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Merge pull request #4 from PhysiCell-Tools/development
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‎VERSION.txt‎

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1.0.0

‎matlab_example/citation and license.txt‎

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This dataset is posted online with the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
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It requires that you cite the source of this dataset for *any* reuse:
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A. Ghaffarizadeh, S.H. Friedman, S.M. Mumenthaler, and P. Macklin.
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PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems.
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PLoS Comput. Biol., 2017 (preprint, in review). DOI: 10.1101/088773.
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Please check http://PhysiCell.MathCancer.org for the most recent citation information as
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this article undergoes peer review.
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For the full text and legal conditions of the CC BY 4.0 license, see:
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https://creativecommons.org/licenses/by/4.0/

‎matlab_example/initial_mesh0.mat‎

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‎matlab_example/output00003696.xml‎

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<?xml version="1.0"?>
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<MultiCellDS version="0.5" type="snapshot/simulation">
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<metadata>
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<software>
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<name>BioFVM</name>
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<version>1.1.6</version>
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<URL>http://BioFVM.MathCancer.org</URL>
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<creator />
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<citation />
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<user />
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</software>
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<citation />
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<current_time units="min">30239.999998</current_time>
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<current_runtime units="sec">191255.188684</current_runtime>
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<created>2017-08-27T04:28:34Z</created>
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<last_modified>2017-08-27T04:28:34Z</last_modified>
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</metadata>
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<microenvironment>
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<domain name="microenvironment">
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<mesh type="Cartesian" uniform="true" regular="true" units="micron">
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<bounding_box type="axis-aligned" units="micron">-750.000000 -750.000000 -750.000000 750.000000 750.000000 750.000000</bounding_box>
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<x_coordinates delimiter=" ">-740.000000 -720.000000 -700.000000 -680.000000 -660.000000 -640.000000 -620.000000 -600.000000 -580.000000 -560.000000 -540.000000 -520.000000 -500.000000 -480.000000 -460.000000 -440.000000 -420.000000 -400.000000 -380.000000 -360.000000 -340.000000 -320.000000 -300.000000 -280.000000 -260.000000 -240.000000 -220.000000 -200.000000 -180.000000 -160.000000 -140.000000 -120.000000 -100.000000 -80.000000 -60.000000 -40.000000 -20.000000 0.000000 20.000000 40.000000 60.000000 80.000000 100.000000 120.000000 140.000000 160.000000 180.000000 200.000000 220.000000 240.000000 260.000000 280.000000 300.000000 320.000000 340.000000 360.000000 380.000000 400.000000 420.000000 440.000000 460.000000 480.000000 500.000000 520.000000 540.000000 560.000000 580.000000 600.000000 620.000000 640.000000 660.000000 680.000000 700.000000 720.000000 740.000000</x_coordinates>
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<y_coordinates delimiter=" ">-740.000000 -720.000000 -700.000000 -680.000000 -660.000000 -640.000000 -620.000000 -600.000000 -580.000000 -560.000000 -540.000000 -520.000000 -500.000000 -480.000000 -460.000000 -440.000000 -420.000000 -400.000000 -380.000000 -360.000000 -340.000000 -320.000000 -300.000000 -280.000000 -260.000000 -240.000000 -220.000000 -200.000000 -180.000000 -160.000000 -140.000000 -120.000000 -100.000000 -80.000000 -60.000000 -40.000000 -20.000000 0.000000 20.000000 40.000000 60.000000 80.000000 100.000000 120.000000 140.000000 160.000000 180.000000 200.000000 220.000000 240.000000 260.000000 280.000000 300.000000 320.000000 340.000000 360.000000 380.000000 400.000000 420.000000 440.000000 460.000000 480.000000 500.000000 520.000000 540.000000 560.000000 580.000000 600.000000 620.000000 640.000000 660.000000 680.000000 700.000000 720.000000 740.000000</y_coordinates>
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<z_coordinates delimiter=" ">-740.000000 -720.000000 -700.000000 -680.000000 -660.000000 -640.000000 -620.000000 -600.000000 -580.000000 -560.000000 -540.000000 -520.000000 -500.000000 -480.000000 -460.000000 -440.000000 -420.000000 -400.000000 -380.000000 -360.000000 -340.000000 -320.000000 -300.000000 -280.000000 -260.000000 -240.000000 -220.000000 -200.000000 -180.000000 -160.000000 -140.000000 -120.000000 -100.000000 -80.000000 -60.000000 -40.000000 -20.000000 0.000000 20.000000 40.000000 60.000000 80.000000 100.000000 120.000000 140.000000 160.000000 180.000000 200.000000 220.000000 240.000000 260.000000 280.000000 300.000000 320.000000 340.000000 360.000000 380.000000 400.000000 420.000000 440.000000 460.000000 480.000000 500.000000 520.000000 540.000000 560.000000 580.000000 600.000000 620.000000 640.000000 660.000000 680.000000 700.000000 720.000000 740.000000</z_coordinates>
