annotate test-data/PhysiCell_settings.xml @ 0:f7f40cc1cfce draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16

<PhysiCell_settings version="devel-version">

    <domain>
        <x_min>-30</x_min>
        <x_max>300</x_max>
        <y_min>-20</y_min>
        <y_max>200</y_max>
        <z_min>-10</z_min>
        <z_max>100</z_max>
        <dx>30</dx>
        <dy>20</dy>
        <dz>10</dz>
        <use_2D>false</use_2D>
    </domain>

    <overall>
        <max_time units="min">1440.0</max_time>
        <time_units>min</time_units>
        <space_units>micron</space_units>
        <dt_diffusion units="min">0.01</dt_diffusion>
        <dt_mechanics units="min">0.1</dt_mechanics>
        <dt_phenotype units="min">6</dt_phenotype>
    </overall>

    <parallel>
        <omp_num_threads>1</omp_num_threads>
    </parallel>

    <save>
        <folder>output</folder>
        <full_data>
            <interval units="min">60</interval>
            <enable>true</enable>
        </full_data>
        <SVG>
            <interval units="min">60</interval>
            <enable>false</enable>
            <plot_substrate enabled="false" limits="false">
                <substrate>water</substrate>
                <colormap>YlOrRd</colormap>
                <min_conc>0</min_conc>
                <max_conc>1</max_conc>
            </plot_substrate>
        </SVG>
        <legacy_data>
            <enable>false</enable>
        </legacy_data>
    </save>

    <options>
        <legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
        <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
        <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
        <random_seed>0</random_seed>
    </options>

    <microenvironment_setup>
        <variable name="oxygen" units="dimensionless" ID="0">
            <physical_parameter_set>
                <diffusion_coefficient units="micron^2/min">1e3</diffusion_coefficient>
                <decay_rate units="1/min">1</decay_rate>
            </physical_parameter_set>
            <initial_condition units="dimensionless">1e3</initial_condition>
            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
            <Dirichlet_options>
                <boundary_value ID="xmin" enabled="False" />
                <boundary_value ID="xmax" enabled="False" />
                <boundary_value ID="ymin" enabled="False" />
                <boundary_value ID="ymax" enabled="False" />
                <boundary_value ID="zmin" enabled="False" />
                <boundary_value ID="zmax" enabled="False" />
            </Dirichlet_options>
        </variable>
        <variable name="water" units="dimensionless" ID="1">
            <physical_parameter_set>
                <diffusion_coefficient units="micron^2/min">1e6</diffusion_coefficient>
                <decay_rate units="1/min">0.001</decay_rate>
            </physical_parameter_set>
            <initial_condition units="dimensionless">1e3</initial_condition>
            <Dirichlet_boundary_condition units="dimensionless" enabled="True">1e3</Dirichlet_boundary_condition>
            <Dirichlet_options>
                <boundary_value ID="xmin" enabled="True">1e3</boundary_value>
                <boundary_value ID="xmax" enabled="True">1e3</boundary_value>
                <boundary_value ID="ymin" enabled="True">1e3</boundary_value>
                <boundary_value ID="ymax" enabled="True">1e3</boundary_value>
                <boundary_value ID="zmin" enabled="True">1e3</boundary_value>
                <boundary_value ID="zmax" enabled="True">1e3</boundary_value>
            </Dirichlet_options>
        </variable>
        <options>
            <calculate_gradients>true</calculate_gradients>
            <track_internalized_substrates_in_each_agent>true</track_internalized_substrates_in_each_agent>
            <initial_condition type="matlab" enabled="false">
                <filename>./config/initial.mat</filename>
            </initial_condition>
            <dirichlet_nodes type="matlab" enabled="false">
                <filename>./config/dirichlet.mat</filename>
            </dirichlet_nodes>
        </options>
    </microenvironment_setup>

