Dutch computing power in the battle against corona

All over the world people are joining forces in the hope of quickly developing a vaccine for the corona virus and a cure for COVID-19. ODISSEI partner SURF is contributing to this by giving researchers accelerated access to high-quality computing facilities and data services. SURF also supports numerous other research initiatives.

Recently, tech giants such as IBM, Amazon Web Service, Google Cloud, Microsoft and the U.S. Department of Energy gave scientists access to their supercomputers to accelerate research related to the COVID-19 virus. Closer to home, scientific research is also supported with extra computing power. The Flemish Supercomputer Centre (VSC), for example, will make their supercomputer BrENIAC available for research into COVID-19 in the next eight weeks, and similar initiatives are now being launched in France, Finland, Germany and Ireland.

SURF and NWO ensure fast access

SURF contributes to accelerating research into the corona virus by giving researchers and research groups accelerated access to, among other things, our advanced high performance computing (HPC) facilities.¬†All corona-related research can start¬†within a few days with the help of a ‘fast track grant’. We do this in collaboration with the Netherlands Organisation for Scientific Research (NWO).

This accelerated procedure applies to all SURF facilities and services, including the national supercomputer Cartesius, the Lisa computing cluster, high-throughput data processing, HPC Cloud, and customised cloud solutions such as Kubernetes. For each of these facilities, the necessary storage and assistance in setting up the software and technical expertise can also be requested.

How to apply?

Researchers can apply directly via: surf.nl/en/coronavirus-and-surf/covid-19-fast-track-for-computing-time-call. Contact helpdesk@surfsara.nl if you need any help and mention ‘COVID-19 Fast Track’. Describe in the proposal how your work will contribute to research on corona and possible virus control. Applicants who receive funding are expected to publish their results open access.

Other activities

Open Access

In addition to accelerating the availability of computing capacity, storage, and expertise, SURF is directly and indirectly involved in numerous other activities relating to corona research. For example, a page has been set up on Openaccess.nl with tips for making papers and research results openly available and for finding and enriching open research information about COVID-19. SURF is working on this as part of the National Open Science Programme. The information on this page is updated daily.

More information: Melanie Imming, melanie.imming@surfsara.nl

Folding at Home

Folding@Home (F@H) allows everyone to use his or her home computer to study the structure of the corona virus and find out how the virus binds to human cells. The only thing interested people have to do, is to download an app from the F@H website. In support of the Folding@Home initiative, SURF also makes compute time available on advanced GPU processors.

More information: Nuno Ferreira, nuno.ferreira@surfsara.nl

FAIR Data Points 

SURF has for many years advocated the Findable, Accessible, Interoperable, Reusable (FAIR) principle as a guideline for the management of scientific data. In order to also be able to use machine learning and artificial intelligence to detect patterns in epidemic outbreaks, it is very important that data is made available in accordance with the FAIR principles. Together with GO FAIR and other national and international partners, we are working on a network of FAIR Data Points (FDPs) to make data on COVID-19 and other virus outbreaks available for research quickly and in the appropriate formats.

More information: Hylke Koers, hylke.koers@surfsara.nl

Pattern recognition via AI

Artificial Intelligence (AI) can be used to recognise fixed patterns in X-rays and CT scans. The SURF Machine Learning team has experience in developing AI applications for detecting pneumonia and other lung diseases on X-rays. Currently, this team is working on the development of two separate AI models: one for detecting COVID-19 patterns in X-rays and one for detecting in CT scans. In the development of the AI models, we will make use of open data and link up with similar national initiatives.

More information: Thomas van Himbergen, thomas.vanhimbergen@surfsara.nl and Valeriu Codreanu, valeriu.codreanu@surfsara.nl.

Quantum chemical calculations on Cartesius

Finding inhibitors for COVID-19 is, given the current global situation, of great importance.  There are already studies leading to potential inhibitors, but more details are needed to further develop an efficient design strategy for powerful inhibitors. SURF is supporting a project by Remco W.A. Havenith and employees of the Stratingh Institute for Chemistry (University of Groningen) with quantum chemical calculations on various potential inhibitors.

More information: Ana da Cunha, ana.dacunha@surfsara.nl

View actual information on SURF and Corona.