Parameters

Parameters

In this page, we list all possible parameters that can be precised in the parameter files in the simulations. We will udpate this list as new parameters are added (or some deleted). The parameter file is composed of different parts, according to the type of parameters to define:

• Simulation
• Cell properties
• Network
• Initial configuration

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Simulation

Parameters that refer to global properties of the simulation, e.g. the numerical time step, are precised in the simulation parameters element. The table below gives the list of possible parameters that can be specified in this section. We precised the default value that is used in PhysiBoSS, and when relevant, a range of plausible values for each parameter.

Parameter name	Default value (advised range)	Description
time_step	0.01 min (0.001-1)	Diffusion time scale (smallest time scale). If no entities are diffusing, can be higher. From 1
mechanics_time_step	0.1 min (0.01-5)	Time scale of motion, cell volume changes. From 1
cell_cycle_time_step	6 min (0.5-10)	Cell cycle time scale, change of cell phase. From 1
maximal time	4320 min	Duration of simulated time
output_intervals	60 min	Frequency at which cells position and states are written to file.
output_densities	600 min	Frequency at which microenvironment densities concentration are written to file.
write_passive_cells	0 (0 or 1)	If write the position of passive cells in output files or not
write_ratio_voxels	0.5 (0-1)	Proportion of microenvironment voxel values to write to output files (writing all of them can be pretty heavy)
number_of_threads	10	Number of threads for parallel computing. Depends on the machine used.
friction_passive_cells	0.0001 (0.00001-1)	How easy will it be to move passive cells (if high, fixed cells).
mode_cell_cycle	0 (0 or 1)	Mode of calculation of the cell cycle: 0, cycling is defined as in 1. 1: cycling is dependant on the boolean network outputs.
number of densities	>= 1	Number of diffusing entities. By default, there is just one (oxygen).
density_0	oxygen	Name of the diffusing densities. Increment the indices in "density_0" to define more than 1 (e.g. <density_1> tnf </density_1>)...
bounding_box_xmin	-200 µm (10-10000)	Definition of the boundray box surrounding all the simulation space
bounding_box_xmax	+200 µm (10-10000)	Definition of the boundray box surrounding all the simulation space
bounding_box_ymin	-200 µm (10-10000)	Definition of the boundray box surrounding all the simulation space
bounding_box_ymax	+200 µm (10-10000)	Definition of the boundray box surrounding all the simulation space
bounding_box_zmin	-200 µm (10-10000)	Definition of the boundray box surrounding all the simulation space
bounding_box_zmax	+200 µm (10-10000)	Definition of the boundray box surrounding all the simulation space
minimum_voxel_size	30 µm (1-50)	Spatial discretisation of the microenvironment. Length of one side of the cube (voxel).
svg_coloring_mode	0 or 1	How to color the cells in svg output: 0, cytoplasmic radius and nuclear radius are colored differently; 1, cells are colored according to their phase

Example of the simulation part of the parameter file:

<simulation>
	<time_step> 0.02 </time_step>
	<mechanics_time_step> 0.1 </mechanics_time_step>
	<cell_cycle_time_step> 2 </cell_cycle_time_step>
	<maximal_time> 1440 </maximal_time>
	<write_passive_cells> 0 </write_passive_cells>
	<mode_cell_cycle> 1  </mode_cell_cycle>
	<number_of_densities> 2 </number_of_densities>
	<density_0> oxygen </density_0>
	<density_1> tnf </density_1>
	<write_ratio_voxels> 0.3 </write_ratio_voxels>
</simulation>

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Cell properties

In this section of the parameter file, the properties common to all cells of one cell line are given. This section will be repeated for each cell line (e.g. if you simulate a cell population composed of 2 different cell lines, there will be 2 `cell_properties` sections in the parameter file). The order in which the cell properties are given in the file correspond to the cell lines in the simulation (cell line 0, cell line 1...).

Parameter name	Default value (advised range)	Description

<cell_properties>
    <polarity_coefficient> 0.1 </polarity_coefficient>
    <motility_amplitude_min> 0.01 </motility_amplitude_min>
    <motility_amplitude_max> 0.01 </motility_amplitude_max>
    <mode_motility> 1 </mode_motility>
    <homotypic_adhesion_min> 2 </homotypic_adhesion_min>
    ....
    <phenotype_number> 3 </phenotype_number>
    <secretion_rate> 0.1 </secretion_rate>
</cell_properties>

<network>
	<network_update_step> 10 </network_update_step>
	<mutation_0>
		<symbol_name> $High_IKK </symbol_name>
		<cell_line> 0 </cell_line>
		<rate> 0.0 </rate>
	</mutation_0>
	<mutation_1>
		<symbol_name> $High_IKK </symbol_name>
		<cell_line> 1 </cell_line>
		<rate> 1.0 </rate>
	</mutation_1>
	<mutation_2>
		<symbol_name> $High_cFLIP </symbol_name>
		<cell_line> 0 </cell_line>
		<rate> 0.0 </rate>
	</mutation_2>
	<mutation_3>
		<symbol_name> $High_cFLIP </symbol_name>
		<cell_line> 1 </cell_line>
		<rate> 1.0 </rate>
	</mutation_3>
</network>

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Initial configuration

Parameter name	Default value (advised range)	Description
sphere_radius	100 µm (10-10000)	If no initial file is provided, length of the initial sphere of cells to create
load_cells_from_file	init.txt	Name of the file containing the initial position of all the cells
create_ecm_from_file	ecm.txt	Name of the file containing the initial value of ECM concentrations (must contains a list of position (x,y,z) and density value).
number_of_passive_celles	0	If no initial file is provided, number of passive cells to add (around the active cells sphere)
time_passive_cells	1000000 min	Change the repulsive capacity of the passive cells during the simulation, after the time given (before not repulsing=phantom cells, after repulsing cells=obstacle). By default, value above max time of simulation: no change
mode_injection	-1 (-1 or 0 or 1)	How injection of a density is simulated. Options are: -1, no injection; 0, injection in all the voxels of the space; 1; injection only in the voxels at the outer boundary of the space
time_add_egf	1000000 min	Time interval between EGF injection (default value is higher than simulation maximal time, so no injection)
time_add_tnf	1000000 min	Time interval between TNF injection (default value is higher than simulation maximal time, so no injection)
duration_add_tnf	10 min	Duration of the pulse injection when there is injection to do
time_remove_tnf	1000000 min	Time at which to clear the microenvironment of all TNF (corresponding by example to a change of solution)
densityName_concentration	7.2 fg/µm^3	Concentration of injected density (name of the density followed by _concentration: e.g. tnf_concentration)
membrane_shape	none	Addition of an outer "membrane" that constrains all the cells inside this geometry. Can be: none, duct or sphere
membrane_length	0	If a shape is defined, length of the geometry (e.g. radius for the sphere)

Example of the initial configuration part of the parameter file:

<initial_configuration>
	<load_cells_from_file> init.txt </load_cells_from_file>
	<membrane_shape> sphere </membrane_shape>	
	<membrane_length> 470 </membrane_length>
	<oxygen_concentration> 40 </oxygen_concentration>
	<tnf_concentration> 1 </tnf_concentration>	
	<mode_injection> 1 </mode_injection>
</initial_configuration>

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References

[1] Ghaffarizadeh A., Heiland R., Friedman S.H, Mumenthaler S.M. and Macklin P. PhysiCell : [an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005991). Plos Computational Biology 2018