Department of Science and Technology’s COARE Supercomputing Facility continues to support Covid-19-centric initiatives

It has been more than a year since the COVID-19 pandemic devastated the world, affecting the global economy and altering lives. The Philippines was not spared, and the nation has been hit hard. With the virus claiming more than 20,000 lives and the total number of cases is still climbing past the one million mark, there is a need to intensify our efforts in battling this highly infectious disease.

Since March 2020, the Computing and Archiving Research Environment (COARE), the supercomputing facility housed at the Advanced Science and Technology Institute of the Department of Science and Technology (DOST-ASTI), has been instrumental in expanding our knowledge about the virus. Through the continuous allocation of its supercomputing resources, the facility did not only aid a plethora of research institutions in their high-computing and data storage needs, but it also helped propel the nation’s collective efforts to shed light on COVID-19.

Here is a look at how COARE’s supercomputing facility contributed to the efforts of the  government and research institutions regarding their COVID-19-centric research initiatives from the dawn of the pandemic up to the present.

Feasibility Analysis of Syndromic Surveillance using Spatio-Temporal Epidemiological Modeler (FASSSTER) for LGU Epidemiology Surveillance Units

FASSSTER was officially turned over to the DOH in September 2020. It is a pandemic intelligence monitoring platform that aids national government agencies, local government units (LGUs), and the Inter-Agency Task Force on Emerging Infectious Diseases (IATF) in their real-time decision-making processes, 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. Since March 2020, the COARE facility has been of crucial help to FASSSTER, providing access to its virtual cloud services to help them in their mathematical models and data warehouse needs.

The COVID-19 dashboard of FASSSTER.

Safe, Swift & Smart Passage (S-PaSS) 

COARE has provided large storage and compute resources to the Safe, Swift & Smart Passage application or S-PaSS, a web-based system developed by the DOST Regional Office VI to manage the travels of Locally Stranded Individuals (LSIs), Returning Overseas Filipinos (ROFs), Authorized Persons Outside of Residence (APORs), and Emergency Travelers (ETs). To manage travel and mobility in and out of the country and across provinces and regions, the IATF, LGUs, and the Philippine National Police (PNP) adopted the said travel management system. With the expected scale-up of the application, COARE is ready to provide additional compute and storage resources to support its nationwide adoption.

The interface of the web-based S-PaSS system.

COVID-19 Operations Center Monitoring Dashboard & Data Platform: Department of Science and Technology – Advanced Science and Technology Institute (DOST-ASTI) and SyCip Gorres Velayo & Company (SGV & Co)

DOST-ASTI, in cooperation with SyCip Gorres Velayo & Company (SGV & Co.), developed the COVID-19 Operations Center Monitoring Dashboard and Data Platform to help LGUs in managing, tracking, and monitoring COVID-19 cases. The system consolidates COVID-19 data that LGUs can view through an easy-access dashboard. It includes visualization features like heat maps and charts for monitoring, designed for municipality up to the barangay level. It also includes 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 COVID-19 Operations Center Monitoring Dashboard & Data Platform.

SafeTravelPH: University of the Philippines Diliman (UPD) and Department of Transportation (DOTr) – Land Transportation Franchising and Regulatory Board

This collaborative research aims to enhance the quality and safety in public transport through the deployment of SafeTravelPH, a crowdsourcing app and dashboard that provides an integrated system for real-time fleet monitoring and evaluation of public transport services. Through the establishment of an information exchange platform, this app aims to set up parameters and performance indicators for fuel-efficient public transport operations through the promotion of eco-driving practices and safe commuting through real-time data feeds and commuter-contributed alerts. COARE assisted in the SafeTravelPH research through the provision of Science Cloud services.

The crowdsourcing application of SafeTravelPH.

CovCheck Application: University of the Philippines Cebu (UPC)

The Department of Computer Science and the FireCheck team of the University of the Philippines Cebu has developed the web application called CovCheck. It enables LGUs in Cebu to manage and respond to the transmission of COVID-19 through the collection of data from people who have self-assessed and self-reported for COVID-19 symptoms. CovCheck also features Quarantine Buddy, an application that allows the LGU to monitor residents who are admitted to their quarantine facilities. At present, COARE has helped UP Cebu’s CovCheck by hosting their web application in its virtual servers.

The COVID-19 web application of UP Cebu’s CovCheck.

COVID-19 Analysis; COVID19 Assembly; Evolutionary analysis of SARS-CoV-2 : UP Philippine Genome Center (UP-PGC)

The Philippine Genome Center of the University of the Philippines-Diliman is a genome-focused institution that currently prioritizes research pursuits on COVID-19. The PGC’s current activities center on phylogenetic analysis, computational studies, evolutionary analysis, molecular biology, and in silico detection of COVID-19. From the onset of the pandemic, COARE has given support to the PGC by providing its researchers an access to the facility’s supercomputing services.

Screenshot from the Philippine Genome Center’s virtual conference, “OnePGC”, held on December 10, 2020.

Advancing Antivirals thru Combined Computational Design and Emerging Omics to Leverage Repurposed and Natural Drugs for SARS-CoV-2 Therapeutics (ACCELER8): UP Manila College of Arts and Sciences (UPM CAS) / UP-PGC Mindanao / De La Salle University (DLSU) Manila

Faculty members and scientists from the University of the Philippines-Manila, Philippine Genome Center-Mindanao, and the De La Salle University Manila are working on the ACCELER8 research project to be able to identify antiviral inhibitors of SARSCoV-2 from repurposed, commercially available drugs and Philippine natural product compounds. COARE has given ACCELER8 researchers an access to its supercomputing services to help them conduct simulations and data analysis on computational drug design and omics, supported by in silico and in vitro screening.

The research and resource portal of De La Salle University that lists the research works, activities, and initiatives related to COVID-19.

Telemedicine Network of the Philippines (TNP) 

Aside from the resources provided by COARE, DOST-ASTI’s high-speed network, PREGINET, has been a crucial tool for COVID-19-related activities, especially in advancing telemedicine initiatives. The only national research and education network of the country, PREGINET has been working closely with the Telemedicine Network of the Philippines to facilitate and support online events and educational webinars significant to healthcare practitioners in the local and international scenes. Since the pandemic started, the activities conducted related to telemedicine focused more in expanding useful knowledge about COVID-19.

A telemedicine initiative during the Philippine Association of Laparoscopic and Endoscopic Surgeons (PALES) Virtual Congress 2020.

Amid the availability of COVID-19 vaccines worldwide and the ceaseless plight of the medical community in giving assistance to COVID-19 patients, the end is still far from sight for this virulent disease. However, through the support of supercomputing facilities such as COARE, researchers are empowered to create data-driven systems, platforms, and applications, and work on research initiatives that allows us to get closer to uncovering the facets of this virus.

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