annotate test-data/initial.xml @ 0:8f7513d34212 draft default tip

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

<?xml version="1.0"?>
<MultiCellDS version="2" type="snapshot/simulation">
	<metadata>
		<software>
			<name>PhysiCell</name>
			<version>1.14.1</version>
			<URL>http://physicell.org</URL>
			<creator>
				<orcid-identifier>
					<path>0000-0002-9925-0151</path>
					<given-names>Paul</given-names>
					<family-name>Macklin</family-name>
					<email>[e-mail]</email>
					<url>http://MathCancer.org</url>
					<organization-name>Indiana University &amp; PhysiCell Project</organization-name>
					<department-name>Intelligent Systems Engineering</department-name>
				</orcid-identifier>
			</creator>
			<citation>
				<text>A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin. PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991</text>
				<DOI>10.1371/journal.pcbi.1005991</DOI>
				<URL>https://dx.doi.org/PMC5841829</URL>
				<PMID>29474446</PMID>
				<PMCID>PMC5841829</PMCID>
			</citation>
			<user />
		</software>
		<citation />
		<current_time units="min">0.000000</current_time>
		<current_runtime units="sec">0.008479</current_runtime>
		<created>2025-01-05T08:14:32Z</created>
		<last_modified>2025-01-05T08:14:32Z</last_modified>
	</metadata>
	<microenvironment>
		<domain name="microenvironment">
			<mesh type="Cartesian" uniform="false" regular="true" units="micron">
				<bounding_box type="axis-aligned" units="micron">-30.000000 -20.000000 -10.000000 300.000000 200.000000 100.000000</bounding_box>
				<x_coordinates delimiter=" ">-15 15 45 75 105 135 165 195 225 255 285</x_coordinates>
				<y_coordinates delimiter=" ">-10 10 30 50 70 90 110 130 150 170 190</y_coordinates>
				<z_coordinates delimiter=" ">-5 5 15 25 35 45 55 65 75 85 95</z_coordinates>
				<voxels type="matlab">
					<filename>initial_mesh0.mat</filename>
				</voxels>
			</mesh>
			<variables>
				<variable name="oxygen" units="dimensionless" ID="0">
					<physical_parameter_set>
						<conditions />
						<diffusion_coefficient units="micron^2/min">1000.000000</diffusion_coefficient>
						<decay_rate units="1/min">1.000000</decay_rate>
					</physical_parameter_set>
				</variable>
				<variable name="water" units="dimensionless" ID="1">
					<physical_parameter_set>
						<conditions />
						<diffusion_coefficient units="micron^2/min">1000000.000000</diffusion_coefficient>
						<decay_rate units="1/min">0.001000</decay_rate>
					</physical_parameter_set>
				</variable>
			</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="PhysiCell" data_version="2">
						<cell_types>
							<type ID="0" type="0">default</type>
							<type ID="1" type="1">blood_cells</type>
						</cell_types>
						<labels>
							<label index="0" size="1" units="none">ID</label>
							<label index="1" size="3" units="microns">position</label>
							<label index="4" size="1" units="cubic microns">total_volume</label>
							<label index="5" size="1" units="none">cell_type</label>
							<label index="6" size="1" units="none">cycle_model</label>
							<label index="7" size="1" units="none">current_phase</label>
							<label index="8" size="1" units="min">elapsed_time_in_phase</label>
							<label index="9" size="1" units="cubic microns">nuclear_volume</label>
							<label index="10" size="1" units="cubic microns">cytoplasmic_volume</label>
							<label index="11" size="1" units="none">fluid_fraction</label>
							<label index="12" size="1" units="none">calcified_fraction</label>
							<label index="13" size="3" units="none">orientation</label>
							<label index="16" size="1" units="none">polarity</label>
							<label index="17" size="3" units="micron/min">velocity</label>
							<label index="20" size="1" units="none">pressure</label>
							<label index="21" size="1" units="none">number_of_nuclei</label>
							<label index="22" size="1" units="min">total_attack_time</label>
							<label index="23" size="1" units="none">contact_with_basement_membrane</label>
							<label index="24" size="1" units="1/min">current_cycle_phase_exit_rate</label>
							<label index="25" size="1" units="min">elapsed_time_in_phase</label>
							<label index="26" size="1" units="none">dead</label>
							<label index="27" size="1" units="none">current_death_model</label>
							<label index="28" size="2" units="1/min">death_rates</label>
							<label index="30" size="1" units="1/min">cytoplasmic_biomass_change_rate</label>
							<label index="31" size="1" units="1/min">nuclear_biomass_change_rate</label>
							<label index="32" size="1" units="1/min">fluid_change_rate</label>
