High-level research infrastructures support COVID-19 research

Scientists and researchers are hard at work on solutions to overcome the COVID-19 disease and to manage the effects of the coronavirus pandemic. This requires ready access to good research infrastructures: tools and equipment, data networks and databases, and open access research materials and services that facilitate research and promote research collaboration.

The coronavirus pandemic has shown that even in exceptional circumstances, it is possible to mount an effective response – provided that competent staff and the necessary international and national preparedness are in place. The foundation for this lies in the long-term development of research infrastructures. Indeed, research infrastructures funded by the Academy of Finland are crucial to the science community ’s efforts to understand the characteristics of the SARS-CoV-2 virus and the effects of the epidemic.

How have these research infrastructures been used during the corona pandemic, and how will they be used in different fields of science and research as we move forward? We are publishing a series of short pieces to shed light on these questions.

High-performance computing (HPC) supercomputers harnessed to support COVID-19 research

During the coronavirus pandemic both academic research and tuition have largely moved online. The data network for universities and research in Finland, Funet, is operated by CSC - IT Centre for Science. The role of the company is to ensure that there is adequate network capacity for all users and that licences for web conferencing, for instance, are set up.

“You could say we’re providing a kind of security of supply service,” says CSC Managing Director Kimmo Koski. “We have a sound foundation for IT services and infrastructure, and we’re well prepared to operate in exceptional circumstances.”

The investments made over time in building a fault-tolerant and reliable communications environment have certainly paid off: “The network has held up to the massive surge in user demand, and we’ve been able to quickly solve any emerging problems,” Koski continues.

CSC is also involved in several European corona research projects. It has made prioritised computing capacity available for research purposes and for official studies related to the COVID-19 epidemic. Furthermore, CSC gave researchers access to its supercomputer Puhti at very short notice. Thanks to the high computing capacity and close multidisciplinary cooperation, the first results were obtained within about one week.

“COVID-19 projects have used about one-third of the capacity of our supercomputer, and at times up to around one-half of total capacity has been in use. For instance, the computer has been used in a joint modelling project involving four Finnish research organisations, in which the focus is to investigate the airborne transmission of the coronavirus,” Koski explains.

CSC is currently working to give researchers the tools they need to work even faster and with better models. One of the world’s most powerful supercomputers, the EuroHPC pre-exascale supercomputer LUMI will be installed in CSC’s Kajaani datacentre. An exceptionally large pan-European investment, the new supercomputer is scheduled to go live in early 2021.

“LUMI offers a vast amount of computing capacity for simulations, the use of AI methods and heavy data analytics within the same system. What’s more, the supercomputer’s user and resource management are designed by default to support multinational research projects,” Koski says.

Via the ELIXIR node (European Life Science Infrastructure for Biological Information) operated by CSC, the company is also involved in building the COVID-19 data portal launched by the European Commission and the EMBL’s European Bioinformatics Institute.

“The aim is to create a computing environment where it is possible to analyse not only publicly available molecular biology information about the virus pathogen, but also sensitive genome data about the human host organism, for example. The findings and outcomes will have a direct effect among others on healthcare decision-making,” Koski concludes.

Read more:

• Open access and storage of research data must be ensured even in exceptional times
• International infrastructure services for molecular biology and bioinformatics support coronavirus research
• Imaging technologies play key part in virus research: Finland has cutting-edge expertise
• Virus vector laboratory applies gene transfer technology to tackle corona pandemic