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ELIXIR ELIXIR Annual Report 2018 Annual Report 2018 Contents ELIXIR ELIXIR Annual Report 2018 Report Annual Annual Report 2018 Contents 2 Foreword by Robert Gentleman, Chair of Scientific Advisory Board 3 Foreword by ELIXIR Director 5 Platforms 8 Tools: Services and connectors to drive access and exploitation 10 Data: Sustaining Europe’s life science data infrastructure 12 Compute: Access, exchange and storage 14 Interoperability: Integration of data and services 17 Training: Professional skills for managing and exploiting data 20 Platform leaders 21 Use Cases and Communities 23 Human data 24 Rare diseases 25 Marine metagenomics 26 Plant sciences 27 Use Case leaders 28 New ELIXIR Communities 29 Members 39 2017 Highlights 43 EU Grants 44 ELIXIR-EXCELERATE 46 Collaboration with other Research Infrastructures 49 Supporting activities 50 Capacity building and Node development 51 Industry engagement 53 International collaboration 54 Impact and sustainability 55 Communications 57 Governance 59 ELIXIR Hub staff 61 Governance Committees and financial data 62 ELIXIR Committees 65 Implementation studies in 2017 69 Financial data Foreword by Robert Gentleman The past year has seen a remarkable increase in the technical and scientific activities of ELIXIR, ranging from the selection of ELIXIR Implementation Studies by peer review for the first time, to the delivery of activities across all of the ELIXIR Platforms and Use Cases, to the results of ELIXIR collaborations with its European and international partners. As Chair of the ELIXIR Scientific Advisory Board (SAB), I have watched the development of ELIXIR in 2017 in great detail, and – as we stated in our regular SAB reports – the rate of progress in the implementation of the ELIXIR Scientific Programme has been phenomenal. The selection and publication of the ELIXIR Core Data Resources was not only the highlight of 2017, I have had the privilege of engaging with ELIXIR and but of the entire programming cycle of 2014–2018. its members through my role on the ELIXIR Scientific By establishing the initial list of ELIXIR Core Data Advisory Board since the early days of ELIXIR. Resources, ELIXIR has defined the best practices in I am proud of the impact that the SAB has had and I assessing the quality of biological data provision and continue to be impressed by the energy and effort of its has gained worldwide recognition as an authority in members. It has been enormously interesting to watch this field. This directly feeds into the global case to and help guide the development of ELIXIR, and I am sustain core data resources. looking forward to seeing it build and develop further. Another important milestone in 2017 was the creation I believe that the future of ELIXIR is very bright and of new ELIXIR Communities. Although each of the that it will leverage the potential of life-science data for three new communities created – the Proteomics, maximum impact on research, innovation and society Metabolomics and the Galaxy community – have at large. different requirements, they provide very good opportunities to develop strong technical activities that Robert Gentleman will benefit their respective user groups. Chair of ELIXIR Scientific Advisory Board (2013-2017) In 2017, we also saw the beginning of the development of the ELIXIR Scientific Programme for 2019–2023, the strategic document that lays out the priorities and objectives for the next five years. I’ve been pleased to see ELIXIR reaching out to ELIXIR Nodes in the development of this programme. It will be crucial in 2018 to maintain this vibrant dialogue to ensure the Programme responds to the needs of the life science community in Europe. 2 ELIXIR Annual Report 2017 Foreword by ELIXIR Director This Annual Report illustrates the growth and maturity of our research infrastructure, highlighting the efforts of the 650 plus national experts involved in ELIXIR through our 21 ELIXIR Nodes, which collectively span over 200 institutes across Europe. As I reflect on the major achievements of 2017, there are several events and themes that stand out: the publication of the initial list of ELIXIR Core Data Resources, the collective efforts in ELIXIR- EXCELERATE that resulted in a highly successful mid- term review, and the implementation of FAIR principles across our data resources and services. Long-term sustainability A key goal for ELIXIR, ever since the planning began for a distributed European data infrastructure, has been The quality of our work in ELIXIR-EXCELERATE to develop a new model that ensures the long-term was also recognised by the European Commission; sustainability of the key life science databases and ELIXIR-EXCELERATE was cited as an early success knowledgebases. In 2017, we made several important story in the analysis of the Horizon 2020 Research