							<label index="33" size="1" units="1/min">calcification_rate</label>
							<label index="34" size="1" units="cubic microns">target_solid_cytoplasmic</label>
							<label index="35" size="1" units="cubic microns">target_solid_nuclear</label>
							<label index="36" size="1" units="none">target_fluid_fraction</label>
							<label index="37" size="1" units="microns">radius</label>
							<label index="38" size="1" units="microns">nuclear_radius</label>
							<label index="39" size="1" units="square microns">surface_area</label>
							<label index="40" size="1" units="micron/min">cell_cell_adhesion_strength</label>
							<label index="41" size="1" units="micron/min">cell_BM_adhesion_strength</label>
							<label index="42" size="1" units="micron/min">cell_cell_repulsion_strength</label>
							<label index="43" size="1" units="micron/min">cell_BM_repulsion_strength</label>
							<label index="44" size="2" units="none">cell_adhesion_affinities</label>
							<label index="46" size="1" units="none">relative_maximum_adhesion_distance</label>
							<label index="47" size="1" units="none">maximum_number_of_attachments</label>
							<label index="48" size="1" units="1/min">attachment_elastic_constant</label>
							<label index="49" size="1" units="1/min">attachment_rate</label>
							<label index="50" size="1" units="1/min">detachment_rate</label>
							<label index="51" size="1" units="none">is_motile</label>
							<label index="52" size="1" units="min">persistence_time</label>
							<label index="53" size="1" units="micron/min">migration_speed</label>
							<label index="54" size="3" units="none">migration_bias_direction</label>
							<label index="57" size="1" units="none">migration_bias</label>
							<label index="58" size="3" units="micron/min">motility_vector</label>
							<label index="61" size="1" units="none">chemotaxis_index</label>
							<label index="62" size="1" units="none">chemotaxis_direction</label>
							<label index="63" size="2" units="none">chemotactic_sensitivities</label>
							<label index="65" size="2" units="1/min">secretion_rates</label>
							<label index="67" size="2" units="1/min">uptake_rates</label>
							<label index="69" size="2" units="stuff/cubic micron">saturation_densities</label>
							<label index="71" size="2" units="stuff/min">net_export_rates</label>
							<label index="73" size="2" units="stuff">internalized_total_substrates</label>
							<label index="75" size="2" units="none">fraction_released_at_death</label>
							<label index="77" size="2" units="none">fraction_transferred_when_ingested</label>
							<label index="79" size="1" units="1/min">apoptotic_phagocytosis_rate</label>
							<label index="80" size="1" units="1/min">necrotic_phagocytosis_rate</label>
							<label index="81" size="1" units="1/min">other_dead_phagocytosis_rate</label>
							<label index="82" size="2" units="1/min">live_phagocytosis_rates</label>
							<label index="84" size="2" units="1/min">attack_rates</label>
							<label index="86" size="2" units="none">immunogenicities</label>
							<label index="88" size="1" units="none">attack_target</label>
							<label index="89" size="1" units="1/min">attack_damage_rate</label>
							<label index="90" size="1" units="min">attack_duration</label>
							<label index="91" size="1" units="none">attack_total_damage_delivered</label>
							<label index="92" size="2" units="1/min">fusion_rates</label>
							<label index="94" size="2" units="1/min">transformation_rates</label>
							<label index="96" size="2" units="none">asymmetric_division_probabilities</label>
							<label index="98" size="1" units="none">damage</label>
							<label index="99" size="1" units="1/min">damage_rate</label>
							<label index="100" size="1" units="1/min">damage_repair_rate</label>
							<label index="101" size="1" units="dimensionless">sample</label>
						</labels>
						<filename>initial_cells.mat</filename>
					</simplified_data>
					<neighbor_graph type="text" source="PhysiCell" data_version="2">
						<filename>initial_cell_neighbor_graph.txt</filename>
					</neighbor_graph>
					<attached_cells_graph type="text" source="PhysiCell" data_version="2">
						<filename>initial_attached_cells_graph.txt</filename>
					</attached_cells_graph>
					<spring_attached_cells_graph type="text" source="PhysiCell" data_version="2">
						<filename>initial_spring_attached_cells_graph.txt</filename>
					</spring_attached_cells_graph>
				</custom>
			</cell_population>
		</cell_populations>
	</cellular_information>
</MultiCellDS>