    <cell_definitions>
        <cell_definition name="default" ID="0">
            <phenotype>
                <cycle code="6" name="Flow cytometry model (separated)">
                    <phase_transition_rates units="1/min">
                        <rate start_index="0" end_index="1" fixed_duration="false">0.003333</rate>
                        <rate start_index="1" end_index="2" fixed_duration="true">0.002083</rate>
                        <rate start_index="2" end_index="3" fixed_duration="true">0.004167</rate>
                        <rate start_index="3" end_index="0" fixed_duration="true">0.016667</rate>
                    </phase_transition_rates>
                </cycle>
                <death>
                    <model code="100" name="apoptosis">
                        <death_rate units="1/min">5.31667e-05</death_rate>
                        <phase_durations units="min">
                            <duration index="0" fixed_duration="true">516</duration>
                        </phase_durations>
                        <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>
                        <phase_durations units="min">
                            <duration index="0" fixed_duration="true">0</duration>
                            <duration index="1" fixed_duration="true">86400</duration>
                        </phase_durations>
                        <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_fraction units="dimensionless">0.75</fluid_fraction>
                    <nuclear units="micron^3">540</nuclear>
                    <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>
                <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="blood_cells">1.0</cell_adhesion_affinity>
                        <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>
                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                    <attachment_rate units="1/min">0.05</attachment_rate>
                    <detachment_rate units="1/min">0.03</detachment_rate>
                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
                </mechanics>
                <motility>
                    <speed units="micron/min">1</speed>
                    <persistence_time units="min">1</persistence_time>
                    <migration_bias units="dimensionless">.2</migration_bias>
                    <options>
                        <enabled>true</enabled>
                        <use_2D>true</use_2D>
                        <chemotaxis>
                            <enabled>true</enabled>
                            <substrate>oxygen</substrate>
                            <direction>1</direction>
                        </chemotaxis>
                        <advanced_chemotaxis>
                            <enabled>false</enabled>
                            <normalize_each_gradient>false</normalize_each_gradient>
                            <chemotactic_sensitivities>
                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
                                <chemotactic_sensitivity substrate="water">0.0</chemotactic_sensitivity>
                            </chemotactic_sensitivities>
                        </advanced_chemotaxis>
                    </options>
                </motility>
                <secretion>
                    <substrate name="oxygen">
                        <secretion_rate units="1/min">0</secretion_rate>
                        <secretion_target units="substrate density">0</secretion_target>
                        <uptake_rate units="1/min">10</uptake_rate>
                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
                    </substrate>
                    <substrate name="water">
                        <secretion_rate units="1/min">5</secretion_rate>
                        <secretion_target units="substrate density">15</secretion_target>
                        <uptake_rate units="1/min">0</uptake_rate>
                        <net_export_rate units="total substrate/min">0</net_export_rate>
                    </substrate>
                </secretion>
                <cell_interactions>
                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
                    <live_phagocytosis_rates>
                        <phagocytosis_rate name="blood_cells" units="1/min">0.001</phagocytosis_rate>
                        <phagocytosis_rate name="default" units="1/min">0.0</phagocytosis_rate>
                    </live_phagocytosis_rates>
                    <attack_rates>
                        <attack_rate name="blood_cells" units="1/min">0.0025</attack_rate>
                        <attack_rate name="default" units="1/min">0.0</attack_rate>
                    </attack_rates>
                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
                    <attack_duration units="min">0.1</attack_duration>
                    <fusion_rates>
                        <fusion_rate name="blood_cells" units="1/min">0.0</fusion_rate>
                        <fusion_rate name="default" units="1/min">0.005</fusion_rate>
                    </fusion_rates>
                </cell_interactions>
                <cell_transformations>
                    <transformation_rates>
                        <transformation_rate name="blood_cells" units="1/min">0.0</transformation_rate>
                        <transformation_rate name="default" units="1/min">0.0</transformation_rate>
                    </transformation_rates>
                </cell_transformations>
                <cell_integrity>
                    <damage_rate units="1/min">0.0</damage_rate>
                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
                </cell_integrity>
            </phenotype>
            <custom_data>
                <sample conserved="false" units="dimensionless" description="">1.0</sample>
            </custom_data>
            <initial_parameter_distributions enabled="false">
          </initial_parameter_distributions>
        </cell_definition>
        <cell_definition name="blood_cells" ID="1">
            <phenotype>
                <cycle code="5" name="live">
                    <phase_durations units="min">
