How DOST-ASTI’s Supercomputing Facility aids in advancing COVID-19 research initiatives
Science research specialists at the supercomputing facility of DOST-ASTI.
The number of global deaths due to the Novel Coronavirus-2019 (COVID-19) has surpassed a million by the end of September 2020. In the Philippines alone, the Department of Health (DOH) has recorded a nationwide death toll of more than 6,000 as the second week of October rolled in. The unceasing efforts of researchers worldwide in understanding the COVID-19 virus and its epidemiology have been continuously supported by supercomputing facilities that can perform high-speed processing and computations.
In essence, a supercomputing facility is a cluster of computers with the power to process massive amounts of data, speed up research simulations, and provide large amounts of storage space. Such facilities also enable access to virtual machines which can be utilized for cloud-computing. Compared to a regular PC, a supercomputing facility could produce research results a thousand times faster. One of its most notable capabilities is its potential to aid discoveries in multi-disciplinary fields, including medical and health research. Such facilities could initiate advancements in the development of treatments and in the pursuit of researchers to learn more about viruses, such as the COVID-19.
The Computing and Archiving Research Environment, better known as COARE, is a supercomputing facility established in 2014 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 for their research projects. Currently, COARE has allocated its resources to institutions and researchers who are dedicated to uncovering the nature of COVID-19.
The COVID-19 dashboard of FASSSTER. Photo source: DOST-PCHRD
FASSSTER and TanodCOVID
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 platform utilized to guide the government’s real-time decision-making processes for COVID-19.
FASSSTER, which was officially turned over to the DOH on September 2020, aids national government agencies, Local Government Units (LGUs), and the Inter-Agency Task Force on Emerging Infectious Diseases (IATF) in making interventions and implementing programs to address COVID-19 cases in the country. FASSSTER has a fast and secure data warehouse that features multiple modules used for collating, storing, and filtering real-time information sourced from various health records, reports, and parameters. Authorized data from the warehouse are then fed to a dashboard that produces analytical projections and computations that can help with the government’s disease response and decision-making processes.
One component and data source of FASSSTER is TanodCOVID, which helps people track and monitor their 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 developed for Local Government Units to help them in the management, tracking, and monitoring of COVID-19 cases. The system consolidates COVID-19 data LGUs can easily view through a convenient dashboard. It includes visualization 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 has assisted the COVID-19 Operations Center Monitoring System in storing and analyzing their data through the provision of virtual servers.
The Philippine Genome Center at UP Diliman. Photo Source: PGC
Philippine Genome Center Research Initiatives
The Philippine Genome Center (PGC) of the University of the Philippines-Diliman is a genome-focused institution that currently prioritizes research pursuits on COVID-19. COARE has given support to the PGC by providing its researchers access to the facility’s supercomputing services. Currently, the PCG’s activities are centered on phylogenetic analysis, computational studies, evolutionary analysis, molecular biology, and in silico detection of COVID-19.
Folding@Home is an R&D project created to help combat worldwide diseases through pioneering research pursuits carried out through distributed computing. From March to August 2020, COARE volunteered to allocate its supercomputing resources to the COVID-19 research efforts of Folding@Home by installing and delegating a folding node for the project. Through this node, Folding@Home was able to utilize COARE’s resources for their computational drug design, protein folding, molecular dynamics, and other COVID-19-related computer simulations.
The COVID-19 web application of UP Cebu’s CovCheck. Photo Source: CovCheck
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 called CovCheck. The web application 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 UP Cebu’s CovCheck by hosting their web application in the virtual servers of COARE.
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 called ACCELER8, or Advancing Antivirals thru Combined Computational Design and Emerging Omics to Leverage Repurposed and Natural Drugs for SARS-CoV-2 Therapeutics, in an effort to contribute to the fight against COVID-19. COARE has given ACCELR8 researchers access to its supercomputing services to help them conduct simulations and data analysis on computational drug design and omics, that are supported by in silico and in vitro screening.
As the COVID-19 virus continues to ravage the world through the rise of the global death toll and the emergence of new cases, the support of supercomputing facilities such as COARE and the relentless pursuit of researchers are helping shed light to our understanding of the virus—one research project at a time.
Have questions about our supercomputing facility? For more information about the Computing and Archiving Research Environment, you may visit our wiki and Facebook. You may also send us an e-mail at firstname.lastname@example.org.
The Computing and Archiving Research Environment (COARE) is one of the services offered by the Department of Science and Technology’s Advanced Science and Technology (DOST-ASTI) that fosters collaboration among institutions by enabling multiple data integration between ASTI-initiated projects and other collaborative projects with other agencies that have high requirements for data storage and high-performance computing. The COARE facility provides a platform for easy storage, analysis, and sharing of scientific data by providing the following services: High-Performance Computing (HPC), Science Cloud, and Data Archiving.