initial.xml 7.64 KB
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<?xml version="1.0"?>
<MultiCellDS version="0.5" type="snapshot/simulation">
	<metadata>
		<software>
			<name>BioFVM</name>
			<version>1.1.7</version>
			<URL>http://BioFVM.MathCancer.org</URL>
			<creator />
			<citation />
			<user />
		</software>
		<citation />
		<current_time units="min">0.000000</current_time>
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		<current_runtime units="sec">0.123792</current_runtime>
		<created>2020-10-26T18:40:36Z</created>
		<last_modified>2020-10-26T18:40:36Z</last_modified>
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	</metadata>
	<microenvironment>
		<domain name="microenvironment">
			<mesh type="Cartesian" uniform="true" regular="true" units="micron">
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				<bounding_box type="axis-aligned" units="micron">-400.000000 -400.000000 -10.000000 400.000000 400.000000 10.000000</bounding_box>
				<x_coordinates delimiter=" ">-390.000000 -370.000000 -350.000000 -330.000000 -310.000000 -290.000000 -270.000000 -250.000000 -230.000000 -210.000000 -190.000000 -170.000000 -150.000000 -130.000000 -110.000000 -90.000000 -70.000000 -50.000000 -30.000000 -10.000000 10.000000 30.000000 50.000000 70.000000 90.000000 110.000000 130.000000 150.000000 170.000000 190.000000 210.000000 230.000000 250.000000 270.000000 290.000000 310.000000 330.000000 350.000000 370.000000 390.000000</x_coordinates>
				<y_coordinates delimiter=" ">-390.000000 -370.000000 -350.000000 -330.000000 -310.000000 -290.000000 -270.000000 -250.000000 -230.000000 -210.000000 -190.000000 -170.000000 -150.000000 -130.000000 -110.000000 -90.000000 -70.000000 -50.000000 -30.000000 -10.000000 10.000000 30.000000 50.000000 70.000000 90.000000 110.000000 130.000000 150.000000 170.000000 190.000000 210.000000 230.000000 250.000000 270.000000 290.000000 310.000000 330.000000 350.000000 370.000000 390.000000</y_coordinates>
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				<z_coordinates delimiter=" ">0.000000</z_coordinates>
				<voxels type="matlab">
					<filename>initial_mesh0.mat</filename>
				</voxels>
			</mesh>
			<variables>
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				<variable name="virion" units="virion/micron^3" ID="0">
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					<physical_parameter_set>
						<conditions />
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						<diffusion_coefficient units="micron^2/min">2.500000</diffusion_coefficient>
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						<decay_rate units="1/min">0.000000</decay_rate>
					</physical_parameter_set>
				</variable>
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				<variable name="assembled virion" units="virion/micron^3" ID="1">
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					<physical_parameter_set>
						<conditions />
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						<diffusion_coefficient units="micron^2/min">2.500000</diffusion_coefficient>
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						<decay_rate units="1/min">0.000000</decay_rate>
					</physical_parameter_set>
				</variable>
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				<variable name="interferon 1" units="mol/micron^3" ID="2">
					<physical_parameter_set>
						<conditions />
						<diffusion_coefficient units="micron^2/min">555.560000</diffusion_coefficient>
						<decay_rate units="1/min">0.010200</decay_rate>
					</physical_parameter_set>
				</variable>
				<variable name="pro-inflammatory cytokine" units="mol/micron^3" ID="3">
					<physical_parameter_set>
						<conditions />
						<diffusion_coefficient units="micron^2/min">555.560000</diffusion_coefficient>
						<decay_rate units="1/min">0.010200</decay_rate>
					</physical_parameter_set>
				</variable>
				<variable name="chemokine" units="mol/micron^3" ID="4">
					<physical_parameter_set>
						<conditions />
						<diffusion_coefficient units="micron^2/min">555.560000</diffusion_coefficient>
						<decay_rate units="1/min">0.010200</decay_rate>
					</physical_parameter_set>
				</variable>
				<variable name="debris" units="mol/micron^3" ID="5">
					<physical_parameter_set>
						<conditions />
						<diffusion_coefficient units="micron^2/min">555.560000</diffusion_coefficient>
