November 25, 2020

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DOST-ASTI’s supercomputing enabling Philippine COVID-19 research

The pandemic has caused widespread devastation across the world with cases inching towards 43 million even as the death toll crosses a million. The Philippines is also struggling to deal with the COVID-19. The country has recorded 370 thousand cases with fatalities touching 7,000 in this last week of October.

Researchers across the world are working ceaselessly to try and get a comprehensive picture of the virus, its epidemiology and management. Such large-scale, glocal research has been made possible with supercomputing facilities that can perform high-speed processing and computations.

Wide interconnectivity and global reach give it the capacity to empower multi-disciplinary efforts in medical and health research across facilities and experts spread across wide geographical areas. The incredible processing and analytic powers drive advancements in the development of treatments, vaccine and management of all diseases and pandemics, such as the COVID-19. Supercomputing facilities can process massive amounts of data, speed up simulations and provide large amounts of space need to store data and analytics. These capabilities allow access to virtual machines, massive cloud applications and coordination on a global scale – produce results a thousand times faster.

The Computing and Archiving Research Environment (COARE) is a supercomputing facility at the Department of Science and Technology-Advanced Science and Technology Institute (DOST-ASTI). The facility provides free services to researchers, scientists and students who need high computational resources, access to virtual machines and data archiving services. Currently, COARE has allocated its resources to institutions and researchers dedicated to dealing with COVID-19.


Developed by the Ateneo de Manila University’s Ateneo Center for Computing Competency and Research (ADMU-ACCCRe) and in collaboration with the University of the Philippines Manila-National Telehealth Center (UP-NTCH) and the Department of Health-Epidemiology Bureau, the Feasibility Analysis of Syndromic Surveillance using Spatio-Temporal Epidemiological Modeler (FASSSTER) is a pandemic intelligence monitoring that assists the government’s real-time decision-making processes for COVID-19.

FASSSTER’s data warehouse features multiple modules used for collating, storing and filtering real-time information sourced from various health records and reports. Data from the warehouse is fed to a dashboard that produces analytical projections and computations that help decision-making processes and disease response.

One component and data source of FASSSTER is TanodCOVID, which helps people track and monitor COVID-19 symptoms and report it to their local health authorities through a self-reporting tool. Since March 2020, the COARE facility has been of crucial help to FASSSTER and TanodCOVID, providing access to its virtual cloud services to help them in their complex mathematical models and data warehouse needs.

COVID-19 Operations Center Monitoring System

The COVID-19 Operations Center Monitoring System is a data platform used by Local Government Units to help in management, tracking and monitoring of COVID-19 cases. The system consolidates COVID-19 data that is easily viewed on a dashboard. It includes visualisation features like heat maps and charts for monitoring at the municipality up to the barangay level and modules for encoding patient information and assigning patient records for contact tracing. COARE assists this platform by storing and analysing data through virtual servers.

Philippine Genome Center Research Initiatives

The Philippine Genome Center (PGC) of the University of the Philippines-Diliman is a genome-focused institution that currently prioritising research on COVID-19 – centred on phylogenetic analysis, computational studies, evolutionary analysis, molecular biology and in silico detection of COVID-19. COARE supports PGC by providing researchers access to the facility’s supercomputing services.

Folding@Home Project

Folding@Home is an R&D project that helps combat worldwide diseases through research carried out through distributed computing. From March 2020, COARE offered its supercomputing resources to F@H research efforts by installing a dedicated folding node. Through this node, the project was able to utilise COARE’s resources for computational drug design, protein folding, molecular dynamics, and other COVID-19-related computer simulations.

University of the Philippines Cebu’s CovCheck Application

The Department of Computer Science and the FireCheck team of the University of the Philippines Cebu is developing a web application, CovCheck, that enables Local Government Units to manage and respond to the transmission of COVID-19 through the collection of data from constituents who have self-assessed and self-reported for COVID-19 symptoms. At present, COARE has helped by hosting the web application on its virtual servers.

ACCELER8 Project for SARS-CoV-2 Therapeutics

Faculty members and scientists from the University of the Philippines-Manila, Philippine Genome Center-Mindanao, and De La Salle University Manila are working on a research project – Advancing Antivirals through Combined Computational Design and Emerging Omics to Leverage Repurposed and Natural Drugs for SARS-CoV-2 Therapeutics (ACCELER8). COARE has given ACCELR8 researchers access to its supercomputing services to help them conduct simulations and data analysis on computational drug design and omics.