ELIXIR-NL obtained a position on the NWO ‘National Roadmap for Large-Scale Scientific Infrastructure’ in 2016. Our Roadmap ambition was to build a professional research data infrastructure, enabling scientists and innovators to contribute and re-use data, tools, and models, and to compute in a modular environment. An ‘app store-type’ protected environment would enable scientists to collaborate efficiently in order to answer complex research questions. In addition, we wanted to establish a national network of data managers to support this infrastructure.
Since the proposal was not funded by NWO, other ways have been sought to realize the goals of ELIXIR-NL.
Life science domains
When the proposal was submitted, Health-RI was a new initiative. Now that Health-RI is established and funded, it will invest in several Dutch nodes of health research infrastructures, including the health-directed components of ELIXIR. Via newly established Data Competence Centers in the institutes, the infrastructure will also be extended to serve as a backbone for other life science domains. We envisage a broad and scalable facility that eventually will support all data analytics and stewardship in the Dutch life sciences.
The ELIXIR-NL Roadmap plans were rooted in a strong network of dedicated Dutch professionals that have been collaborating for nearly two decades, for instance within the Netherlands Bioinformatics Centre (2003-2013), the Dutch Techcentre for Life Sciences (ongoing), CTMM-TraIT (2011-2015), Data4lifesciences (2016-2019), the Personal Health Train project (ongoing), the MRI/Cognition cluster (ongoing), and BBMRI-NL (first as two roadmap projects, now ongoing in Health-RI). The original partners from the 2017 roadmap proposal still strongly collaborate on this, and additional parties have joined several of the efforts in the mean time. The original ideas for a Digital Research Environment have progressed to a second generation implementation called anDREa that is in use in several academic institutes in The Netherlands and has an independent organisation for its governance.
Our Roadmap ambition is to build and support a professional research data infrastructure, enabling scientists and innovators to contribute and re-use data, tools, and models, and to compute in a modular environment.
Modern life scientists use a variety of advanced technologies, such as genomics, proteomics, metabolomics, and imaging techniques. These technologies offer unprecedented opportunities to unravel the complexity of life and answer research questions of great societal relevance. However, they also bring challenges, in particular because they produce large and complex data sets that call for specialised ICT resources and data expertise.
As a result of these developments, scientific excellence now requires collaborative, multidisciplinary approaches, i.e., open science. Structural collaboration between domain scientists and data scientists is an essential element of modern data-driven science. Unfortunately, our current science system insufficiently supports cross-domain and cross-technology approaches. This has resulted in fragmented, sub-optimal solutions, in particular for digital scientific infrastructures. We urgently need to improve this situation.
- Watch our video about Open Science.
The Netherlands is considered a guiding country in open science, for instance because of its leading role in the design of the European Open Science Cloud and the FAIR Data principles (Findable, Accessible, Interoperable, and Reusable). Our country has a strong digital infrastructure and collaborative culture. This renders us eminently equipped to perform the daunting task of developing an efficient research data infrastructure. Our ambition will be realised by a strong network of dedicated Dutch professionals that have been collaborating for nearly two decades. We constitute a national consortium (ELIXIR-NL) with close international links.
Our ambition is to build an infrastructure that resembles the ‘app store’ environments of Apple and Android, enabling scientists to contribute and re-use data, tools, and models, and to compute in a modular environment. Within this infrastructure, the core backbone for semantic and syntactic interoperability allows tools, compute platforms, and data to work together seamlessly in variable, customised combinations. (Interoperability enables humans and computers to unambiguously recognise whether items in different data sources refer to the same thing, see ‘About FAIR Data‘.) Academic and industrial groups will be contributors as well as users, collectively building a professional digital research infrastructure that is geared towards complex, yet reproducible and low-overhead scientific research. The infrastructure will facilitate optimal translation into societal applications.