                        <duration index="0" fixed_duration="false">1388.888889</duration>
                    </phase_durations>
                </cycle>
                <death>
                    <model code="100" name="apoptosis">
                        <death_rate units="1/min">5.31667e-05</death_rate>
                        <phase_transition_rates units="1/min">
                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</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>
                        <phase_transition_rates units="1/min">
                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
                        </phase_transition_rates>
                        <parameters>
                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</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-05</cytoplasmic_biomass_change_rate>
                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
                            <calcification_rate units="1/min">7e-05</calcification_rate>
                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
                        </parameters>
                    </model>
                </death>
                <volume>
                    <total units="micron^3">2494</total>
                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
                    <nuclear units="micron^3">540</nuclear>
                    <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">0.0</calcified_fraction>
                    <calcification_rate units="1/min">0.0</calcification_rate>
                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
                </volume>
                <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="blood_cells">1.0</cell_adhesion_affinity>
                        <cell_adhesion_affinity name="default">1.0</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>
                    <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>
                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
                </mechanics>
                <motility>
                    <speed units="micron/min">2.5</speed>
                    <persistence_time units="min">1.0</persistence_time>
                    <migration_bias units="dimensionless">.5</migration_bias>
                    <options>
                        <enabled>true</enabled>
                        <use_2D>true</use_2D>
                        <chemotaxis>
                            <enabled>true</enabled>
                            <substrate>water</substrate>
                            <direction>1</direction>
                        </chemotaxis>
                        <advanced_chemotaxis>
                            <enabled>false</enabled>
                            <normalize_each_gradient>false</normalize_each_gradient>
                            <chemotactic_sensitivities>
                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
                                <chemotactic_sensitivity substrate="water">0.0</chemotactic_sensitivity>
                            </chemotactic_sensitivities>
                        </advanced_chemotaxis>
                    </options>
                </motility>
                <secretion>
                    <substrate name="oxygen">
                        <secretion_rate units="1/min">1000</secretion_rate>
                        <secretion_target units="substrate density">50000</secretion_target>
                        <uptake_rate units="1/min">0</uptake_rate>
                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
                    </substrate>
                    <substrate name="water">
                        <secretion_rate units="1/min">0</secretion_rate>
                        <secretion_target units="substrate density">1.0</secretion_target>
                        <uptake_rate units="1/min">10</uptake_rate>
                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
                    </substrate>
                </secretion>
                <cell_interactions>
                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
                    <live_phagocytosis_rates>
                        <phagocytosis_rate name="blood_cells" units="1/min">0.0</phagocytosis_rate>
                        <phagocytosis_rate name="default" units="1/min">0.0005</phagocytosis_rate>
                    </live_phagocytosis_rates>
                    <attack_rates>
                        <attack_rate name="blood_cells" units="1/min">0</attack_rate>
                        <attack_rate name="default" units="1/min">0.006</attack_rate>
                    </attack_rates>
                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
                    <attack_duration units="min">0.1</attack_duration>
                    <fusion_rates>
                        <fusion_rate name="blood_cells" units="1/min">0.0</fusion_rate>
                        <fusion_rate name="default" units="1/min">0.0</fusion_rate>
                    </fusion_rates>
                </cell_interactions>
                <cell_transformations>
                    <transformation_rates>
                        <transformation_rate name="blood_cells" units="1/min">0.0</transformation_rate>
                        <transformation_rate name="default" units="1/min">0.0</transformation_rate>
                    </transformation_rates>
                </cell_transformations>
                <cell_integrity>
                    <damage_rate units="1/min">0.0</damage_rate>
                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
                </cell_integrity>
            </phenotype>
            <custom_data>
                <sample conserved="false" units="dimensionless" description="">0.0</sample>
            </custom_data>
            <initial_parameter_distributions enabled="false">
          </initial_parameter_distributions>
        </cell_definition>
    </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="3.0" 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" description="">0</random_seed>
        <number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">64</number_of_cells>
    </user_parameters>
</PhysiCell_settings>