Preparedness in the North of Europe – how our services support the battle against COVID-19

Photo: Hannu Mourujärvi/CSC

Preparedness in the North of Europe – how our services support the battle against COVID-19

In early 2020, a new disease spread rapidly around the world paralyzing the global economy and causing casualties in unprecedented scale; suddenly, services for managing and computing on sensitive human data related to this disease were in high demand.

Though we were not prepared for this disease as a society, the Nordic countries have been working together with their other ELIXIR colleagues on data services and tools for researchers to understand this viral infection affecting patients in our hospitals.

People up in the North of Europe still prepare for a bad day. As the summer fades away, our forests are full of people of all ages picking berries and mushrooms in order to prepare for the cold, dark, and ever so long winter. The vitamins from that harvest will help us to survive until the next summer. And there is nothing better than a shed filled to the brim with dry firewood as the snow starts to fall on us. Though our survival may not any more depend on the inventory of our wood shed or fully packed larder, our basic instincts still kick in year after year.

The modern Nordic person collects, processes and preserves also data as if it may indeed help us to survive. In ELIXIR, our responsibility is to build the required infrastructure to support our national researchers. Suddenly in the spring, we were asked if we had the infrastructure ready – the winter had fallen on us.  

Designing interoperable Nordic data services and the supporting infrastructure has not been an easy task. We started small by solving individual Nordic use cases, and during the journey we have mastered the challenges of implementing secure and scalable data management services that can also support connections to similar services across Europe, and beyond. The host organisation of ELIXIR Finland, CSC – IT Center for Science Ltd, is a traditional high performance computing centre for research. Our key insight was when we understood the close relationship between data and compute processes. Neither of them can fly alone.

In Finland, we have now implemented a completely new set of services for managing sensitive human data that have access to our computing environments. We look at this from the data life cycle point of view. Researchers need a service for each step of their research project, from data generation to data archival and data analysis. And mind the gap: in the future, both data itself and compute resources will need to be federated to support all the legal, ethical, and/or societal requirements.

As the data generation moves closer to healthcare, the number of data points increases rapidly and there will be a point of no return at the horizon. It does not help if you host the most powerful supercomputer if it cannot access the required data.

Two of the important pieces in our strategy are Federated EGA and ELIXIR Cloud. These are the services that are now being developed to manage genome-phenome data in a federated manner and for enabling computation on these data across Europe. At the heart of these new services are international standards, such as those developed within Global Alliance for Genomics and Health (GA4GH).

We have analysed the Nordic use cases to contribute to the development of these standards. We have also aligned the Finnish roadmap for the sensitive data management services with Europe-wide objectives and participated in deep collaborations with our Nordic colleagues to ensure that sufficient resources and competences exist for completing the work in the northern part of Europe.

For example, the Nordic e-Infrastructure Collaboration (NeIC) has facilitated the collaboration in the NeIC Tryggve project that supported Nordic collaboration at the European level with the other ELIXIR Nodes. I find it rather unique that we are able to put our own organisation’s objectives aside and work together towards common European goals, like we have been doing when building the EGA federation with our Nordic colleagues and EGA hosting organisations EMBL-EBI and CRG.
Coming back to this spring, I remember how everyone seemed to have urgent ideas on how to support the battle against COVID-19 pandemic. These ideas were not necessarily compliant with our ongoing work at ELIXIR Finland, nor did they align with our agreed priorities. We soon understood that changing the focus would cause significant delays to the development of the sensitive data services that were equally urgently needed by the Nordic researchers. Only by running an extra mile, we were able to contribute also to short-term goals, such as the ELIXIR COVID-19 Hackathon.

The Finnish Federated EGA service will soon be released to the wild and the collaboration with our Nordic colleagues continues in the new NeIC Heilsa “Tryggvedottir” project. We have also plans to integrate our national service with the new European COVID-19 Research Data Portal coordinated by the EMBL-EBI with tight links to ELIXIR. We work again with our European colleagues together within the ELIXIR-CONVERGE project to adapt our Federated EGA services on the COVID-19 research requirements. As the second wave of COVID-19 is now with us, it is good to remember that every winter will be followed by spring. 

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Juha Törnroos

Team lead at CSC – IT Center for Science and ELIXIR Finland