Computing Covid-19: Virtual quantitative biosciences workshop dives deep into the use of computational modeling in response to epidemics

July 12, 2021

Throughout the past year, virtual communication has been necessary but challenging. Yet, with the increase in virtual events, there have been unexpected benefits to scientific collaboration and education. These benefits were obvious as over 100 young scientists from Georgia Tech and around the world gathered around their laptops for this year’s virtual iteration of the annual Quantitative Biosciences Modeling Workshop. The hands-on workshop in May of 2021 aimed to teach scientists of all backgrounds and skill levels about how to use computational models to focus on the problem that has been on everyone’s mind for over a year: epidemics.

“The ongoing Covid-19 pandemic made it easy to pick a topic,” says Aaron Pfenning, one of the first-year PhD students in Quantitative Biosciences at Georgia Tech who was responsible for organizing the workshop. Open to graduate students, scientists, and faculty members across the world, the hands-on workshop provided an introduction to how computational modeling is applied to understand and combat epidemics. “The entire workshop was based on a single lab from a class we took in the fall, Foundations in Quantitative Biosciences,” explained Leo Wood, another first-year PhD student involved in organizing the workshop. “But that was enough to fill two days of workshop, and really taught our students a lot.”

The two-day virtual workshop was split into two components: public lectures and hands-on small group sessions. The plenary lectures spurred meaningful discussion on the past, present, and future of using computational models to respond to epidemics. Later, the Applied Bioinformatics Laboratory (ABiL) provided detailed a demonstration on how to create interactive tools dashboards using R Shiny. Between public talks, registered attendees took part in small group sessions. In these sessions, attendees were grouped by computer programming experience, and received hands-on instruction in developing computational models in their preferred programming language from graduate students and postdoctoral volunteers from Georgia Tech.

A map and pie chart describing where workshop attendees were attending from. Attendees hailed from 20 countries around the world and 15 states within the U.S.
A map and pie chart describing where workshop attendees were attending from. Attendees hailed from 19 countries around the world and 15 states within the U.S.

Yet, planning a workshop is not without its challenges, especially when it is virtual. “It definitely made it harder to enable socializing and networking which is particularly important for people early in their career,” explained Pfenning. Despite these challenges, Pfenning noticed unforeseen benefits to the workshop’s virtual nature. “At the same time, we had a greater outreach, though, as people across different time zones attended.” The workshop, typically attended only by students in the Atlanta area, was open to students across the world. Leo Wood was also taken aback by the international attendance, describing “In my [small group] session alone, I had one person in South Africa and one person in Germany.”

Sabrina Li, a PhD student in the School of Geography & Environment at Oxford University, found the workshop particularly useful for her work. “As someone that currently works on COVID-19 modeling,” Li explained, “I wanted to improve my understanding of the models and assumptions used by many studies in the literature.” Li, who discovered the workshop through Twitter, says she found the public talks engaging, and thought the hands-on sessions served as a great introduction to modeling biomedical data. “Given that I come from a non-epidemiology/biomedical sciences background, I appreciated the introductory content and theory, which helped me to better understand the math and logic used to formulate the models.”

For those who missed the workshop, the materials from the small group sessions, as well as recordings of the public lectures, are available online. Keep an eye out for next year’s Quantitative Biosciences Modeling Workshop – there are many more topics to explore through a modeling lens.