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Modern ode-energy-sample & Makefile Typo correction #185

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Jul 28, 2023
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Modern ode-energy-sample & Makefile Typo correction #185

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be1d9e9
Modernized ode-energy-sample model
furkankurtoglu Jul 27, 2023
34e95ab
PhyisiCell_rules.o typo is corrected
furkankurtoglu Jul 28, 2023
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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_contai

PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_basic_signaling.o \
PhysiCell_signal_behavior.o PhyisiCell_rules.o
PhysiCell_signal_behavior.o PhysiCell_rules.o

PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
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146 changes: 118 additions & 28 deletions sample_projects_intracellular/ode/ode_energy/config/PhysiCell_settings.xml
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Expand Up @@ -35,7 +35,7 @@
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project #
# Copyright (c) 2015-2021, Paul Macklin and the PhysiCell Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
Expand Down Expand Up @@ -87,7 +87,7 @@
</domain>

<overall>
<max_time units="min">1440</max_time> <!-- 5 days * 24 h * 60 min -->
<max_time units="min">1440</max_time> <!-- 1 days * 24 h * 60 min -->
<time_units>min</time_units>
<space_units>micron</space_units>

Expand Down Expand Up @@ -120,7 +120,8 @@

<options>
<legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
<disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
<virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
<disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
</options>

<microenvironment_setup>
Expand All @@ -131,26 +132,29 @@
</physical_parameter_set>
<initial_condition units="mmHg">38</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="false">0</Dirichlet_boundary_condition>
</variable>
</variable>

<variable name="glucose" units="mM" ID="1">


<variable name="glucose" units="mM" ID="1">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">300.0</diffusion_coefficient>
<decay_rate units="1/min">0.0</decay_rate>
</physical_parameter_set>
<initial_condition units="mM">50</initial_condition>
<Dirichlet_boundary_condition units="mM" enabled="false">0.0</Dirichlet_boundary_condition>
<Dirichlet_boundary_condition units="mM" enabled="false">0</Dirichlet_boundary_condition>
</variable>


<variable name="lactate" units="mM" ID="2">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">300.0</diffusion_coefficient>
<decay_rate units="1/min">0.0</decay_rate>
</physical_parameter_set>
<initial_condition units="mM">0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="false">0.0</Dirichlet_boundary_condition>
<initial_condition units="mmHg">0</initial_condition>
<Dirichlet_boundary_condition units="mM" enabled="false">0</Dirichlet_boundary_condition>
</variable>

<options>
<calculate_gradients>false</calculate_gradients>
<track_internalized_substrates_in_each_agent>true</track_internalized_substrates_in_each_agent>
Expand All @@ -169,51 +173,99 @@
<cell_definition name="default" ID="0">
<phenotype>
<cycle code="5" name="live">
<!-- using higher than normal significant digits to match divisions in default code -->
<transition_rates units="1/min">
<rate start_index="0" end_index="0" fixed_duration="false">0.0000000001</rate>
</transition_rates>
</cycle>
<phase_transition_rates units="1/min">
<rate start_index="0" end_index="0" fixed_duration="false">0.0</rate>
</phase_transition_rates>
</cycle>

<death>
<model code="100" name="apoptosis">
<death_rate units="1/min">0.0</death_rate>
<phase_transition_rates units="1/min">
<rate start_index="0" end_index="1" fixed_duration="true">0.0</rate>
</phase_transition_rates>
<parameters>
<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</parameters>
</model>

<model code="101" name="necrosis">
<death_rate units="1/min">0.0</death_rate>
<!-- use phase_transition_rates OR phase_durations -->
<!-- necrosis uses phase_duration[0] = 0 so that it always immediately
tries to transition and instead checks volume against the rupture
volume -->
<phase_transition_rates units="1/min">
<rate start_index="0" end_index="1" fixed_duration="false">0.0</rate>
<rate start_index="1" end_index="2" fixed_duration="false">0.0</rate>
</phase_transition_rates>

<parameters>
<unlysed_fluid_change_rate units="1/min">1.11667e-2</unlysed_fluid_change_rate>
<lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">2.16667e-3</nuclear_biomass_change_rate>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</parameters>
</model>
</death>

