DTL acts as the Dutch node of ELIXIR, the European data infrastructure for the life sciences. ELIXIR-NL is building a digital environment to make life science research data accessible and exchangeable. Our focus is on the FAIR Data principles (i.e., research data should be Findable, Accessible, Interoperable, and Reusable for both humans and computers). ELIXIR-NL is an open network of bioinformatics groups in the Netherlands. ELIXIR-NL is not a funding organisation, but it is part of the strategic roadmap for scientific infrastructure of the Dutch government.
- Compute: Computing, storage and network (e-)infrastructure services
- Data: Operation and maintenance/curation of biological (reference) databases
- Tools: Collection and evaluation of software tools used for life sciences
- Interoperability: Standards and tooling for data interoperability and reuse
- Training: Training and Education of researchers and data experts
To ensure that the services developed by the platforms are fit for purpose, ELIXIR collaborates with the scientific community through ELIXIR Communities.
In addition, ELIXIR participates in several EU-funded projects to drive the delivery of various bioinformatics services to the scientific community.
ELIXIR’s Dutch node is active in the Compute, Interoperability, and Training platforms and represented in most of the ELIXIR Communities. The domains Compute, Interoperability, and Training have been selected as topics in which the Dutch bioinformatics community has a clear added value in ELIXIR’s international programme. This has been confirmed at the start of ELIXIR by the International Scientific Advisory Board. ELIXIR-NL also channels the needs of Dutch life science projects to each of the five international platforms.
As a pan-European infrastructure for biological information, ELIXIR evolves towards being a natural partner for all data-intensive life science projects, programmes, and research infrastructures. ELIXIR-NL acts in close alignment with other ESFRI infrastructure nodes in the Netherlands, such as BBMRI-NL, EATRIS-NL, NL-BioImaging AM, and others. This cross-ESFRI-collaboration has resulted, among other things, in the Health-RI initiative.
ELIXIR-NL is the Dutch node in the European research infrastructure ELIXIR, which is distributed over 20 countries that work together using a ‘Hub and Nodes’ model.
- The ELIXIR Hub is like a headquarters and coordinates the work across ELIXIR. The Hub is based at the Wellcome Genome Campus, near Cambridge, UK.
- Each member state of ELIXIR has established an ELIXIR Node, which is a network of organisations that work within ELIXIR. Each Node has a lead organisation that coordinates the local ELIXIR activities. For ELIXIR-NL, this is DTL.
ELIXIR-NL is hosted by DTL and the ELIXIR-NL activities are part of the DTL Data programme. It is governed through the DTL Scientific Advisory Committee and Board. As ELIXIR-NL’s Head of Node, Professor Jaap Heringa (VU) is coordinating the work in the node and representing the Netherlands in the ELIXIR Heads of Nodes Committee.
ELIXIR-NL is an open conglomerate of bioinformatics groups in the Netherlands. In principle, all activities in the realm of life science data in the Netherlands can be considered part of ELIXIR-NL, provided that the institute involved is a DTL partner. The level of involvement of the groups in ELIXIR-NL varies and changes over time. Connections between the groups are maintained through the DTL network.
- The ELIXIR-NL activities are coordinated by a small staff located at the DTL Office in Utrecht.
- The actual projects (i.e., developing or operating resources, tools, and services for ELIXIR) are mostly performed at the DTL partner institutes.
- The ELIXIR-NL strategic team (consisting of members of the DTL Office and representatives from several DTL partner institutes) meets monthly via teleconference and just before strategic international ELIXIR meetings.
ELIXIR-NL and ELIXIR Europe
The relationship between ELIXIR-NL and ELIXIR Europe is formally described in several documents:
- Consortium agreement: forms the legal binding between all ELIXIR nodes and is a single contract between all participating countries, arranging the governance of ELIXIR.
- Collaboration agreement: defines the two-sided relationship between the ELIXIR-NL node and the ELIXIR hub, defining the involvement of the Dutch node in ELIXIR’s activities.
- Node remit: defines the specific expertise that ELIXIR-NL offers to ELIXIR (implying the intention to collaborate with other nodes on these topics) and is approved by the ELIXIR Scientific Advisory Board.
- Service Delivery Plan: defines the concrete services that ELIXIR-NL offers to its ELIXIR partners, is established as an appendix to the collaboration agreement, and is approved by the ELIXIR Scientific Advisory Board.
