXIR.
 

The RDMkit (Research Data Management toolkit for Life Sciences) is a resource for scientists dedicated to managing their data according to best practices. The RDMkit enables users to find the best practices for research data management (RDM) aligned with the FAIR Principles: Findable, Accessible, Interoperable, Reusable. For metabarcoding data management, the lack of clear standards has been widely acknowledged within the literature, inducing initiatives to develop solutions (Shea et al. 2023, Takahashi et al. 2025). The need for a metabarcoding RDMkit page was previously identified during the development of the biodiversity RDMkit page by the ELIXIR Biodiversity community (BC).
A first version was developed, oriented towards marine biology metabarcoding data management including marine examples. But its spectrum should be widened towards different biomes, in collaboration with the ELIXIR BC, Microbiome (MC) but also the Plant (PC), Food & Nutrition (FNC) communities, to cover different examples and the specifics of diverse fields, such as soil, rivers, forest, or animal biomes. Bringing these communities together also presents an opportunity to update and widen the existing Marine metagenomics RDMkit page.
To gather the different expertises, we propose a workshop at the ELIXIR All Hands Meeting to expand the metabarcoding page, update/expand the metagenomic page and identify the putative missing RDMkit pages to cover the different biodiversity and microbiome data analyses. The workshop will gather experts from the BC, MC, PC, FNC, Research Data Management Community (RDMC) and the Interoperability Platform. It will begin with short presentations of the ongoing work on the metabarcoding RDMkit page and the current Marine metagenomics RDMkit page. Then, we will split in three groups to:
1. Review the metabarcoding RDMkit page to include examples based on the participant’s expertise.
2. Develop the metagenomic RDMkit page, identifying gaps  and using content from the existing marine metagenomics page.
3. Identify additional needed resources in the context of biodiversity analysis(e.g., transcriptomics).
The workshop will be concluded with group restitutions and a collective discussion to share findings and identify key takeaways.
This workshop aims to advance both Science and Technology, by enhancing the interoperability of microbiome and biodiversity data analysis, and Nodes and People, by promoting collaboration across ELIXIR Platforms and Communities.
Expected Outcomes:
•       A ready-to-submit metabarcoding RDMkit page
•       A draft of a metagenomic RDMkit page
•       A roadmap for missing RMDkit pages.
•       Strengthened collaborations between the BC, MC, PC, FNC, RDMC and the Interoperability Platform.
 

MCP servers promise unprecedented accessibility of tooling, including ELIXIR services, by connecting to client-side copilots and enhancing their robustness. This has already led to the development of several third-party and some first-party MCP servers for popular ELIXIR services. In response, we have established a registry for biomedical MCP servers (https://biocontext.ai), collecting many of these servers for better FAIR representation.
However, while MCP servers are technically comparable to REST APIs, their development requires a fundamentally different mindset. Traditional APIs expose a predictable, prescriptive interface, whereas MCP servers are designed to empower LLM-driven clients without assumptions about how—or even whether—a particular tool will be used. This inversion of control represents a new paradigm for service design and raises important questions for ELIXIR service providers around evaluation, quality assurance, sustainability, and communication.
This workshop addresses these challenges by bringing together ELIXIR service teams, Platforms, and interested Communities to establish a shared understanding of MCP servers and their role in the ELIXIR ecosystem. Specifically, the workshop aims to:
•       establish a common understanding of MCP servers, their benefits, and their requirements in an ELIXIR context;
•       define criteria for evaluating whether an MCP server is appropriate and useful for an existing ELIXIR service;
•       discuss practical implications for development, testing, deployment, and maintenance of first-party MCP servers;
•       explore approaches for dissemination, qualification, and signalling of trusted MCP servers to the community.
The session will begin with a short introduction to MCP to align participants’ understanding. This will be followed by an interactive discussion among service representatives on experiences with existing third- and first-party MCP servers. Participants will then jointly examine available tooling for MCP server development and testing, and discuss whether shared guidance—such as a checklist, minimal criteria, or informal statute—would be beneficial for ELIXIR-endorsed MCP servers. The workshop will conclude with a discussion on community positioning and discoverability, including mechanisms such as registries or quality “badges” to reach appropriate user groups.
By focusing on concrete service-level questions and shared problem-solving, this workshop contributes to ELIXIR’s Technology and Science tiers while also addressing the People tier through capacity building. It involves Interoperability, Tools, and Data Platform concerns and is subject to interest from the AI Ecosystem Focus Group.
Expected outcomes include a shared understanding of MCP’s role in ELIXIR services, an initial set of evaluation considerations for MCP adoption, and identified next steps for coordination, documentation, or training within the ELIXIR community.
 

We propose an interactive workshop to carry out the FAIR evaluation of digital objects representing training materials, tools, and workflows. The workshop will focus on entries from key ELIXIR registries, namely TeSS, bio.tools, and WorkflowHub, and will use FAIR assessment tools such as FAIR-checker. The workshop will be facilitated by representatives of these tools and services and draw on the combined expertise of the ELIXIR Interoperability, Tools, and Training Platforms.
The main goal of the workshop is to improve guidance for content creators and annotators contributing to these registries through interactive use of FAIR assessment tools. To achieve this, the workshop will identify community best practices for the FAIR annotation of specific digital object types and integrate them into FAIR evaluation processes. These practices will, for example, address the use of specific identifiers and ontologies for metadata fields.
The workshop will bring together contributors of training materials, tools, and workflows to ELIXIR registries, as well as developers and users of FAIR evaluation tools. After a joint introduction, participants will be grouped according to the type of digital object they work with. Each group will work with pre-selected examples and evaluate their FAIRness scores. The results will be reviewed and discussed based on the expertise and established practices of the participating communities. These discussions are expected to highlight gaps both in the implementation of FAIR-related features within the registries and in the design and configuration of the FAIR evaluation mechanisms themselves.
We expect the workshop to significantly influence the development of ELIXIR tools and services. Registry providers will gain insights into improvements and integrations to enhance the FAIRness of their content, while FAIR assessment tool developers will obtain community-driven recommendations to incorporate into their assessment models, enabling more targeted and customisable evaluations. Content providers and curators will benefit from a clearer and more actionable set of best practices to improve the FAIRness of their materials. The outcomes of the workshop will be documented in ELIXIR RDM resources such as RDMkit and the FAIR Cookbook to ensure long-term findability and reuse. Finally, the workshop aims to lay the groundwork for deeper integration between platforms, registries, and metadata standards, fostering more consistent and standardised annotation across ELIXIR.