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<voxels type="matlab">
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<filename>initial_mesh0.mat</filename>
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</voxels>
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</mesh>
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<variables>
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<variable name="oxygen" units="mmHg" ID="0">
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<physical_parameter_set>
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<conditions />
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<diffusion_coefficient units="micron^2/min">100000.000000</diffusion_coefficient>
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<decay_rate units="1/min">0.100000</decay_rate>
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</physical_parameter_set>
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</variable>
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<variable name="immunostimulatory factor" units="dimensionless" ID="1">
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<physical_parameter_set>
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<conditions />
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<diffusion_coefficient units="micron^2/min">1000.000000</diffusion_coefficient>
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<decay_rate units="1/min">0.016000</decay_rate>
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</physical_parameter_set>
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</variable>
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</variables>
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<data type="matlab">
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<filename>output00003696_microenvironment0.mat</filename>
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</data>
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</domain>
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</microenvironment>
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<cellular_information>
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<cell_populations>
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<cell_population type="individual">
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<custom>
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<simplified_data type="matlab" source="BioFVM">
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<filename>output00003696_cells.mat</filename>
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</simplified_data>
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<simplified_data type="matlab" source="PhysiCell">
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<labels>
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<label index="0" size="1">ID</label>
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<label index="1" size="3">position</label>
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<label index="4" size="1">total_volume</label>
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<label index="5" size="1">cell_type</label>
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<label index="6" size="1">cycle_model</label>
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<label index="7" size="1">current_phase</label>
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<label index="8" size="1">elapsed_time_in_phase</label>
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<label index="9" size="1">nuclear_volume</label>
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<label index="10" size="1">cytoplasmic_volume</label>
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<label index="11" size="1">fluid_fraction</label>
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<label index="12" size="1">calcified_fraction</label>
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<label index="13" size="3">orientation</label>
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<label index="16" size="1">polarity</label>
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<label index="17" size="1">migration_speed</label>
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<label index="18" size="3">motility_vector</label>
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<label index="21" size="1">migration_bias</label>
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<label index="22" size="3">motility_bias_direction</label>
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<label index="25" size="1">persistence_time</label>
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<label index="26" size="1">motility_reserved</label>
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<label index="27" size="1">oncoprotein</label>
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<label index="28" size="1">elastic coefficient</label>
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<label index="29" size="1">kill rate</label>
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<label index="30" size="1">attachment lifetime</label>
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<label index="31" size="1">attachment rate</label>
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</labels>
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<filename>output00003696_cells_physicell.mat</filename>
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</simplified_data>
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</custom>
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</cell_population>
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</cell_populations>
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</cellular_information>
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</MultiCellDS>

‎matlab_example/output00003696_cells.mat‎

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‎matlab_example/output00003696_cells_physicell.mat‎

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‎matlab_example/output00003696_microenvironment0.mat‎

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