Importantly, ELIXIR-NL is not a funding organisation.
Membership of ELIXIR Europe
European research infrastructures like ELIXIR are paid for by the member states. The costs for each operation are paid by the country where it is located. The central costs (i.e., the costs of the Hub in the case of in ELIXIR) are paid from membership fees. The distribution of these costs are agreed upon by the member countries in the consortium agreement, and fixed for a period of five years at a time. The Dutch government has so far paid these dues directly to ELIXIR Europe, in the future the government will request that research institutes benefiting from the infrastructure will co-fund.
International Projects: EXCELERATE and CONVERGE.
In 2015, the European Commission prioritised ELIXIR on its roadmap. This resulted in the invitation to write a large proposal for the INFRADEV-3 call of Horizon 2020, which has as goal to help research infrastructures with their construction. The proposal was called EXCELERATE, a contraction of EXCEL and ACCELERATE, and it was funded. EXCELERATE funding helped ELIXIR coordinate and extend national and international data resources to ensure the delivery of world-leading life-science data services.
NWO Roadmap Large-scale Scientific Infrastructure
In 2017, ELIXIR-NL submitted a funding proposal to further develop the Dutch life sciences data infrastructure. Read more about these Roadmap plans in the dedicated section. Although the proposal was not selected for funding by NWO, many of the aims of the infrastructure have been pursued in other ways and at another pace, also as part of collaboration in Health-RI.
- ELIXIR-NL leads work packages and tasks in the ELIXIR Converge project implementing and documenting data management practice over Europe
- Initiatives for ELIXIR communities for Microbial Biotechnology, Toxicology, Metabolomics and Food and Nutrition were set up under Dutch leadership.
- ELIXIR-NL has participated in more than 50 ELIXIR implementation studies over the years, and for example led the ELIXIR implementation study for the analysis of the FAIRness of the ELIXIR Core Data Resources
- ELIXIR-NL has organised several Bring Your Own Data workshops. The main goal of these events is to make research data FAIR using linked data technology, and to combine the data with other FAIR datasets to answer a scientific question. Read more.
- On 25 April 2017, ELIXIR-NL and ELIXIR Germany organised a workshop ‘Future of Metabolomics in ELIXIR’ at Frankfurt Airport, in collaboration with the PhenoMeNal project and the Netherlands Metabolomics Centre. More than 30 persons from 10 countries participated. A report about the workshop is available online.
- ELIXIR-NL organised a workshop on FAIR data and data stewardship in ELIXIR: ‘How to write your own FAIRy Tale’ for the ELIXIR All Hands meeting (March 2017 in Rome). The presentations are available online. In addition, we organised a workshop about the ELIXIR Data Management Planning Portal.
- On 16-19 January 2017, the first European Galaxy Developer Workshop took place in Strasbourg. Galaxy is an open, web-based platform for data-intensive biomedical research. ELIXIR-NL and the Dutch Galaxy Working Group were actively involved in the workshop’s organisation.
- On 13 December 2016, NWO officially presented its ‘Roadmap for Large-Scale Scientific Infrastructure’. The Roadmap contains 33 research facilities and clusters that are eligible for NWO funding in the next four years. One of these 33 is ELIXIR-NL. Read more.
- ELIXIR-NL hosted a Data Carpentry Hackaton and a Data Carpentry Workshop on 22-25 June 2015. Data Carpentry is designed to teach basic concepts, skills and tools for working more effectively with data. Partners involved were ELIXIR-NL, NLeSC, TU/E, UU, WUR, and UMCG. You can find a report of the Data Carpentry Hackathon and Workshop here.
- ELIXIR, Wageningen University, and DTL held a successful two day ELIXIR Innovation and SME Forum in Wageningen on 18-19 March 2015. Read more.
- In 2015, a two-day ELIXIR Training the Trainers workshop was held in Cambridge, England on the subject of ‘best practices in training on NGS Analysis’. This workshop was a great opportunity to discuss what topics to cover in various bioinformatics courses and how to best get these topics across to students. Martijn Herber (Hanze Hogeschool) joined on behalf of the Dutch node of ELIXIR. His report of the meeting can be found here.
- ELIXIR survey ‘training needs in industry’: An ELIXIR-wide survey about training needs in industry was performed in 2015.