To build the ELIXIR-NL infrastructure, we will decompose and re-amalgamate the best modules of existing infrastructure projects into an ‘app store-type’ environment. The infrastructure will combine diverse and distributed data resources in a form that will allow analytics and modelling workflows to leverage the increased information gleaned from truly interlinked data, workflows, and models. In addition, we will establish a national network of data managers to support researchers when using the infrastructure.
Once fully operational, the ELIXIR-NL infrastructure will be a community resource for FAIR data, tools, workflows, and models. It will support research and innovation in academic and industrial organisations, fully enabling cross-disciplinary collaboration. The infrastructure will be an essential constituent of a large number of other projects, consortia, and Roadmap clusters, across the life sciences and data science, for instance Health-RI.
ELIXIR-NL plans to establish the ‘data backbone’ for Health-RI, the Dutch national infrastructure for personalised medicine & health research. To kick-start this, we have incorporated components of the BBMRI-NL Roadmap cluster (biobanking) and the MRI/cognition Roadmap cluster into our plans. These components will serve as key demonstrators for harmonisation of data approaches across the stakeholders of the ELIXIR-NL infrastructure.
Although the ELIXIR-NL infrastructure will initially be geared to empower personalised medicine and health research, the infrastructure will also serve as a backbone for the other life science communities that are active in ELIXIR-NL. We envisage a broad and scalable facility that will grow to support all data analytics and stewardship in the Dutch life sciences. Evidently, the ELIXIR-NL infrastructure will be strongly connected with the European ELIXIR infrastructure.
Sustainability of the infrastructure will be guaranteed first of all because a broad partnership of ‘users’ and ‘providers’ of data, tools, and compute resources will co-create the environment in a user-driven way. Secondly, productising tools when they reach a certain technology readiness level will be smooth, because industrial technology partners are fully engaged in the consortium, as users and providers. We will develop a pay-for-use model of selected services in the infrastructure, which will also sustain the core backbone on which the services run. A comprehensive business model for sustainability will be developed in the coming years.
The ELIXIR-NL Roadmap plans assemble strong Dutch data scientists and life scientists around a common goal. Please do not hesitate to contact us if you want to get involved in ELIXIR-NL.
- Vrije Universiteit Amsterdam
- Global leader in semantic web technology
- Specialisation: Data science and semantics
- Maastricht University
- Lead translational research in Radiation Biology
- Specialisation: Biomedical, clinical research
- University of Groningen
- Lead causal genetic factors of some hereditary diseases
- Specialisation: Human genetics
- Netherlands Cancer Institute
- Lead translational cancer research
- Specialisation: Pathology
- Innovator in healthcare specialised in neurodegenerative diseases and movement disorders
- Specialisation: Neurology, clinical research
- Max Planck Institute
- Lead functional neuroimaging
- Specialisation: Cognitive Neurosciences
- University Medical Centre
- Lead fundamental and translational magnetic resonance research in physiology and metabolism in a range of diseases
- Specialisation: Physical Chemistry, functional medical imaging research
- Wageningen University & Research
- Expert in epidemiology and human nutrition in amongst others Diabetes Mellitus, obesity, and cardiovascular diseases
- Nutrition and Health over the Lifecourse
- Wageningen University & Research
- Head of the Dutch nodes of the ISBE and IBISBA infrastructures (ESFRI)
- Specialisation: Systems & Synthetic Biology, Systems Medicine
- Specialisation: Information management / Medical Informatics
- Member of executive teams of EUDAT and EOSCpilot projects, former member of PRACE-IP executive team, lead of SURF Open Innovation Lab
- Specialisation: High Performance Computing
- BBMRI-NL and UMCG
- Lead and architect of MOLGENIS, core application in a 25fte research data and analysis support centre [GCC]
- Specialisation: Research data software development, biobank data integration
- Member of the internet hall of fame
- Specialisation: ICT Strategy
- Initiator of national XNAT web-service for storage of medical images in multi-center clinical studies
- Specialisation: Image repositories and image processing workflows
- LUMC, GO-FAIR, TU Twente
