Agent Based Simulation of a chronic Influenza infection

For the Modeling and Simulation in Biological Systems class I took in Fall 2016, @megcyan and I analyzed and extended the work of Dobrovolny et al, 2010. As part of the extension, I made an Agent Based Model of the infection in the two target-cell system. (The scripts for creating and analysing this system can be found here). The output is pretty, and this is a visual representation of what a brutal chronic influenza infection can do to the target epithelial cells: