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Merge pull request #41 from PhysiCell-Models/dev
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Updating README and other polishing edits prior to updating preprint
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@johnmetzcar
johnmetzcar authored Mar 13, 2024
2 parents 5f403b0 + b12a652 commit 19709f5
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147 changes: 106 additions & 41 deletions README.md
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44 changes: 19 additions & 25 deletions config/fibrosis.xml
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Expand Up @@ -169,8 +169,6 @@
<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 units="1/min">0.01</attachment_elastic_constant>
<attachment_rate units="1/min">0.0</attachment_rate>
<detachment_rate units="1/min">0.0</detachment_rate>
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<set_relative_equilibrium_distance enabled="true" 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 units="1/min">0.01</attachment_elastic_constant>
<attachment_rate units="1/min">0.0</attachment_rate>
<detachment_rate units="1/min">0.0</detachment_rate>
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<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 units="1/min">0.01</attachment_elastic_constant>
<attachment_rate units="1/min">0.0</attachment_rate>
<detachment_rate units="1/min">0.0</detachment_rate>
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<cell_setup type="string" units="dimensionless" description="single, random, lesion, cells at y = 0, circle of cells, invasive_spheroid, circle_of_fibroblasts, or cells at left boundary/march">None</cell_setup>
<tumor_radius type="double" units="microns" description="Initial cell lesion radius (lesion only)">175</tumor_radius>
<initial_fibroblast_fraction type="double" units="dimensionless" description="Average percentage of fibroblasts initialized (lesion only)">0</initial_fibroblast_fraction>
<oxygen_uptake type="double" units="mmHg/min" description="Default cell oxygen uptake rate">10</oxygen_uptake>
<default_cell_speed type="double" units="microns/minute" description="Base/maximum cell speed">0.5</default_cell_speed>
<default_persistence_time type="double" units="minutes" description="Cell directional persistence time">10.0</default_persistence_time>
<fibroblast_adhesion type="double" units="micron/minute" description="Strength of fibroblast cells\' cell-cell adhesion">10.0</fibroblast_adhesion>
<fibroblast_repulsion type="double" units="micron/minute" description="Strength of fibroblast cells\' cell-cell repulsion">25.0</fibroblast_repulsion>
<inflam_sig_migration_bias_for_fibroblasts type="double" units="dimensionless" description="fibroblast chemotaxis bias">0.95</inflam_sig_migration_bias_for_fibroblasts>
<anisotropy_increase_rate type="double" units="1/min" description="Anisotropy rate of increase">0.004</anisotropy_increase_rate>
<fiber_realignment_rate type="double" units="1/min" description="Fiber rate of realignment">4.0</fiber_realignment_rate>
<default_ECM_density_target type="double" units="dimenionless" description="Cell ECM density target">0.5</default_ECM_density_target>
<default_ECM_production_rate type="double" units="dimenionless" description="Cell ECM production rate">0.001</default_ECM_production_rate>
<oxygen_uptake type="double" units="mmHg/min" description="Deprecated">10</oxygen_uptake>
<default_cell_speed type="double" units="microns/minute" description="Deprecated">0.5</default_cell_speed>
<default_persistence_time type="double" units="minutes" description="Deprecated">10.0</default_persistence_time>
<fibroblast_adhesion type="double" units="micron/minute" description="Deprecated">10.0</fibroblast_adhesion>
<fibroblast_repulsion type="double" units="micron/minute" description="Deprecated">25.0</fibroblast_repulsion>
<inflam_sig_migration_bias_for_fibroblasts type="double" units="dimensionless" description="Deprecated">0.95</inflam_sig_migration_bias_for_fibroblasts>
<anisotropy_increase_rate type="double" units="1/min" description="Deprecated">0.004</anisotropy_increase_rate>
<fiber_realignment_rate type="double" units="1/min" description="Deprecated">4.0</fiber_realignment_rate>
<default_ECM_density_target type="double" units="dimenionless" description="Deprecated">0.5</default_ECM_density_target>
<default_ECM_production_rate type="double" units="dimenionless" description="Deprecated">0.001</default_ECM_production_rate>
<number_of_fibroblasts type="int" units="" description="Number of fibroblasts to initialize">11</number_of_fibroblasts>
<cancer_cell_adhesion type="double" units="micron/minute" description="Strength of follower cells\' cell-cell adhesion">10.0</cancer_cell_adhesion>
<cancer_cell_repulsion type="double" units="micron/minute" description="Strength of follower cells\' cell-cell repulsion">25.0</cancer_cell_repulsion>
<default_chemotaxis_bias type="double" units="dimensionless" description="Follower chemotaxis bias">0.05</default_chemotaxis_bias>
<default_ECM_sensitivity type="double" units="dimensionless" description="Follower ECM orientation sensitivity">1.0</default_ECM_sensitivity>
<rho_L type="double" units="dimensionless" description="Minimum ECM density required for cell motility">0.0</rho_L>
<rho_H type="double" units="dimensionless" description="Maximum ECM density allowing cell motility">1.0</rho_H>
<rho_I type="double" units="dimensionless" description="Ideal ECM density cell motility">0.5</rho_I>
<cancer_cell_adhesion type="double" units="micron/minute" description="Deprecated">10.0</cancer_cell_adhesion>
<cancer_cell_repulsion type="double" units="micron/minute" description="Deprecated">25.0</cancer_cell_repulsion>
<default_chemotaxis_bias type="double" units="dimensionless" description="Deprecated">0.05</default_chemotaxis_bias>
<default_ECM_sensitivity type="double" units="dimensionless" description="Deprecated">1.0</default_ECM_sensitivity>
<rho_L type="double" units="dimensionless" description="Deprecated">0.0</rho_L>
<rho_H type="double" units="dimensionless" description="Deprecated">1.0</rho_H>
<rho_I type="double" units="dimensionless" description="Deprecated">0.5</rho_I>
<default_hysteresis_bias type="double" units="dimensionless" description="Sensitivity to previous direction (hysteresis model only)">1.0</default_hysteresis_bias>
<fibroblast_motility_mode type="bool" units="dimensionless" description="">true</fibroblast_motility_mode>
<cancer_cell_motility_mode type="bool" units="dimensionless" description="">true</cancer_cell_motility_mode>
<fibroblast_motility_mode type="bool" units="dimensionless" description="Deprecated">true</fibroblast_motility_mode>
<cancer_cell_motility_mode type="bool" units="dimensionless" description="Deprecated">true</cancer_cell_motility_mode>
<chemotactic_substrate_decay_rate type="double" units="1/minutes" description="Oxygen decay rate">0.1</chemotactic_substrate_decay_rate>
<chemical_field_setup type="string" units="" description="Starburst, vertical up, horizontal right, angle, or none">none</chemical_field_setup>
<angle_of_chemical_field_gradient type="double" units="" description="Angle of chemical field gradient orientation, specified in degrees">45.0</angle_of_chemical_field_gradient>
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46 changes: 20 additions & 26 deletions config/invasive_carcinoma.xml
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Expand Up @@ -169,8 +169,6 @@
<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 units="1/min">0.01</attachment_elastic_constant>
<attachment_rate units="1/min">0.0</attachment_rate>
<detachment_rate units="1/min">0.0</detachment_rate>
Expand Down Expand Up @@ -321,8 +319,6 @@
<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 units="1/min">0.01</attachment_elastic_constant>
<attachment_rate units="1/min">0.0</attachment_rate>
<detachment_rate units="1/min">0.0</detachment_rate>
Expand Down Expand Up @@ -473,8 +469,6 @@
<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 units="1/min">0.01</attachment_elastic_constant>
<attachment_rate units="1/min">0.0</attachment_rate>
<detachment_rate units="1/min">0.0</detachment_rate>
Expand Down Expand Up @@ -578,27 +572,27 @@
<cell_setup type="string" units="" description="single, random, lesion, cells at y = 0, circle of cells, invasive_spheroid, or cells at left boundary/march">invasive_spheroid</cell_setup>
<tumor_radius type="double" units="microns" description="Initial cell lesion radius (lesion only)">250</tumor_radius>
<initial_fibroblast_fraction type="double" units="dimensionless" description="Average percentage of fibroblasts initialized (lesion only)">0.0</initial_fibroblast_fraction>
<oxygen_uptake type="double" units="mmHg/min" description="Default cell oxygen uptake rate">10</oxygen_uptake>
<default_cell_speed type="double" units="microns/minute" description="Base/maximum cell speed">0.5</default_cell_speed>
<default_persistence_time type="double" units="minutes" description="Cell directional persistence time">10.0</default_persistence_time>
<fibroblast_adhesion type="double" units="micron/minute" description="Strength of fibroblast cells\' cell-cell adhesion">10.0</fibroblast_adhesion>
<fibroblast_repulsion type="double" units="micron/minute" description="Strength of fibroblast cells\' cell-cell repulsion">25.0</fibroblast_repulsion>
<inflam_sig_migration_bias_for_fibroblasts type="double" units="dimensionless" description="fibroblast chemotaxis bias">0.95</inflam_sig_migration_bias_for_fibroblasts>
<anisotropy_increase_rate type="double" units="1/min" description="Anisotropy rate of increase">0.004</anisotropy_increase_rate>
<fiber_realignment_rate type="double" units="1/min" description="Fiber rate of realignment">4.0</fiber_realignment_rate>
<default_ECM_density_target type="double" units="dimenionless" description="Cell ECM density target">0.5</default_ECM_density_target>
<default_ECM_production_rate type="double" units="dimenionless" description="Cell ECM production rate">0.001</default_ECM_production_rate>
<oxygen_uptake type="double" units="mmHg/min" description="Deprecated">10</oxygen_uptake>
<default_cell_speed type="double" units="microns/minute" description="Deprecated">0.5</default_cell_speed>
<default_persistence_time type="double" units="minutes" description="Deprecated">10.0</default_persistence_time>
<fibroblast_adhesion type="double" units="micron/minute" description="Deprecated">10.0</fibroblast_adhesion>
<fibroblast_repulsion type="double" units="micron/minute" description="Deprecated">25.0</fibroblast_repulsion>
<inflam_sig_migration_bias_for_fibroblasts type="double" units="dimensionless" description="Deprecated">0.95</inflam_sig_migration_bias_for_fibroblasts>
<anisotropy_increase_rate type="double" units="1/min" description="Deprecated">0.004</anisotropy_increase_rate>
<fiber_realignment_rate type="double" units="1/min" description="Deprecated">4.0</fiber_realignment_rate>
<default_ECM_density_target type="double" units="dimenionless" description="Deprecated">0.5</default_ECM_density_target>
<default_ECM_production_rate type="double" units="dimenionless" description="Deprecated">0.001</default_ECM_production_rate>
<number_of_fibroblasts type="int" units="" description="Number of fibroblasts to initialize">0</number_of_fibroblasts>
<cancer_cell_adhesion type="double" units="micron/minute" description="Strength of follower cells\' cell-cell adhesion">10.0</cancer_cell_adhesion>
<cancer_cell_repulsion type="double" units="micron/minute" description="Strength of follower cells\' cell-cell repulsion">25.0</cancer_cell_repulsion>
<default_chemotaxis_bias type="double" units="dimensionless" description="Follower chemotaxis bias">0.05</default_chemotaxis_bias>
<default_ECM_sensitivity type="double" units="dimensionless" description="Follower ECM orientation sensitivity">1.0</default_ECM_sensitivity>
<rho_L type="double" units="dimensionless" description="Minimum ECM density required for cell motility">0.0</rho_L>
<rho_H type="double" units="dimensionless" description="Maximum ECM density allowing cell motility">1.0</rho_H>
<rho_I type="double" units="dimensionless" description="Ideal ECM density cell motility">0.5</rho_I>
<default_hysteresis_bias type="double" units="dimensionless" description="Sensitivity to previous direction (hysteresis model only)">1.0</default_hysteresis_bias>
<fibroblast_motility_mode type="bool" units="dimensionless" description="">true</fibroblast_motility_mode>
<cancer_cell_motility_mode type="bool" units="dimensionless" description="">true</cancer_cell_motility_mode>
<cancer_cell_adhesion type="double" units="micron/minute" description="Deprecated">10.0</cancer_cell_adhesion>
<cancer_cell_repulsion type="double" units="micron/minute" description="Deprecated">25.0</cancer_cell_repulsion>
<default_chemotaxis_bias type="double" units="dimensionless" description="Deprecated">0.05</default_chemotaxis_bias>
<default_ECM_sensitivity type="double" units="dimensionless" description="Deprecated">1.0</default_ECM_sensitivity>
<rho_L type="double" units="dimensionless" description="Deprecated">0.0</rho_L>
<rho_H type="double" units="dimensionless" description="Deprecated">1.0</rho_H>
<rho_I type="double" units="dimensionless" description="Deprecated">0.5</rho_I>
<default_hysteresis_bias type="double" units="dimensionless" description="Deprecated">1.0</default_hysteresis_bias>
<fibroblast_motility_mode type="bool" units="dimensionless" description="Deprecated">true</fibroblast_motility_mode>
<cancer_cell_motility_mode type="bool" units="dimensionless" description="Deprecated">true</cancer_cell_motility_mode>
<chemotactic_substrate_decay_rate type="double" units="1/minutes" description="Oxygen decay rate">0.1</chemotactic_substrate_decay_rate>
<chemical_field_setup type="string" units="" description="Starburst, vertical up, horizontal right, angle, or none">none</chemical_field_setup>
<angle_of_chemical_field_gradient type="double" units="" description="Angle of chemical field gradient orientation, specified in degrees">45.0</angle_of_chemical_field_gradient>
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