Agenda

Tim Hubbard, ELIXIR Director, and Andy Smith, Head of External Relations, will welcome everyone to the 10th ELIXIR All Hands Meeting, after which the Head of ELIXIR Sweden will provide an introduction. 

This interactive workshop will help participants understand ELIXIR's structure and operations. It is particularly suitable for people who have been part of ELIXIR for less than two years, but is open to all.

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. They should leave with answers to their questions, and understand where to find further information and how to actively engage with ELIXIR.

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Join us for an interactive workshop aimed at forging collaborative pathways between BioFAIR UK, ELIXIR and the wider European life sciences research community.

The BioFAIR project is a proposed new UK government-funded investment of £34M to develop a federated digital research infrastructure connecting existing life sciences infrastructures which will be assembled largely through the integration of existing services, resources and knowledge.Expected to commence in the summer of 2024, BioFAIR will initially be funded for 5-years and will focus on four core capabilities: data commons, method commons, knowledge centre, and community centre. The capabilities will be validated by pathfinder projects. This infrastructure will support the broad life sciences research communities, initially centred on the four nations of the UK.

However, while BioFAIR's primary focus is on the UK research landscape, we recognise the importance of international collaboration in advancing service development, delivery, and interoperability. This workshop serves as a platform to explore opportunities for cooperation and alignment between BioFAIR, ELIXIR, and the broader European life sciences community.

Participants will engage in dynamic discussions exploring avenues for collaboration, identifying synergies, and addressing challenges across our four core capabilities. We aim to collectively envision pathways for leveraging BioFAIR's infrastructure to enhance research capabilities across the life science research community, by fostering cross-border partnerships and knowledge exchange.

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The public release of ChatGPT at the end of 2022 was a landmark event in the deployment of advanced natural language processing technologies. The combination of a sophisticated language model, enormous compute power and a streamlined user interface is already reshaping the scientific landscape, with many more researchers feeling empowered to incorporate natural language processing into their research.

At the same time, machine learning systems in the realm of life sciences depend on the labour of expert curators for training data which is now potentially more valuable than ever. The increased demand for large, high quality, annotated corpora makes the provision of technology to assist biocuration particularly important.

The purpose of this workshop is to examine the use of tools for various tasks in curation workflows. Such tasks would include literature search and triage, extraction and annotation, collaboration on curation, and literature summarisation. The expanding use of LLMs, either developed bespoke or using off the shelf APIs like ChatGPT will be of particular interest.

The workshop would include demonstrations from teams developing software likely to be of interest to biocurators and biocuration teams who have incorporated LLMs and other machine learning technologies into their curation workflows, and discussion of gaps in service provision and possible opportunities to develop and adapt emerging technologies to assist biocurators. By bringing together biocurators, tool developers, and others interested in natural language processing, we hope to identify avenues for new collaborations across disciplines.

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As a pan-european initiative, ELIXIR members collaborate across multiple countries with different cultures and expectations. These diverse perspectives and collaboration drive better research and innovation, but for truly meaningful collaborations we need to think carefully about pathways and potential barriers to participation.

If a collaborator’s suggestions to a project get continuously ignored, or if key decisions are made in conversations they have no access to, chances are they will stop contributing to that project. For science to be truly collaborative and accessible, we should learn to recognise inequities in science and act to change them, supporting researchers in embedding ethical values in scientific projects and discussing the societal impacts of their work.

When we witness oppression (such as racism, sexism, queerphobia, or ableism), sometimes we are so shocked we can’t react quickly, can’t figure out what to do, or do something that turns out to be more harmful than helpful. This is true even for people who have experience and education in supporting members of marginalised groups in their communities.

Education and practice can help. This Ally Skills Workshop equips participants with actionable, practical skills to use their societal advantages. It will focus on teaching people with privilege how to support members of marginalised groups in their daily lives by taking small, simple, everyday actions—and then making systemic changes to prevent oppression in the first place. We use the phrase “ally skills” instead of “allies” because it emphasises that actions are what make a difference, not self-identification as a supporter by itself.

Format: The workshop will start with a general introduction to Ally Skills followed by breakout sessions in small groups to discuss and practise handling a potential scenario where using ally skills could make a difference. In addition to the workshop lead, a dedicated pair of facilitators - one in-person, one remote- will ensure that virtual and in-person participants are equally involved and supported.

This workshop is designed for people who are voluntarily attending the workshop, who already agree that oppression exists, that it should stop, and that they personally would like to help end it. The workshop is meant to equip all allies, including marginalised groups who want to use their skills to support other marginalised groups. It does not teach marginalised groups how to respond to oppression targeting them.