<volume>
<total units="micron^3">2494</total>
<fluid_change_rate units="1/min">0.0</fluid_change_rate>
<fluid_fraction units="dimensionless">0.75</fluid_fraction>
<nuclear units="micron^3">540</nuclear>
<fluid_change_rate units="1/min">0.5</fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">0.045</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">0.55</nuclear_biomass_change_rate>
<fluid_change_rate units="1/min">0.05</fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>

<calcified_fraction units="dimensionless">0</calcified_fraction>
<calcification_rate units="1/min">0</calcification_rate>

<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</volume>

<motility>
<speed units="micron/min">0.0</speed>

<mechanics>
<cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
<cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
<relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
<cell_adhesion_affinities>
<cell_adhesion_affinity name="default">1</cell_adhesion_affinity>
</cell_adhesion_affinities>
<options>
<set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
<set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
</options>
<cell_BM_adhesion_strength units="micron/min">4.0</cell_BM_adhesion_strength>
<cell_BM_repulsion_strength units="micron/min">10.0</cell_BM_repulsion_strength>
<attachment_elastic_constant type="double" units="1/min">0.01</attachment_elastic_constant>
<attachment_rate type="double" units="1/min">0.0</attachment_rate>
<detachment_rate type="double" units="1/min">0.0</detachment_rate>
</mechanics>

<motility>
<speed units="micron/min">0.0</speed>
<persistence_time units="min">0.1</persistence_time>
<migration_bias units="dimensionless">.9</migration_bias>

<options>
<enabled>true</enabled>
<use_2D>true</use_2D>
<chemotaxis>
<chemotaxis>
<enabled>false</enabled>
<substrate>oxygen</substrate>
<direction>1</direction>
</chemotaxis>
</options>
</motility>
<secretion>
<secretion>
<substrate name="oxygen">
<secretion_rate units="1/min">0.0</secretion_rate>
<secretion_target units="substrate density">0.0</secretion_target>
Expand All @@ -233,7 +285,26 @@
<net_export_rate units="total substrate/min">0</net_export_rate>
</substrate>
</secretion>


<cell_interactions>
<dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
<live_phagocytosis_rates>
<phagocytosis_rate name="default" units="1/min">0</phagocytosis_rate>
</live_phagocytosis_rates>
<attack_rates>
<attack_rate name="default" units="1/min">0</attack_rate>
</attack_rates>
<damage_rate units="1/min">1</damage_rate>
<fusion_rates>
<fusion_rate name="default" units="1/min">0</fusion_rate>
</fusion_rates>
</cell_interactions>
<cell_transformations>
<transformation_rates>
<transformation_rate name="default" units="1/min">0</transformation_rate>
</transformation_rates>
</cell_transformations>

<intracellular type="roadrunner">
<sbml_filename>./config/Toy_Metabolic_Model.xml</sbml_filename>
<intracellular_dt>0.01</intracellular_dt>
Expand All @@ -245,15 +316,34 @@
<map PC_phenotype="ssr_lactate" sbml_species="Lac_Secretion_Rate"></map>
<map PC_phenotype="ctr_0_0" sbml_species="Transition_Rate"></map>
</intracellular>

<molecular />
</phenotype>
<custom_data>
<custom_data>
<intra_oxy units="mmHg">0.0</intra_oxy>
<intra_glu units="mM">0.0</intra_glu>
<intra_lac units="mM">0.0</intra_lac>
<intra_energy units="dimensionless">0.0</intra_energy>
</custom_data>
</cell_definition>
</cell_definitions>
</cell_definitions>

<initial_conditions>
<cell_positions type="csv" enabled="false">
<folder>./config</folder>
<filename>cells.csv</filename>
</cell_positions>
</initial_conditions>

<cell_rules>
<rulesets>
<ruleset protocol="CBHG" version="2.0" format="csv" enabled="false">
<folder>./config</folder>
<filename>cell_rules.csv</filename>
</ruleset>
</rulesets>
<settings />
</cell_rules>

<user_parameters>
<random_seed type="int" units="dimensionless">0</random_seed>
Expand Down
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