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Updating README and other polishing edits prior to updating preprint #41

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merged 5 commits into from
Mar 13, 2024
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Updating README and other polishing edits prior to updating preprint #41

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f705ec5
Adding in output forlder for leader-follower model.
johnmetzcar Mar 6, 2024
f41bb88
Updated README. Minor edits to other files - including update to brin…
johnmetzcar Mar 12, 2024
305542f
Updating READMEs still. Updated model config files to note which user…
johnmetzcar Mar 12, 2024
616ae48
Updated ECM density and anisotropy to be more readily available to re…
johnmetzcar Mar 13, 2024
b12a652
Found a missing config file and two recently added imaging scripts.
johnmetzcar Mar 13, 2024
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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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Original file line number Diff line number Diff line change
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 @@ -320,8 +318,6 @@
<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>
Expand Down Expand Up @@ -471,8 +467,6 @@
<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 @@ -575,27 +569,27 @@
<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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Original file line number Diff line number Diff line change
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>
Expand Down
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