The open-source CompuCell3D program is allowing researchers to model COVID-19.
Researchers from the Biocomplexity Institute at the Luddy School of Informatics, Computing, and Engineering recently showcased the use of a cutting-edge computational model of COVID-19 for an international research community to allow them to better understand the spread of the disease.
A series of webinars using multicellular computational models of COVID-19 in CompuCell3D were designed to present the model in a form that could easily be used via a cloud-based version of the model on nanoHUB. It provided examples of how the model could be used and modified by other researchers while teaching the modeling tools at a level that allows the model to be used by researchers from the undergraduate level to professional researchers in biology and computer science.
“The webinar emerged from one we developed specifically for our ad hoc group of collaborators in COVID-19 modeling,” said Jim Sluka, a research scientist at the Biocomplexity Institute. “After developing and giving the seminar to that group, we decided it was of sufficient interest to give publicly. Overall, the model represents a cutting-edge application of advanced computational biology, computer science, and cloud-based research in a rapidly evolving area.”
The webinars attracted more than 170 researchers from around the world. The model exhibits basic patterns of infection dynamics, including widespread infection, slowed infection, recurrence, containment, and clearance. It allows researchers to simulate tissue-specific effects of COVID-19 and its possible response to treatments, which can allow rapid development of methods to combat the disease.
The success of the webinars has led to the planning of future events.
“Several attendees have asked about a third webinar focused on developing their own models, with their own particular interests, using our model as a framework,” Sluka said. “In addition, we have modified our yearly two-week summer course in multiscale biological modeling to include COVID-19 applications.”
“Our researchers at the Luddy School continue to take the lead in helping a world-wide community battle COVID-19,” said Kay Connelly, the associate dean for research at the Luddy School. “Webinars such as this open so many opportunities for collaboration, and it creates exactly the kind of cross-disciplinary research that can help us make strides against the pandemic.”