Students develop a SARS-CoV-2 immune response framework that could allow researchers and medical professionals to improve prognosis and personalized treatment.
A team of students and postdoctoral fellows from the Luddy School of Informatics, Computing, and Engineering’s Department of Intelligent Systems Engineering and the Indiana University Biocomplexity Institute were part of a hackathon in mid-April to develop a SARS-CoV-2 immune response framework that could allow researchers and medical professionals to improve prognosis and personalized treatment.
The Global Hack, a 48-hour online hackathon, featured more than 12,000 participants from more than 100 countries and was designed to encourage sharing and the rapid development of ideas to be developed into solutions to issues raised by the COVID-19 pandemic. The Luddy team developed a multiscale model of initial SARS-CoV-2 exposure and infection using CompuCell3D, an open-source modeling and simulation environment of the spatiotemporal dynamics of virtual tissue at the cellular and subcellular levels. The model simulated the complex molecular and cellular interactions driving early progression of the disease.
“We wanted to test the potential for a collaborative model development in the most extreme circumstances,” said ISE postdoctoral fellow T.J. Sego, who was the leader of the group. “Some students came into this hackathon with minimal experience in coding and computational modeling, but with a bit of guidance and the online manuals we’ve written for CompuCell3D, everyone was able to jump in and contribute.”
The project, which was conceived by ISE Ph.D. student Josua Aponte-Serrano, organized the simulation into modules that allowed researchers from diverse backgrounds to isolate different components of the model. Each module then could be deployed, validated, and extended independently. The simulation also described properties and interactions between generalized susceptible and immune cells and their extracellular environment. At the cellular level, some of these characteristics include changes typically associated with viral infection such as release of newly assembled viral particles and cell death due to viral load.
The group included ISE Ph.D. student Juliano Gianlupi, and Kira Breithaupt from IU’s Department of Psychological and Brain Sciences, as well as students from George Washington University. The group used a Zoom meeting room to collaborate, and the students came from a diverse set of academic backgrounds and levels of coding experience.
“Considering the size of the crisis we’re all enduring, it was great to see so many people come together for a single cause,” Sego said. “Most of us barely slept, but we wanted to do what we could to help.”
The hackathon featured tracks for researchers to follow, including categories such as crisis response, economy, environment, health and wellness, work, education, and more.