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Biomedical research is witnessing a paradigm shift driven by the growing need for collaboration across stakeholders from different domains. In this era, secure data access and analysis are fundamental requirements; however, we are confronted by an inherent dilemma - the need to harness the power of collective analysis while safeguarding data privacy and complying with data protection regulations. This is the challenge that the use of federated analysis seeks to address.

The usage of federated analysis is linked to several ongoing developments associated with ELIXIR; including GDI, EUCAIM, BY-COVID, EOSC4Cancer and technology-oriented projects like EuroScienceGateway and EOSC-ENTRUST. These multiple parallel developments create an imperative need to establish unifying guidelines to harmonise these efforts, guaranteeing synchronised development and coherence in the evolution of the different projects.

This workshop objective will be to identify federated analysis key developmental technologies, assess their maturity level and their suitability for different data types through a collective discussion, enhancing the knowledge exchange between the ELIXIR members working on different projects, platforms and communities.

Within the context of this workshop, we will:

• Interactively discuss, e.g. through a World-cafe set-up, and aim to define common terminology and requisites for federated analysis and its underlying federated infrastructure, considering commonalities and differences with other approaches.
• Pinpoint synergies and gaps across ELIXIR platforms, communities and projects encouraging debate between different teams on tackling them.
• Discuss which elements should be considered for evaluating the technology maturity levels.
• Identify relevant initiatives, projects and organisations to engage with regarding secure federated analysis.

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Our vision for the ELIXIR Human Data Community is to establish a federated and interoperable ecosystem of services that enables access to genomic and biomolecular data on a population scale across borders,  to accelerate research and contribute to improving human health. 
The successful completion of the Beyond 1 Million  Genomes (B1MG) project and the commencement of The European Genomic Data Infrastructure (GDI) have created momentum across Europe and globally; therefore building on the success and expanding the knowledge gained from the ELIXIR HDCs communities, B1MG and its ongoing implementation phase through GDI is critical. By leveraging these achievements and fostering new relationships we aim to expand the global network in this field.

This session will focus on the latest developments in Human Genomics from experts in Australia, Switzerland and the U.K. providing an overview of the current landscape, advancements and key challenges, including ways that ELIXIR can support activities to align efforts towards approaching a federated ecosystem.

Feedback from this session will allow us to establish further engagement mechanisms to facilitate the required level of knowledge transfer to ensure interoperability between ELIXIR, other Research Infrastructures and the wider scientific genomic community. 
 

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The main theme of the mini-symposium is towards finding the appropriate connections and building bridges between the planned efforts across the ELIXIR Training Platform, and the activities of the ELIXIR Science Tier. This bidirectional interaction will be facilitated by flash presentations of the individual Work Packages in the TrP, complemented by an overview of the different Science Priorities with Training in mind. Ultimately, the session will conclude with an open Panel discussion, towards identifying the most viable synergies in the short-term, while also building a longer-term connection across the key elements of the Science Tier.

The ELIXIR Training Platform (TrP) is building a network of training resources and services, aiming for collaboration, visibility, and standardisation. SPLASH, a digital hub, showcases core services like TeSS, enhancing the training life cycle. Work Packages focus on infrastructure, guidelines, and Train-the-Trainer resources. Collaboration across ELIXIR entities is essential, as are standardised guidelines and a supportive community for knowledge sharing. The project's success will transform training delivery within the community.
 

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This session by the ELIXIR Data Platform explores cutting-edge developments in sharing, using, annotating and curating life science data. It also goes beyond data itself to look at work underway to grant better credit and recognition to those who create and curate life science data. We'll discuss tools that facilitate literature curation, such as Triage using LLM-based models, and better annotation, such as text and table standardisation using NLP. We'll discuss different business models for curating databases comparing community-driven and professionalised approaches. We'll look at initiatives that track contributions to repositories and knowledge bases at a very granular level, and how research assessment in Europe is changing to acknowledge the importance of previously underappreciated experts. We'll consider how standardised formats can simplify the complex world of multi-omics data deposition and integration and directly improve public health responses and support biodiversity research.

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This workshop will contribute to the ELIXIR Programme interdisciplinary collaborations, by linking the ELIXIR Plant Science Community, the ELIXIR Biodiversity Community and external partners, including the French PNDB and the German NFDI4Biodiversity. In addition, two other projects involving ELIXIR, BiCIKL (Biodiversity Community Integrated Knowledge Library) and PHENET (Tools and methods for extended plant PHENotyping and EnviroTyping services of European Research Infrastructure), will participate in this collaboration.

