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config.xml
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config.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!--
/*
###############################################################################
# If you use PhysiCell in your project, please cite PhysiCell and the version #
# number, such as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# See VERSION.txt or call get_PhysiCell_version() to get the current version #
# x.y.z. Call display_citations() to get detailed information on all cite-#
# able software used in your PhysiCell application. #
# #
# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
# as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
# with BioFVM [2] to solve the transport equations. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
# llelized diffusive transport solver for 3-D biological simulations, #
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
###############################################################################
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
# modification, are permitted provided that the following conditions are met: #
# #
# 1. Redistributions of source code must retain the above copyright notice, #
# this list of conditions and the following disclaimer. #
# #
# 2. Redistributions in binary form must reproduce the above copyright #
# notice, this list of conditions and the following disclaimer in the #
# documentation and/or other materials provided with the distribution. #
# #
# 3. Neither the name of the copyright holder nor the names of its #
# contributors may be used to endorse or promote products derived from this #
# software without specific prior written permission. #
# #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
# POSSIBILITY OF SUCH DAMAGE. #
# #
###############################################################################
*/
-->
<!--
<user_details />
-->
<PhysiCell_settings version="devel-version">
<domain>
<x_min>-1000</x_min>
<x_max>1000</x_max>
<y_min>-1000</y_min>
<y_max>1000</y_max>
<z_min>-10</z_min>
<z_max>10</z_max>
<dx>20</dx>
<dy>20</dy>
<dz>20</dz>
<use_2D>true</use_2D>
</domain>
<overall>
<max_time units="min">60</max_time>
<time_units>min</time_units>
<space_units>micron</space_units>
</overall>
<parallel>
<omp_num_threads>4</omp_num_threads>
</parallel>
<save>
<folder>output</folder> <!-- use . for root -->
<full_data>
<interval units="min">10</interval>
<enable>true</enable>
</full_data>
<SVG>
<interval units="min">10</interval>
<enable>true</enable>
</SVG>
<legacy_data>
<enable>false</enable>
</legacy_data>
</save>
<user_parameters>
<random_seed type="int" units="dimensionless" hidden="true">0</random_seed>
<!-- for microenvironment setup -->
<cargo_signal_D type="double" units="micron/min^2" description="cargo signal diffusion coefficient">1e3</cargo_signal_D>
<cargo_signal_decay type="double" units="1/min" description="cargo signal decay rate">.4</cargo_signal_decay> <!-- 50 micron length scale -->
<director_signal_D type="double" units="micron/min^2" description="director signal diffusion coefficient">1e3</director_signal_D>
<director_signal_decay type="double" units="1/min" description="director signal decay rate">.1</director_signal_decay> <!-- 100 micron length scale -->
<!-- for cell definitions -->
<elastic_coefficient type="double" units="1/min" description="elastic coefficient of cells">0.05</elastic_coefficient>
<worker_motility_persistence_time type="double" units="min" description="persistance time for worker motility">5.0</worker_motility_persistence_time>
<worker_migration_speed type="double" units="micron/min" description="speed of worker cells">5.0</worker_migration_speed>
<attached_worker_migration_bias type="double" description="migration bias of attached workers">1.0</attached_worker_migration_bias>
<unattached_worker_migration_bias type="double" description="migration bias of unattached workers">0.5</unattached_worker_migration_bias>
<!-- tissue setup -->
<number_of_directors type="int" units="none" description="# of director cells">15</number_of_directors>
<number_of_cargo_clusters type="int" units="none" description="# of cargo clusters">100</number_of_cargo_clusters>
<number_of_workers type="int" units="none" description="# of worker cells">50</number_of_workers>
<!-- cargo parameters -->
<drop_threshold type="double" units="dimensionless" description="threshold to drop cargo">0.4</drop_threshold>
<!-- colors -->
<worker_color type="string" units="none" description="color of worker cells">red</worker_color>
<cargo_color type="string" units="none" description="color of cargo cells">blue</cargo_color>
<director_color type="string" units="none" description="color of director cells">limegreen</director_color>
</user_parameters>
</PhysiCell_settings>