steps towards this goal. Infrastructures programme published in May 2017 by the European Commission. In Prague, during the ISMB conference in July, we announced the initial list of ELIXIR Core Data Resources. It was the culmination of many months of committed FAIR principles effort by our Data Platform, Heads of Nodes, Scientific In September, we published a position paper on Advisory Board, our external evaluators and – not least – FAIR Data Management in the life sciences, setting the representatives of all the ELIXIR data resources who out our view on the guiding principles on FAIR Data embraced the process and participated in it. Management. The position paper confirmed our commitment to supporting the FAIR data principles Our work to establish ELIXIR Core Data Resources, and within the framework of the European Open Science the very positive reactions we have received about these Cloud (EOSC). resources from the community, also strengthened our position in the dialogue with global funders. Throughout Good examples of how we support FAIR data are the 2017, ELIXIR was an active participant in the initiative continued success of the Bioschemas Community. to establish a global coalition to sustain core data In 2017, Bioschemas held a series of workshops and resources, initially facilitated by the Human Frontier hackathons to engage with the life-science community Science Program Organization. and encourage their members to adopt and use the Bioschemas specifications and make their data ELIXIR-EXCELERATE discoverable by others. As more ELIXIR resources adopt the Bioschemas markup, we are building a In May 2017, our flagship project ELIXIR-EXCELERATE key component of ELIXIR FAIR data infrastructure. received very positive feedback on the activities and results of the first half of this project. During the project’s mid-term review meeting in May in Brussels, we had a very fruitful discussion with our external reviewer and received many useful recommendations for our future work. ELIXIR Annual Report 2017 3 Looking ahead The year 2018 is the last year of our current Scientific Programme and we are working hard on the next ELIXIR Scientific Programme for 2019–2023. As a strategic document to set the future direction of ELIXIR, this new programme reflects the priorities and activities of ELIXIR Members and the needs of our user communities. Development of the ELIXIR 2019–23 Scientific Programme is a considerable undertaking that involves the large community of ELIXIR Node experts, the leaders of ELIXIR Platforms and Use Cases, and the Heads of ELIXIR Nodes. I would like to take the opportunity to thank all of those involved in the work to develop the vision of ELIXIR in 2023, including those working on the technical roadmaps that will take us there, and on the development and delivery of services that have earned us the trust and commitment of users. I look forward to the continued success of ELIXIR in this transformative era in the life sciences. Niklas Blomberg 4 ELIXIR Annual Report 2017 Platforms ELIXIR Platforms ELIXIR activities are structured around five Platforms and a growing portfolio of Use Cases (see the Use Case section). The Platforms form the basic units of operation within ELIXIR, drawing on technical expertise and resources from ELIXIR Nodes. ELIXIR Platforms are built on the real and changing needs of established research communities. They are led by senior scientists from ELIXIR Nodes and are supported by a Platform coordinator at the ELIXIR Hub. The ELIXIR Platforms comprise: • Data: Sustaining Europe’s life-science data infrastructure • Tools: Services and connectors to drive access and exploitation • Interoperability: Supporting the discovery, integration and analysis of biological data • Compute: Storage, computing and authentication / access services • Training: Professional skills for managing and exploiting data The activities of the Platforms are primarily funded by the ELIXIR-EXCELERATE project, in which each Platform is represented by a Work Package. Each Platform also manages an expanding set of ELIXIR Implementation Studies, funded through the ELIXIR Hub budget. Additional activities are funded through other EU grants (CORBEL, EOSC and others). 6 ELIXIR Annual Report 2017 Platforms Communities Data Rare diseases Human data Training Marine metagenomics Compute Plant science Proteomics Interoperability Metabolomics Tools Galaxy ELIXIR Annual Report 2017 7 Tools Services and connectors for access and exploitation The ELIXIR Tools Platform supports the The Tools Platform also started a joint Implementation discovery, quality and sustainability of Study with the ELIXIR Training Platform to integrate 4 software resources, initially from ELIXIR ELIXIR portals from a user perspective . In addition, the Nodes, and later
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