The workshop will consist of presentations, flash talks, hands-on and a panel discussion to share knowledge on specific initiatives (e.g. ELIXIR Communities and partner projects). With this structure, attendees will be able to explore the initiatives relations, highlight their data management practices, challenges and the integration of training efforts. In addition, the workshop will feature a high-level presentation on the Biodiversity, Food Security and Pathogen (BFSP) strategic theme of the new ELIXIR programme, clarifying the potential synergies in relevant ELIXIR Communities and ongoing projects. As part of the flash talks, a presentation will focus on a holobiont project detailing the interactions between plants and their surrounding microbial communities, providing a different perspective on biodiversity. To maximise audience engagement, participants will be asked to participate in the panel discussion to encourage a dynamic exchange of ideas.

The Communities will use this workshop to further refine their roadmaps and strategically incorporate insights from the panel discussions in a hands-on session. The workshop will facilitate a lively dialogue bringing together experts and practitioners from the fields of plant science, biodiversity and data management. This interaction will foster innovative solutions and insights by identifying common challenges and opportunities. The overarching goal is to promote the development of common standards, best practices and training materials. This workshop is highly relevant to the overall objectives of the ELIXIR Programme as it promotes interoperability and collaboration between the different areas of life sciences. By bringing together the Plant Science and Biodiversity Communities, we aim to improve the ability of the ELIXIR network to manage and utilise a wide range of biological data. The involvement of external partners PNDB and NFDI4Biodiversity, as well as AnaEE and EMPHASIS through PHENET will further increase the reach of ELIXIR's collaborative efforts at European level. Ultimately, the outcomes of this workshop will contribute to building a collaborative and networked European life sciences research community and further align the objectives of the ELIXIR programme, particularly the scientific priority area of “Biodiversity, Food Security and Pathogens”.

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This workshop will showcase how ELIXIR members at all levels can engage with ELIXIR’s Interoperability Platform (EIP) to strengthen their expertise and access information resources. It is organised by the EIP and focuses on the activities that drive its transition to a sustainable framework for enabling real-world data integration and reuse by promoting and supporting interoperability, data management and FAIR principles.

The workshop objectives are to: 1) highlight opportunities for the wider ELIXIR community to engage with activities organised under the new EIP programme to pave the way for synergistic activities across Nodes, Platforms, Communities and projects; and 2) support ELIXIR members in sharing and discussing expertise and learnings from related activities to seed the EIP programme. The intended audience is ELIXIR community members engaged in data integration/reuse challenges and who would like to liaise with the EIP activities. Furthermore, since it will also promote the broader EIP ecosystem and the scope of the EIP programme, anyone is welcome to participate.

The EIP’s transition to a sustainable framework centres on mature Products that enable FAIRification and responsible RDM, data integration and analysis; specific Processes that use (or need) Products; and broader Practices that enable a user to succeed. Each of “the Three Ps” (Products, Processes, Practices) are addressed by tasks and deliverables in the new EIP programme:

• Growing the FAIR-enabling portfolio of products (WP2)
• Standardising processes for FAIR data management (WP3)
• Establishing best practices for interoperable data management and use (WP4)

During the first part of the workshop, participants will be introduced to the EIP vision with examples of opportunities to engage and potential liaison strategies. The second part focuses on discussions to identify ‘target’ ELIXIR communities to work with for the EIP’s initial tasks. The workshop concludes with reflections on the next steps to take across the EIP programme WPs and future touching points across the EIP and activities in the wider ELIXIR community.

The expected outcome is an outline of future interactions between the wider ELIXIR community and the EIP programme including examples of resources and learnings that should inform its work. Beyond the contributions to the EIP, participants will be equipped with a better understanding of how they can leverage the EIP and its current offerings/activities in their own communities. The broader impact includes strengthening ELIXIR’s advancements around federation and FAIR data across the scientific programme’s themes grounded in the “the Three Ps” of the EIP.

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This workshop will be an interactive session on strengthening ELIXIR's global partnerships in two areas – partnerships with relevant global initiatives (e.g. GA4GH, Australian BioCommons, NIH, RDA), as well as internationally, including partner networks / institutes in countries beyond Europe (i.e. Latin America, Africa).

