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‎Makefile‎

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‎config/PhysiCell_settings.xml‎

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‎config/cell_rules.csv‎

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‎config/cells.csv‎

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‎custom_modules/custom.cpp‎

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/*
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###############################################################################
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# If you use PhysiCell in your project, please cite PhysiCell and the version #
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# number, such as below: #
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# #
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# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
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# #
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# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
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# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
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# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
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# DOI: 10.1371/journal.pcbi.1005991 #
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# #
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# See VERSION.txt or call get_PhysiCell_version() to get the current version #
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# x.y.z. Call display_citations() to get detailed information on all cite-#
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# able software used in your PhysiCell application. #
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# #
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# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
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# as below: #
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# #
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# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
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# with BioFVM [2] to solve the transport equations. #
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# #
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# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
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# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
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# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
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# DOI: 10.1371/journal.pcbi.1005991 #
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# #
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# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
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# llelized diffusive transport solver for 3-D biological simulations, #
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# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
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# #
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###############################################################################
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# #
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# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
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# #
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# Copyright (c) 2015-2021, Paul Macklin and the PhysiCell Project #
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# All rights reserved. #
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# #
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# Redistribution and use in source and binary forms, with or without #
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# modification, are permitted provided that the following conditions are met: #
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# #
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# 1. Redistributions of source code must retain the above copyright notice, #
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# this list of conditions and the following disclaimer. #
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# #
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# 2. Redistributions in binary form must reproduce the above copyright #
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# notice, this list of conditions and the following disclaimer in the #
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# documentation and/or other materials provided with the distribution. #
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# #
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# 3. Neither the name of the copyright holder nor the names of its #
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# contributors may be used to endorse or promote products derived from this #
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# software without specific prior written permission. #
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# #
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
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# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
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# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
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# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
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# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
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# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
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# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
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# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
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# POSSIBILITY OF SUCH DAMAGE. #
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# #
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###############################################################################
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*/
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#include "./custom.h"
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void create_cell_types( void )
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{
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// set the random seed
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if (parameters.ints.find_index("random_seed") != -1)
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{
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SeedRandom(parameters.ints("random_seed"));
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}
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/*
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Put any modifications to default cell definition here if you
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want to have "inherited" by other cell types.
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This is a good place to set default functions.
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*/
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initialize_default_cell_definition();
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cell_defaults.phenotype.secretion.sync_to_microenvironment( &microenvironment );
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cell_defaults.functions.volume_update_function = standard_volume_update_function;
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cell_defaults.functions.update_velocity = standard_update_cell_velocity;
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cell_defaults.functions.update_migration_bias = NULL;
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cell_defaults.functions.update_phenotype = NULL; // update_cell_and_death_parameters_O2_based;
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cell_defaults.functions.custom_cell_rule = NULL;
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cell_defaults.functions.contact_function = NULL;
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cell_defaults.functions.add_cell_basement_membrane_interactions = NULL;
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cell_defaults.functions.calculate_distance_to_membrane = NULL;
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/*
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This parses the cell definitions in the XML config file.
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*/
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initialize_cell_definitions_from_pugixml();
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/*
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This builds the map of cell definitions and summarizes the setup.
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*/
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build_cell_definitions_maps();
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/*
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This intializes cell signal and response dictionaries
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*/
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setup_signal_behavior_dictionaries();
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/*
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Cell rule definitions
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*/
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setup_cell_rules();
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/*
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Put any modifications to individual cell definitions here.
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This is a good place to set custom functions.
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*/
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cell_defaults.functions.update_phenotype = phenotype_function;
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cell_defaults.functions.custom_cell_rule = custom_function;
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cell_defaults.functions.contact_function = contact_function;
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/*
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This builds the map of cell definitions and summarizes the setup.
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*/
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display_cell_definitions( std::cout );
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return;
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}
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void setup_microenvironment( void )
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{
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// set domain parameters
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// put any custom code to set non-homogeneous initial conditions or
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// extra Dirichlet nodes here.
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// initialize BioFVM
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initialize_microenvironment();
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return;
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}
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void setup_tissue( void )
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{
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double Xmin = microenvironment.mesh.bounding_box[0];
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double Ymin = microenvironment.mesh.bounding_box[1];
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double Zmin = microenvironment.mesh.bounding_box[2];
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double Xmax = microenvironment.mesh.bounding_box[3];
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double Ymax = microenvironment.mesh.bounding_box[4];
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double Zmax = microenvironment.mesh.bounding_box[5];
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if( default_microenvironment_options.simulate_2D == true )
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{
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Zmin = 0.0;
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Zmax = 0.0;
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}
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double Xrange = Xmax - Xmin;
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double Yrange = Ymax - Ymin;
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double Zrange = Zmax - Zmin;
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// create some of each type of cell
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Cell* pC;
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for( int k=0; k < cell_definitions_by_index.size() ; k++ )
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{
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Cell_Definition* pCD = cell_definitions_by_index[k];
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std::cout << "Placing cells of type " << pCD->name << " ... " << std::endl;
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for( int n = 0 ; n < parameters.ints("number_of_cells") ; n++ )
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{
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std::vector<double> position = {0,0,0};
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position[0] = Xmin + UniformRandom()*Xrange;
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position[1] = Ymin + UniformRandom()*Yrange;
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position[2] = Zmin + UniformRandom()*Zrange;
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pC = create_cell( *pCD );
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pC->assign_position( position );
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}
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}
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std::cout << std::endl;
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// load cells from your CSV file (if enabled)
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load_cells_from_pugixml();
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set_parameters_from_distributions();
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return;
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}
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std::vector<std::string> my_coloring_function( Cell* pCell )
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{ return paint_by_number_cell_coloring(pCell); }
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void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt )
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{ return; }
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void custom_function( Cell* pCell, Phenotype& phenotype , double dt )
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{ return; }
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void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt )
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{ return; }

