TABLE 1

Main input parameters of Infectio

ParameterTypeDefaultDescription
cells_xInteger5Model size defined by the number of the horizontal cells in the hexagonal lattice (y size is computed automatically to maintain the lattice)
pauseOnCAIterationsFlag (0 or 1)0Wait for key stroke or user input after every iteration
virus Flags.Flag (0 or 1)0Should the images be displayed with or without PSE particles
plotImagesWithParts
virusFlags.Flag (0 or 1)0Advection: true, apply flow; false, do not
isAdvectionEnabled
TotalTimeStepsHPIInteger10Total time steps for the model to run in hours postinfection
virusFlags.Flag (0 or 1)1Switches the cell-to-cell spread on and off
isSpreadCell2CellLimitedByTime
virusFlags.Flag (0 or 1)0Switches the cell-free spread on and off
isCellFreeSpreadEnabled
initialC2cInfectionInteger1Number of initially infected cells
SensorFlag (0 or 1)0Save all workspace variable at certain hours p.i. during the simulation
CellDeathFlagFlag (0 or 1)0Allow death of uninfected cells
CellLysDistFlagString“unif”Cell lysis probability distribution flag for lytic cell-free spread: unif, norm, exp
SavePrticlesPlotFlagFlag (0 or 1)0Saves the PSE particle plots
virusTypeString“VACV-WR”Select one of the preset viruses; new presets for viruses with experimentally measured parameters can be definied in capse/src/matlab/+caps/+config/parameters.m and capse/src/matlab/+caps/+config/flags.m
PrimaryLysisFlagFlag (0 or 1)0Defines whether the initially infected cell lyses to initiate spread