- FAIR Digital Object Architecture
- Specialisation: Ontology Engineering/Requirements Engineering
- Maastricht University
- Prime architect of distributed learning
- Specialisation: Distributed learning, Medical Physics
- Donders Institute
- Project leader of pilot project Donders Institute Research Data Management
- Specialisation: Technical Infrastructure
- VU University Medical Centre
- Prime architect of the Health-RI initiative
- Specialisation: Medical Informatics
- Maastricht University
- Driver of Open PHACTS, Co-founder of WikiPathways
- Specialisation: Bioinformatics
- Leads the Translational Research IT (TraIT) program (used by >3000 scientists in >300 projects) and the Data4lifesciences programs of the Dutch University Medical Centers)
- Integrator of Radboudumc multi-omics and clinical resources. Main applicant of the xOMICS roadmap proposal
- Specialisation: Personalised Healthcare
- The Hyve
- CEO and founder of a 30fte company providing development support for open source software)
- Specialisation: Open source
- Aridhia Informatics
- As Product owner/architect delivered DRE to Scottish, English and Dutch research communities as well as EU H2020/IMI consortia
- Specialisation: Digital Research Environment (DRE)
- Vrije Universiteit Amsterdam
- SBE; VICI laureate; Midterm Career Award (2014) from the Lactic Acid Bacteria Industrial Platform
- Specialisation: Systems Biology
The ELIXIR-NL Roadmap plans are rooted in a strong network of dedicated Dutch professionals that have been collaborating for nearly two decades. The following key infrastructures lay the foundation for the ELIXIR-NL Digital Research Infrastructure:
- ELIXIR-NL has its roots in the Dutch bioinformatics and computational (systems) biology community. Hosted by DTL, it constitutes the Dutch node in the ESFRI landmark ELIXIR. ELIXIR-NL has prepared a nationwide infrastructure for data interoperability, reference data, bioinformatics tools, training, and IT. ELIXIR-NL groups are the key driver of the global FAIR data initiative, delivering key infrastructure for data stewardship, from tools for software engineers to training for FAIR data stewards.
- SURF has developed high capacity storage, network, and computational infrastructures for all Dutch science & education organisations. SURF also coordinates the development of collective data stewardship policies and research support across Dutch research institutions. Together with BBMRI and CTMM/TraIT, SURF runs the national research support desk supporting professionally run installations of biomedical applications. SURF and NWO have jointly set up the Netherlands eScience Center (NLeSC) which develops and applies domain-overarching software and methods for the national scientific community, including computational workflows, FAIR and linked data, machine learning, and data visualisation.
- DRE, the Digital Research Environment, was developed at Radboudumc as a secure user-driven collaboration platform, bringing together data and tools for digital biomedical research projects. The DRE platform now supports a great variety of studies and is being piloted by all UMCs and several other research organisations.
- EuroCAT, at Maastricht UMC, has, together with industrial partners, developed advanced distributed learning technology at a global scale in over 25 hospitals from five continents using FAIR technology. This approach has enabled combined analytics when datasets cannot be shared (e.g., privacy sensitive datasets). This approach has inspired the development of the Personal Health Train
- The MRI/Cognition cluster assembles the five internationally outstanding centres in the Netherlands operating 7T MRI instruments as core of the very strong Dutch cognitive neuroscience and brain-imaging fields. These groups collect and process huge volumes of brain imaging data, with unique interoperability properties, advancing the international field both technically and scientifically.
- The BBMRI-NL cluster brings together over 200 biobanks, with expertise on managing biomedical samples and all associated data, including ~omics and imaging. It forms the national node in the BBMRI-ERIC ESFRI, where it plays an important role in the common IT infrastructure, with the setup and maintenance of the biobank catalogue, expertise on biobank data interoperability, and ELSI services for access to patient material and privacy-sensitive data.
- News item ‘ELIXIR-NL will coordinate data approaches of Dutch life sciences facilities‘
- Interview ‘Hans van Duijn’s view on the NWO Roadmap‘
- NWO’s press release about the Roadmap
- Roadmap brochure with list of selected facilities and clusters
- Website large-scale research infrastructures