BSC Uses Bioinformatics, AI, and Marenostrum Supercomputer in Fight Against COVID-19

April 1, 2020

April 1, 2020 — Barcelona Supercomputing Center (BSC) collaborates in the fight against the coronavirus from different areas: the application of bioinformatics for the research on the virus and its possible treatments, the use of artificial intelligence and natural language processing to analyze the data about the spread and impact of the pandemic and the use of the MareNostrum 4 supercomputer to enable the fight against the coronavirus.

Image courtesy of BSC.

Bioinformatics to search for treatments

From the bioinformatics side, the BSC is an example of how bioinformatics and supercomputers are nowadays an indispensable tool for research centers that have experimental laboratories to accelerate the fight against the coronavirus. Bioinformatics is used for research on the virus and its possible treatments, analyzing the coronavirus genome and its successive mutations, and searching for drugs and immune therapies (antibodies and vaccines).

Genomics

Understanding how the virus has evolved through different epidemics (such as the SARS epidemic in 2003, MERS in 2012, or the current COVID-19) is important because it allows us to understand how it is possible for the virus to pass from one species to another and what changes it has to undergo to make possible this transmission. It sheds light on the virus mode of transmission and the mechanisms it uses to interact with our immune system and the immune system of other species. This is crucial when looking for treatments and 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 analyzed 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, hosted and managed by Barcelona Supercomputing Center, are used.

Search for treatments

Another important aspect is the search for treatments against the diseases caused by the coronavirus, including simulations that reproduce in silico the possible routes that can be exploited to attack this virus.

This process is known in research as “docking” and 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.

Computer search or drug screening 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.

To carry out this work, researchers at the BSC use different computer programs, including the PELE molecular interaction modeling software developed at BSC. This software and the power of the MareNostrum 4 supercomputer enable thousands of computational experiments to be performed optimizing the binding of drugs and proteins in a fast and effective way.

At the BSC, research on the virus and its possible treatments are carried out in close collaboration between the groups of Alfonso Valencia, ICREA researcher, director of the BSC Life Sciences Department and leader of the Computational biology group, Víctor Guallar, also ICREA researcher, head of the Electronic and atomic protein modeling team and maximum promoter of the PELE software and Toni Gabaldón, ICREA researcher and head of the Comparative genomics group. All of them work in cooperation with the BSC operations team, who are in charge of providing them with the computational resources needed.

Currently, there are two projects that channel the research carried out at BSC on the coronavirus and its possible treatments: EXSCALATE4CoV (E4C), funded by the European Commission under the H2020 program, and a collaborative project with the centers of research IrsiCaixa and CreSa-IRTA.

E4C especially emphasizes on basic and applied research to search for drugs while the collaboration with IrsiCaixa and CreSa-IRTA is more focused on the search for immunological therapies supported by genomic research and bioinformatics tools.

Artificial intelligence to analyze the spread and social impact of the pandemic

BSC’s High Performance Artificial Intelligence (HPAI) research group collaborates with UNICEF and IBM on a project that aims to analyze 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.

The same team of BSC’s artificial intelligence experts collaborates with Mexican researchers and other researchers at the center in the creation of a data collection and analysis system to assist in decision-making to deal with COVID-19, which expansion is found there, still at a fairly early stage. The project is carried out in collaboration with Mexico City, Nuevo León and Jalisco: http://dash.covid19.geoint.mx/

MareNostrum 4 and users support

The MareNostrum 4 supercomputer, which despite the current circumstances is still in full operation, provides the necessary computational capacity to accelerate ongoing investigations against the coronavirus.

The BSC’s Department of Life Sciences is using it for its own research, but the center also made it available to research teams or external entities that need high-performance computing for their research against the coronavirus.

The BSC Operations Department provides support in the use of the MareNostrum 4, both to internal and external researchers.

About BSC

Barcelona Supercomputing Center-Centro Nacional de Supercomputación (BSC-CNS) is the national supercomputing centre in Spain. The center is specialised in high performance computing (HPC) and manage MareNostrum, one of the most powerful supercomputers in Europe, located in the Torre Girona chapel. BSC is involved in a number of projects to design and develop energy efficient and high performance chips, based on open architectures like RISC-V, for use within future exascale supercomputers and other high performance domains. The centre leads the pillar of the European Processor Project (EPI), creating a high performance accelerator based on RISC-V. More information: www.bsc.es


Source: Barcelona Supercomputing Center

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