How data science was used to solve the pandemic

The first mentorship session of the semester, “How Data Science was Used to Solve the Pandemic,” took place online on Saturday, November 25, 2023, at 1:00 PM. It was announced the day before and livestreamed on the UP Data Science Society Facebook page.

Speaker

John Michael C. Egana is a Junior Research Analyst at the Core Facility for Bioinformatics of the Philippine Genome Center and a graduate student of the Department of Computer Science in UP Diliman. His research interests include computational biology, insect and plant transcriptomics, and viral phylodynamics.

What the session covered

Mr. Egana described two methods of disease surveillance. Epidemiological surveillance is the continuous collection, analysis, and interpretation of health-related data. Genomic surveillance uses sequencing to identify SARS-CoV-2 variants. Both fed the COVID-19 Tracker, the dashboard managed by the Department of Health, whose public data drop covered daily confirmed cases, hospitalization rate, vaccination rate, testing positivity rate, and death rate, and which was used for policy making, forecasting, and resource allocation.

He defined mutation, lineage, variant, genomic sequencing, and genomic surveillance, walked through the PANGO lineage classification of SARS-CoV-2, and explained how data science supports mathematical modeling and forecasting in epidemiologic surveillance. The Philippine Genome Center showed its own visualizations, including the V map of where SARS-CoV-2 lineages were found in the country. Open data shared through organizations such as Epi-CoV made global genomic epidemiology and real-time surveillance possible.

Mr. Egana also talked about the difficulties his team faced, from sampling to computationally expensive analyses, and how the center answered them by building tools, a data-sharing platform called PANDASH, and by integrating software from different professions. He closed by saying that the pandemic was a problem that needed many approaches and kinds of expertise, and that data science was one of the tools that gave unique insight into it.

The recap was written by Elaine M. Pelicano with photos by Diego M. Bacud. Three days later, on November 28, 2023, the society held its mentorship workshop with Dr. Syrus Gomari on data-driven solutions for community problems.