This respository contains the code to implement the model and results presented in Multicellular Spatial Model of RNA Virus Replication and Interferon Responses Reveals Factors Controlling Plaque Growth Dynamics: https://www.biorxiv.org/content/10.1101/2021.03.16.435618v1
The directory Simulation_Code contains the code to simulate the model using CompuCell3D (CC3D). Users need a local version of CC3D to execute the code and clone this repository to their local machines.
Inside the directory, users can find the main simulation file: IFNModel.cc3d. To execute the base simulation lunch CompuCell3D and load the simulation file: File > Open Simulation File (.cc3d).
Locate the main simulation file IFNModel.cc3d and execute the simulation by hitting the Run button.
Since configuration files are not shared in this repository, display configurations might be slightly different for each user. By default, CC3D displays a single graphic window showing the Cell_Field, which corresponds to the cell lattice colored by their different types. To display the extracellular species (Virus and IFN), click on the New Graphics Window button.
In the new graphics window, choose the specific extracellular species of interest from the pulldown menu.
Continue stepping forward the simulation by hitting the Run button. Users will be able to see the progression of the viral plaque, and the concentration of extracellular Virus and IFN in the simulation domains.
