Nordic e-Infrastructure actions against COVID-19
The COVID-19 pandemic is impacting every corner of the world at scales previously unimaginable. It is becoming increasingly clear that an international crisis at this scale demands international solutions, and collaboration across borders is a vital necessity in the fight against the virus. In the Nordic and Baltic region, providers of e-infrastructure are getting engaged in the fight against the pandemic to support in the ways they can. For example, when researchers are conducting research on the coronavirus, they need access to data and computing resources. National providers of e-infrastructure services in the Nordic and Baltic region have been quick to respond to these various needs and challenges by for example giving prioritised access to their High Performance Computing resources for COVID-19 research. At NeIC we celebrate this supportive action, and have collected an overview over some of the supportive measures taken by our partners across the region.
In Finland the national provider of e-infrastructure, CSC - IT Center for Science Ltd., offers compute and data services for COVID-19 data analysis. It has opened a priority lane facilitating coronavirus research and provides access to supercomputing and management of data across national borders. The intention is to provide researchers with access to CSC’s compute and data resources and enable them to leverage modern Cloud and HPC computing environments. This is done as part of ELIXIR’s coordinated response to the COVID-19 pandemic.
COVID-19 gets priority on all CSC’s compute resources, and more than 10 projects studying various aspects of COVID-19 have already indicated a need for the resources made available by CSC. One of these is a larger study between Aalto University, the Finnish Meteorological Institute, VTT Technical Research Centre of Finland and the University of Helsinki. These partners have brought together a multidisciplinary group of researchers to model how the extremely small droplets that leave the respiratory tract when coughing, sneezing or talking are transported in air currents. Dozens of researchers are involved, ranging from fluid dynamics physicists to specialists in virology, medical technology and infectious diseases. The project will model the coughing of a person moving around indoors. For the modeling work, the researchers are using a supercomputer that CSC has made available at very short notice. You can find more information about the study here.
SNIC, the national provider of e-infrastructure in Sweden supports initiatives for COVID-19 related research by offering special access to High Performance Computing resources for these initiatives. So far there are three projects on SNIC resources regarding COVID-19.
The Swedish SciLifeLab is also active in supporting COVID-19 research in mainly two ways. The first is a programme focused on testing the SARS-Cov-2 virus. Knut and Alice Wallenberg Foundation announced a 50 MSEK donation to academic laboratories at SciLifeLab, Karolinska Institutet and Uppsala University with the aim of contributing to the scale-up of testing and diagnosis of the corona virus disease COVID-19. The second part, the SciLifeLab Open Call for Proposals, is a call launched nationwide by SciLifeLab. The aim is to create a comprehensive national program to combat the corona epidemic. Proposals should focus on coordination of samples, studies and data; technology development; or research projects. See more information here.
In Denmark the National Lifescience Center (and its supercomputing centre Computerome) together with the Danish National Genome Center (NGC) are coordinating the activity surrounding COVID-19 on the national level. They have set up a dedicated e-infrastructure to analyse the data and monitor the situation.
Also, several ELIXIR Denmark members are involved in collaborative projects analysing data from Danish clinical COVID-19 samples and from existing biobanks matching those samples. In addition to this, they are also trying to gather information on tools and workflows of interest related to COVID-19. You can find a collection of these here.
The Estonian national e-infrastructure provider, ETAIS (University of Tartu (UT)), together with the Estonian node of ELIXIR are facilitating studies related to COVID-19. The server koroona.ut.ee hosts a survey for the general public on the spread of the coronavirus including disease symptoms, confirmed diagnoses and contacts to the infected. In addition to the survey the server also hosts a variety of Coronavirus analysis tools.
As part of ELIXIR’s coordinated response to the COVID-19 ETAIS has set up a Graphical User Interface dashboard to bring the SARS-CoV-2 sequence data analysis to lab scientists and is providing priority access to HPC resources as required.
Because of the pandemic the hospitals are currently not performing routine ultrasound scans for pregnancies. The Estonian state has provided funding for prenatal genome screening. ETAIS/ UT is providing compute resources for the private company doing the noninvasive antenatal lab tests.
The Norwegian e-infrastructure provider, Sigma2, is prepared to give expedited access to resources for work related to combating COVID-19 and the immediate consequences of it. This includes access to HPC for data of sensitive as well as non-sensitive nature. At present Sigma2 is not aware of any research groups within Norway that could effectively use access to resources. However, Sigma2 is prepared to respond immediately if needed. Interested researchers are encouraged to contact Sigma2 at firstname.lastname@example.org. For more information please read here.
The Norwegian national eInfrastructure for research on sensitive data, Tjenester for Sensitive Data (TSD), hosts three different COVID-19 research projects at the moment. The most prominent one is www.koronastudien.no (the Corona Study) by Oslo University hospital. Here more than 100.000 persons in Norway have consented to their data on Corona being extracted from patient records subsequent to and during a possible future hospitalisation due to Corona.
Also, the Norwegian node of ELIXIR will collaborate with the National Institute of Public Health (NIPH/FHI) and other institutions that are sequencing and analysing SARS-CoV-2 within the Norwegian population, aiming to make data available for the research community.
The priority in Tryggve2 is Nordic sensitive data management, including e-infrastructure that gives the possibility to share cross-border data without compromising data privacy. Several Covid-19 studies will, apart from SARS-CoV-2 sequence and molecular data, also contain sensitive human data such and genome sequences, epidemiological data as well as patient-related phenotype data combined with the virus sequence data. All these human data need to be stored in a secure manner compliant to GDPR, and made accessible via controlled access for national and cross-border access. For this purpose, the federated EGA technology has been in development in The Nordic countries with the support of Tryggve2 and Nordic ELIXIR nodes to enable this process. It is therefore important that the ongoing work on federated EGA development and establishment of the Nordic EGA nodes is intensified in the light of the Covid-19 pandemic.
Within the last week, Tryggve also received six new use case proposal for integrations across the healthcare data space. One of these proposals was selected and already indicated to be possible at least in the Nordic setting, and is in line with European goalsetting, and the global COVID-19 hackathon.
At a Nordic scale, NeIC is discussing possible activities in response to the COVID-19 crisis from a Nordic perspective. Some examples of such activities are:
1) Obtaining access to all Nordic sequence data available in gisaid.org (Global Initiative on Sharing All Influenza Data) and developing a resource to undertake evolutionary mapping of all available data. This could be used as a backbone to facilitate further samples to be mapped and analysed in the context of Nordic strains, and to also map Nordic interchanges.
2) Using open source tools for transparent, reproducible analyses of viral datasets.
3) Ensuring secure cloud infrastructure for sharing and analysing COVID-19 datasets that allows the users to bring and enhance the analyses with their own data and tools.
4) Assisting in setting up FAIR data points for the accessibility of content on regional, national or local scale. Patient journal data can be shared using FAIR data points to enable access and analysis of (sensitive) data across multiple sites via local / national FDPs that can be accessed without data leaving the institution or country.
5) TSD is today used to collect consents to extract patient journal data for those of the respondents that will be hospitalised due to COVID-19. The study utilizes the TSD digital dynamic consent form, which could be used also in other Nordic countries. This would enable the same very rapid and digital collection of consents and questionnaires within the Nordics, giving larger cohorts and better data.
These are just a snapshot of the many creative ideas and suggestions that have been proposed to us, where NeIC could take a coordinating role on behalf of the Nordic countries. NeIC is currently looking into ways in which we could help our Nordic partners better in their support for COVID-19 research. Watch this space for further information regarding new NeIC initiatives responding to the COVID-19 crisis in the time to come.