BSC research on COVID-19

The Barcelona Supercomputing Center’s (BSC) team is working from home to maintain the center’s research activity and the support for users of our supercomputing infrastructures. As an example, our fusion group continues working in the search of a clean energy using online meetings to coordinate and share the work.

The aim of this post is to discuss the numerous ways in which our center is devoted to the fight against coronavirus including new research projects that have been started related to it. Also, it will highlight external investigations aimed at fighting the pandemic which have been granted priority access to the MareNostrum 4 supercomputer and other BSC infrastructures.

Understanding how the virus is transmitted and the mechanisms it uses to interact with our immune system and the immune system of other species is crucial when looking for treatments and also for the prevention and prediction of eventual future outbreaks. This study is carried out on data available in public databases that house genomic sequences of the different virus mutations and animal species. The information is analysed with computer programs specifically designed for it, some developed in the BSC itself and others by other teams. The processing of these data requires great computational capacity and therefore the high-performance computing resources of MareNostrum 4 supercomputer are used.

Another important aspect is the search for treatments with the process known as “docking” that consists in simulating in the computer the interactions between the virus and the molecules that could be used to make vaccines, antibody treatments or drug treatments. To carry out this process, the researchers use the knowledge generated in the research of the virus genome, information on the structures of its virus proteins and data on drugs and other inorganic molecules, which are stored in computer libraries that contain millions of chemical compounds and the results obtained in previous experiments, collected over years by the scientific community.

The computer search is very helpful in speeding up the process of finding and validating disease treatments and vaccines, as it greatly cuts the time and investment required for the first phase of this research. Any treatment or vaccine that computer models predict may be successful must subsequently be validated in experimental laboratories, animal testing, and clinical research, and refined in constant collaboration between different research participants. In the case of BSC, the researchers use different computer programs, including the in-house PELE molecular interaction modelling software.

Fusion group online meeting (#BSCatHome).

Currently, there are two projects that channel the research carried out at BSC on the coronavirus and its possible treatments: EXSCALATE4CoV (E4C) focused on the search for drugs, funded by the European Commission under the H2020 program, and a collaborative project with the centres of research IrsiCaixa and CreSa-IRTA which is focused on the search for immunological therapies supported by genomic research and bioinformatics tools.

BSC’s High Performance Artificial Intelligence (HPAI) research group collaborates with UNICEF and IBM on a project that aims to analyse the socioeconomic impact of the virus locally and globally, with an emphasis on social distancing. The goal is to find impact indicators, patterns and statistics that serve the UN and local authorities to take better and faster measurements. The group that carries out the project is currently made up of about 40 people from eight different countries, and focuses on the cases of three cities: New York, Tokyo and Barcelona. HPAI leads the case of Barcelona.

Furthermore, the BSC user support service is assisting the Government of Spain and the Generalitat in screening public purchase contracts to locate medical equipment (especially respirators) acquired by centres that are not dedicated to health care and that may be susceptible to be transferred to health centers. In total, more than 850,000 documents have been screened using big data technologies and the service is still on-going.

Another collaboration is the project performed with the Hospital Universitario 12 de Octubre and with the Hospital Clínic Barcelona for the development of methodologies with natural language processing for the analysis of clinical reports of those affected by COVID-19.

In our BSC department of Computer Applications in Science and Engineering (CASE), a group of researchers has collaborated with the adaptation of the infectious diseases simulator Epigraph, to the characteristics of COVID-19 to simulate the spread of the current pandemic in Spain. The adaptation has been done with the supervision of the National Center for Epidemiology (CNE) and the Consortium Center for Biomedical Research Network (CIBER).

Further external projects to which the BSC provides infrastructure and user service support include the following:

  • Hosting of a chest X-ray medical imaging data set to collaborate in the development of open-source artificial intelligence tools to aid the early detection of COVID-19 infection and pneumonia. The data set has been prepared by the Bioinformatics and Statistics Unit of the Príncipe Felipe Research Center.
  • Molecular dynamics and sequence design simulations for the optimization of antibodies against SARS-COV-2. Collaboration between researchers from the Physics-Chemistry Department of the University of Barcelona at the National Center for Biotechnology and the University of Edinburgh.
  • The University of Valencia (UV) will use 23.3 million processor hours of MareNostrum 4 to simulate the chemical reactivity of the SARS-COV-2 protease and obtain information that helps design drugs that are useful for inhibiting it and, therefore, prevent the virus from replicating.

The UV has obtained access to MareNostrum 4 through the PRACE COVID-19 Fast Track Call, an extraordinary procedure by which the most powerful public supercomputers in Europe have been made available to research on COVID-19, which are included in the European infrastructure PRACE.

It is important to note that the PRACE COVID-19 Fast Track Call is open until further notice. Applications are evaluated within one week and start as soon as possible when awarded. This call applies, among others, to the following topics:

  • Biomolecular research to understand the mechanisms of the virus infection
  • Bioinformatics research to understand mutations, evolution, etc.
  • Bio-simulations to develop therapeutics and/or vaccines
  • Epidemiologic analysis to understand and forecast the spread of the disease
  • Other analyses to understand and mitigate the impact of the pandemic

We hope that this post has given you an idea of the numerous ways in which our center  is working together with the local and global scientific community to fight against COVID-19 pandemic and to return to normality as soon as possible.

In the meantime, do take care of yourself to take care of all!

Source: BSC news

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