‎custom_modules/custom.h‎

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/*
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###############################################################################
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# If you use PhysiCell in your project, please cite PhysiCell and the version #
4+
# number, such as below: #
5+
# #
6+
# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
7+
# #
8+
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
9+
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
10+
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
11+
# DOI: 10.1371/journal.pcbi.1005991 #
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# #
13+
# See VERSION.txt or call get_PhysiCell_version() to get the current version #
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# x.y.z. Call display_citations() to get detailed information on all cite-#
15+
# able software used in your PhysiCell application. #
16+
# #
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# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
18+
# as below: #
19+
# #
20+
# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
21+
# with BioFVM [2] to solve the transport equations. #
22+
# #
23+
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
24+
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
25+
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
26+
# DOI: 10.1371/journal.pcbi.1005991 #
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# #
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# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
29+
# llelized diffusive transport solver for 3-D biological simulations, #
30+
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
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# #
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###############################################################################
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# #
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# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
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# #
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# Copyright (c) 2015-2021, Paul Macklin and the PhysiCell Project #
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# All rights reserved. #
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# #
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# Redistribution and use in source and binary forms, with or without #
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# modification, are permitted provided that the following conditions are met: #
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# #
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# 1. Redistributions of source code must retain the above copyright notice, #
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# this list of conditions and the following disclaimer. #
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# #
45+
# 2. Redistributions in binary form must reproduce the above copyright #
46+
# notice, this list of conditions and the following disclaimer in the #
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# documentation and/or other materials provided with the distribution. #
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# #
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# 3. Neither the name of the copyright holder nor the names of its #
50+
# contributors may be used to endorse or promote products derived from this #
51+
# software without specific prior written permission. #
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# #
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
54+
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
55+
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
56+
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
57+
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
58+
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
59+
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
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# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
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# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
62+
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
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# POSSIBILITY OF SUCH DAMAGE. #
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# #
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###############################################################################
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*/
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#include "../core/PhysiCell.h"
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#include "../modules/PhysiCell_standard_modules.h"
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using namespace BioFVM;
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using namespace PhysiCell;
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// setup functions to help us along
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void create_cell_types( void );
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void setup_tissue( void );
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// set up the BioFVM microenvironment
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void setup_microenvironment( void );
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// custom pathology coloring function
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std::vector<std::string> my_coloring_function( Cell* );
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// custom functions can go here
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void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt );
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void custom_function( Cell* pCell, Phenotype& phenotype , double dt );
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void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt );
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