The session will be divided into two panel discussions, followed by an interactive Q&A. The conversation will start with a panel of representatives from different ELIXIR Nodes and relevant initiatives to provide a short overview of existing ELIXIR partnerships (e.g. GA4GH, NIH) and allow for questions about ongoing activities and progress. The session is intended to create an interactive environment for the audience to contribute with thoughts and discussions about current collaborations and which areas / partners / initiatives ELIXIR should develop / strengthen in terms of collaborations or partnerships going forward. The second part of the session will focus on ELIXIR Node activities in countries beyond Europe and explore possibilities for creating synergies and increasing ELIXIR’s visibility and impact internationally.

Conversation points will also aim to highlight key outcomes and impacts of recent collaborations, identify enabling factors and barriers, as well as next steps, notably as part of the upcoming ELIXIR Scientific Programme for 2024-2028 & the ELIXIR-STEERS project.

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This workshop proposal aims to harness the collective experience of some ELIXIR entities, alongside contributors from diverse backgrounds. The focus is on enhancing the ELIXIR Training Platform (TrP) activities, with a special emphasis on open-source solutions to address technical challenges for the creation of inclusive training material. Embracing a “call for help” framework, we invite participation from all ELIXIR entities, as we intend to pool together the wider possible range of expertise. The Galaxy Community, the Compute Platform and the Generative AI discussion group have expressed interest to join the workshop.

In particular, we aim to explore open-source solutions (possibly with assistance of generative AI) solving urgent issues faced by the Training Platform such as video editing, incorporation of subtitles, multi-modal streaming, translation to different languages, and other accessibility measures.

The workshop will consist of interactions with experts that could already have some solutions in place (e.g. the Galaxy Training Network) providing an opportunity for advertisement of their solution in exchange of the experience that they will contribute. After an introduction of the TrP challenges and aims, attendees will work in group tables, each dedicated to a specific technical issue, enabling guided interactions with the experts’ tools and gaining a practical understanding of how to apply them to other training contexts. Participants will be encouraged to share how they have solved similar problems in the entities that they represent. In those cases where we will not be able to identify internal relevant expertise, we will use the workshop to explore how other international communities are addressing the issues.

The outcome of this workshop will be a detailed summary report. This report will comprehensively list and describe the specific challenges discussed during the workshop and solutions collected (tools and/or strategies). Additionally, it will possibly include a draft plan on how to integrate these technical solutions into the existing Training Platform activities. This initiative aligns with ELIXIR’s goal of fostering collaboration and knowledge exchange across its diverse entities. By collecting in this document the possible solutions related to the technical challenges of training activities, and by sharing the report publicly on Zenodo, we expect to have an impact well beyond ELIXIR itself, fostering a more effective and accessible learning environment across Life Sciences in Europe.

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This workshop aims to establish a connection among the ELIXIR communities, platforms, and focus groups, all with an interest in industry engagement as part of the new scientific program 2024-2028. This will contribute to building the capacity of the ELIXIR members in engaging with industry and aligning with ELIXIR’s innovation and Industry Strategy and the Nodes’ priorities.

Considering the issues of i) lack of incentive in industry engagement, ii) diverse maturity among ELIXIR resources, diverse collaborations and expectations among different partners, and iii) rules, standards and recommendations issues for data sharing, this workshop is an opportunity to share current and past experiences and discuss future aspects on the topic.

The 90-minute workshop will entail an introduction to the upcoming plan on industry engagement in the new program, followed by short talks by different ELIXIR communities with industry engagement experience or interest in engaging, and a structured discussion among attendees on how to tackle common problems in public-private partnerships . The joint discussion will contribute to a better understanding of the steps of building collaborations, management of expectations, and what is needed to achieve and overcome limitations.

The workshop will build capacity on:

• Identifying industry-ELIXIR interactions in the different community domains.
• Opportunities in building beneficial collaborations.
• Planning joint activities and synergized resources among the communities around challenging issues.
• Blueprint engaging activities for strengthening industry involvement among ELIXIR communities, platforms and focus groups.

Everyone working within the ELIXIR network on industrial engagement, has experience with industry connections, or wants to participate in the topics of this workshop is highly welcome to participate. Your feedback is appreciated!

The outcome of the workshop will be to identify best practices and services used, or with a potential to be used, by industry and explore activities for bridging the gap between research and industrial applications within the ELIXIR framework. The partners of the WP5 industry engagement in the Nodes Tier of the 2024-2028 programme will then use the outcome of this workshop to enrich the corresponding planned activities.

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The dinner will take place in Uppsala Castle which is in walking distance from the venue.  Join us for networking, delicious food and entertainment!