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European research community preparing for next pandemic

The aim of the BeYond-COVID project (By-COVID) is to make COVID-19 data collected in different European countries available to researchers, hospitals and public administrations. Identifying data, combining it from different sources and integrating it for analysis is a major undertaking, one that has been taken up by no fewer than 53 organisations from 19 countries.   The Finnish organisations involved are Tampere University and the Finnish Institute for Health and Welfare (THL). Data collected in Finland at THL has been processed in the CSC – IT Center for Science.

According to THL research professor Markus Perola, the By-COVID project is simply preparing for the next pandemic by analysing the COVID-19 data.

“We are now piloting how this kind of collaboration can be done when the next pandemic comes. This seems to be necessary.”

There is a genuine need for data harmonisation between European countries, Perola says.

“For instance, different countries may have very different ideas about what is considered essential in COVID infection chains.”

Perola uses CSC’s computing and sensitive data storage and analysis services for almost all his research. In addition to genetic data, he makes extensive use of register data. In the By-COVID project, his research team has used Finnish communicable disease registers and mortality data from Statistics Finland. The data will be used for joint analyses in the By-COVID project. THL’s raw data is available in CSC’s sensitive data services, but it is kept within Finland. The By-COVID project is also collecting information about the virus itself. This is open research data.

“THL is participating in one work package which involves federated analysis of register data from different countries. The project will extract specific issues from different registers and combine them to move towards a common analysis across Europe.”

The register data collected from Finland includes all Finnish residents who have a personal identity code.

According to Perola, it is necessary to collect and analyse this kind of data. In his view, it would be unethical not to use the important data that is collected on European citizens.

“Why collect data if you’re not going to use it? Statistics are important, but they’re enough to translate the information into clinical work or social policy-making. This requires peer-reviewed scientific research, and that is what By-COVID provides.”

The project will end in autumn 2024.

COVID-19 portal

 

A portal with COVID-19 data is available on the By-COVID project website. The project is coordinated by the ELIXIR infrastructure, whose member organisation EMBL-EBI has compiled the main coronavirus datasets on the portal. Researchers can use the portal to analyse the COVID-19 reference data. It contains more than 8 million COVID sequences.

The Research council of Finland funded the Finnish ELIXIR Node’s CSC experiment, where data from the CSC portal was analysed and tested on the Finnish LUMI supercomputer. The work supports the By-COVID project: an important role of the CSC is to promote the use of supercomputers in data-intensive computing.

According to Tommi Nyrönen, Director of the ELIXIR Finland node, the project overcame many of the technical challenges of data management.

“Computational work at the EMBL-EBI European Bioinformatics Institute enabled the analysis of the COVID-19 viral data, and this work was done in collaboration with experts from the CSC and EMBL-EBI. With European supercomputing, we can now transfer hundreds of thousands of virus data points daily between computing centres with the help of European research networks.”

As a result, the capacity of a supercomputer will be needed in the future to analyse all the data.

“This is essential for a rapid response in the event of a new pandemic, and also to update the data available on the COVID-19 portal.”

 

Ari Turunen

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FIRI

Article was supported by the Research council of Finland grant No: 345591 for ELIXIR European Life-Sciences Infrastructure for Biological Information (FIRI 2021)

CSC – IT Center for Science

is a non-profit, state-owned company administered by the Ministry of Education and Culture. CSC maintains and develops the state-owned, centralised IT infrastructure.

https://www.csc.fi/en/

https://research.csc.fi/cloud-computing

 

ELIXIR

builds infrastructure in support of the biological sector. It brings together the leading organisations of 21 European countries and the EMBL European Molecular Biology Laboratory to form a common infrastructure for biological information. CSC – IT Center for Science is the Finnish centre within this infrastructure.

https://www.elixir-finland.org