About ELIXIR-NL

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. It 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.

ELIXIR Europe
ELIXIR is the European research infrastructure (ESFRI) dealing with all aspects of data in all branches of life sciences. ELIXIR Europe has grouped its activities into five platforms:

  • 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 in four specific domains, the so-called Use Cases:

  • Marine
  • Rare disease
  • Human data
  • Plants

In addition, ELIXIR participates in several EU-funded projects to drive the delivery of various bioinformatics services to the scientific community, e.g., EXCELERATE and CORBEL.

ELIXIR-NL
ELIXIR’s Dutch node is active in the Compute, Interoperability, and Training platforms and in the Use Cases Rare disease, Human data, and Plants. 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 by the ELIXIR International Scientific Advisory Board. ELIXIR-NL also channels the needs of Dutch life science projects to each of the five international platforms.

Other ESFRIs
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 governance
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.

Professor Heringa

ELIXIR-NL organisation
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 operational team (consisting of members of the DTL Office and representatives from several DTL partner institutes) meets via teleconference every two weeks on Tuesday mornings 10:30-11:15. In these meetings, we inform each other about the progress of our projects, international meetings we attended, etc.
  • 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.

Representation in ELIXIR Board

  • Ruben Kok (DTL), vice chair
  • Bea Pauw, (NWO) administrative delegate

Representation in ELIXIR Heads of Nodes Committee

  • Jaap Heringa (VU Amsterdam)

Representation in ELIXIR Technical Coordinators group

  • Rob Hooft (DTL)

Representation in ELIXIR Training Coordinators group

  • Celia van Gelder (DTL)

Representation in ELIXIR Platforms

Compute Platform

  • Irene Nooren (SURFsara)
  • Christine Staiger (SURFsara)
  • Paul van Dijk (SURFnet)
  • Niels van Dijk, (SURFnet)
  • Fokke Dijkstra (RUG)

Interoperability Platform

  • Chris Evelo (Maastricht University), Platform coordinator
  • Rob Hooft (DTL)
  • Mascha Jansen (DTL)

Training Platform

  • Celia van Gelder (DTL), Platform coordinator
  • Irene Nooren (SURFsara)
  • Sanne Abeln (VU)
  • Mateusz Kuzak (NLeSC), Software Carpentry, Data Carpentry
  • Leon Mei (LUMC) , Chair NL Working Group Galaxy
  • Andrew Stubbs, Working Group Galaxy
  • Chris Evelo (Maastricht University), e- learning
  • Frederieke Ehrhart (Maastricht University), e- learning

Representation in ELIXIR Use Cases

Human Data/ WP9 ELIXIR EXCELERATE

  • Morris Swertz (UMCG, Beacons Implementation study)
  • Sanne Abeln (VU)
  • David van Enckevort (UMCG, Beacons Implementation study)

Rare diseases/ WP8 ELIXIR EXCELERATE

  • Marco Roos (LUMC), Use case lead
  • Mark Thompson (LUMC)
  • David van Enckevort (UMCG)

Plants/ WP7 ELIXIR EXCELERATE

  • Richard Finkers (WUR)

Representation in ELIXIR projects

ELIXIR-EXCELERATE

  • See above.

CORBEL

  • Morris Swertz (UMCG)
  • Jan-Willem Boiten (Lygature)

Implementation studies

  • ELIXIR Beacons (Morris Swertz, David van Enckevort)
  • Bioschemas (Morris Swertz)
  • 2017 Beacon project (Morris Swertz)
  • Data management planning portal (Rob Hooft) & DMP training (Celia van Gelder)
  • Molecular data (Frederieke Ehrhart, Chris Evelo, Marco Roos)
  • Rare disease pilot (Marco Roos)
  • TraIT pilot (Sanne Abeln, Jochem Bijlard)
  • Software/Data carpentry (Mateusz Kuzak)

ELIXIR-NL Operational Team

  • Katy Wolstencroft (Leiden University)
  • Fokke Dijkstra (RUG)
  • Jaap Heringa (VU)
  • Irene Nooren (SURFsara)
  • Marco Roos (LUMC)
  • Morris Swertz (UMCG)
  • Chris Evelo (Maastricht University)
  • Richard Finkers (WUR)
  • Celia van Gelder (DTL)
  • Rob Hooft (DTL)

ELIXIR-NL Office

  • Jacintha van Beemen, project support
  • Linda van den Berg, communications
  • Femke Francissen, community
  • Merlijn van Rijswijk, contracts
  • Leonie Hek, finances

DTL has reserved a small budget (initially EUR 10k) to make sure that ELIXIR-NL is represented in relevant international meetings that the DTL staff cannot personally attend. Please contact Rob Hooft if you want to apply for this travel fund.

Conditions

  • The person applying for the travel fund has an intrinsic motivation to visit the meeting, as shown by investing his or her own time.
  • At the meeting, the representant represents ELIXIR-NL visibly and audibly.
  • ELIXIR-NL has a good cause to be represented at the meeting.
  • Only one person per meeting can use this fund.
  • It is not possible to obtain funding if another ELIXIR-NL representative will visit the meeting.
  • This fund can only be used if there is no other money that could reasonably be used to attend the meeting.
  • This fund does not pay people who are partner in a project that contains money for ELIXIR travel.
  • Demands for funds should be placed before the trip takes place.
  • A report of the meeting and interactions and/or contacts is expected quickly after the meeting.
  • Final judgment call on eligibility is with the DTL office.

Reimbursement

  • Reimbursement after the trip and report.
  • Costs of a reasonable hotel night + economical travel tickets.
  • Be reasonable.
  • Keep receipts and deliver with the declaration.

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 pays these dues directly to ELIXIR Europe.

EXCELERATE
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 will help 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 teamed up with Eurocat (Radboud UMC) and Digital Research Environment (Maastricht UMC) to further develop the Dutch life sciences data infrastructure. The team submitted a funding proposal on 1 June 2017. Read more about NWO’s Roadmap Large-scale Scientific Infrastructure in the section below.

The list below contains some examples of past activities of ELIXIR-NL. Please consult the news archive for a more complete overview and subscribe to the DTL newsletter to stay informed.

  • ELIXIR-NL has organised several Bring Your Own Data workshops in the past few years. The main goal of these three-day 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. ELIXIR-NL has been asked to coordinate the data approach of the life science facilities. 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.

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, which was asked to team up with Eurocat (Radboud UMC) and Digital Research Environment (Maastricht UMC) to further develop the Dutch life sciences data infrastructure. The team submitted a funding proposal on 1 June 2017.

More information