						<decay_rate units="1/min">0.010200</decay_rate>
					</physical_parameter_set>
				</variable>
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			</variables>
			<data type="matlab">
				<filename>initial_microenvironment0.mat</filename>
			</data>
		</domain>
	</microenvironment>
	<cellular_information>
		<cell_populations>
			<cell_population type="individual">
				<custom>
					<simplified_data type="matlab" source="BioFVM">
						<filename>initial_cells.mat</filename>
					</simplified_data>
					<simplified_data type="matlab" source="PhysiCell">
						<labels>
							<label index="0" size="1">ID</label>
							<label index="1" size="3">position</label>
							<label index="4" size="1">total_volume</label>
							<label index="5" size="1">cell_type</label>
							<label index="6" size="1">cycle_model</label>
							<label index="7" size="1">current_phase</label>
							<label index="8" size="1">elapsed_time_in_phase</label>
							<label index="9" size="1">nuclear_volume</label>
							<label index="10" size="1">cytoplasmic_volume</label>
							<label index="11" size="1">fluid_fraction</label>
							<label index="12" size="1">calcified_fraction</label>
							<label index="13" size="3">orientation</label>
							<label index="16" size="1">polarity</label>
							<label index="17" size="1">migration_speed</label>
							<label index="18" size="3">motility_vector</label>
							<label index="21" size="1">migration_bias</label>
							<label index="22" size="3">motility_bias_direction</label>
							<label index="25" size="1">persistence_time</label>
							<label index="26" size="1">motility_reserved</label>
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							<label index="27" size="1">virion</label>
							<label index="28" size="1">uncoated_virion</label>
							<label index="29" size="1">viral_RNA</label>
							<label index="30" size="1">viral_protein</label>
							<label index="31" size="1">assembled_virion</label>
							<label index="32" size="1">virion_uncoating_rate</label>
							<label index="33" size="1">uncoated_to_RNA_rate</label>
							<label index="34" size="1">protein_synthesis_rate</label>
							<label index="35" size="1">virion_assembly_rate</label>
							<label index="36" size="1">virion_export_rate</label>
							<label index="37" size="1">unbound_external_ACE2</label>
							<label index="38" size="1">bound_external_ACE2</label>
							<label index="39" size="1">unbound_internal_ACE2</label>
							<label index="40" size="1">bound_internal_ACE2</label>
							<label index="41" size="1">ACE2_binding_rate</label>
							<label index="42" size="1">ACE2_endocytosis_rate</label>
							<label index="43" size="1">ACE2_cargo_release_rate</label>
							<label index="44" size="1">ACE2_recycling_rate</label>
							<label index="45" size="1">max_infected_apoptosis_rate</label>
							<label index="46" size="1">max_apoptosis_half_max</label>
							<label index="47" size="1">apoptosis_hill_power</label>
							<label index="48" size="1">virus_fraction_released_at_death</label>
							<label index="49" size="1">infected_cell_chemokine_secretion_rate</label>
							<label index="50" size="1">debris_secretion_rate</label>
							<label index="51" size="1">infected_cell_chemokine_secretion_activated</label>
							<label index="52" size="1">TCell_contact_time</label>
							<label index="53" size="1">cell_attachment_rate</label>
							<label index="54" size="1">cell_attachment_lifetime</label>
							<label index="55" size="1">TCell_contact_death_threshold</label>
							<label index="56" size="1">max_attachment_distance</label>
							<label index="57" size="1">elastic_attachment_coefficient</label>
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							<label index="58" size="1">phagocytosis_rate</label>
							<label index="59" size="1">sensitivity_to_debris_chemotaxis</label>
							<label index="60" size="1">sensitivity_to_chemokine_chemotaxis</label>
							<label index="61" size="1">activated_speed</label>
							<label index="62" size="1">activated_cytokine_secretion_rate</label>
							<label index="63" size="1">activated_immune_cell</label>
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						</labels>
						<filename>initial_cells_physicell.mat</filename>
					</simplified_data>
				</custom>
			</cell_population>
		</cell_populations>
	</cellular_information>
</MultiCellDS>