⬣ What host, viral, or environmental factors are predictive of pandemic emergence and spread in different populations?
⬣ How can complex data-sources be integrated to create tools for public health intervention?
⬣ What are the urgently needed ‘dream applications’ for future pandemic prevention and management?
Congratulations to the winning teams!
First Place: Team 3 - Exploring COVID-19 mutation rate covariates
In order to explore the factors that lead to faster pathogen evolution, Team 3 linked geographic information from sequenced COVID genomes to the degree of divergence from inferred ancestral states, and built a Shiny app hosted on GitHub that correlates arbitrary geographic metadata with these divergence rates.
Second Place: Team 2 - Zoo-Cov
Team 2 created an interactive application/web app that can identify putative host-shifts where recent human-hosted SARS-CoV-2 sequences have evolved and infected a non-human host.
Third Place: Team 4 - Social Cost
Team 4 addressed vaccine and resource distribution and disparities as well as vaccine hesitancy by providing the public with pertinent and easily accessible data on COVID-19 cases and risk factors/vulnerability indices, as well as social media-derived sentiment analysis.
- A closing-ceremony accouncement from Dr. Rays Jiang
“Congrats on the winning teams! Congrats Jenna Oberstaller and Janelle Donglasan for recreating the vital space for forging our team spirit. My fellow pandemic codathon companions, congratulations to all. In this surreal time, we have done it across the digital space- “Collaborative coding against pandemic”, with passion and dedications, no less than the old pre-covid world. We have put flesh and blood into the abstract concepts to tackle this global pandemic- e.g. harnessing pandemic social sentiments, tracking variants in space time, predicting of hotspots, decoding breath microbiome, machine learning of vaccination side effect, delineating zoonotic and reverse zoonotic variants. Importantly, some truly innovative concepts and tools emerged for the first time in the depth of this pandemic, like “deep learning for harnessing spatial data”, “forecasting air microbiome”, and “personalized vaccinations”. We are physically far apart, yet, people have been telling me how excited, upset, disappointed and joyous they are. I am amazed that how our team camaraderie can form and intensify in this digital space, almost in a mysterious way. Today marks the beginning of the next phase - bringing our prototypes and ideas and sharing with the world in the form of papers, projects and collaborations, all shall flourish against this pandemic.”
Presentations from the Keynote Symposium are below:
Data-driven, systems-modelling approaches to forecasting Pandemics by Dr. Edwin Michael, Professor Center for Global Health Infectious Disease Research, USF
Early warning system for SARS-CoV-2 Variants of Concern by Dr. Richard Scheuermann, Director J. Craig Venter Institute at La Jolla Campus
If you missed the USF Intro to Codeathons Genomics Forum, you can catch up here.
Special thanks to our sponsors, organizers, and collaborators!