├── .github └── workflows │ ├── build_binaries.yml │ └── tests.yml ├── .gitignore ├── BioFVM ├── BioFVM.h ├── BioFVM_MultiCellDS.cpp ├── BioFVM_MultiCellDS.h ├── BioFVM_agent_container.cpp ├── BioFVM_agent_container.h ├── BioFVM_basic_agent.cpp ├── BioFVM_basic_agent.h ├── BioFVM_matlab.cpp ├── BioFVM_matlab.h ├── BioFVM_mesh.cpp ├── BioFVM_mesh.h ├── BioFVM_microenvironment.cpp ├── BioFVM_microenvironment.h ├── BioFVM_solvers.cpp ├── BioFVM_solvers.h ├── BioFVM_utilities.cpp ├── BioFVM_utilities.h ├── BioFVM_vector.cpp ├── BioFVM_vector.h ├── pugiconfig.hpp ├── pugixml.cpp └── pugixml.hpp ├── CITATION.txt ├── Makefile ├── README.md ├── VERSION.txt ├── addons ├── PhysiBoSS │ ├── setup_libmaboss.py │ └── src │ │ ├── maboss_intracellular.cpp │ │ ├── maboss_intracellular.h │ │ ├── maboss_network.cpp │ │ ├── maboss_network.h │ │ ├── utils.cpp │ │ └── utils.h ├── PhysiMeSS │ ├── PhysiMeSS.cpp │ ├── PhysiMeSS.h │ ├── PhysiMeSS_agent.cpp │ ├── PhysiMeSS_agent.h │ ├── PhysiMeSS_cell.cpp │ ├── PhysiMeSS_cell.h │ ├── PhysiMeSS_fibre.cpp │ ├── PhysiMeSS_fibre.h │ └── README.md ├── dFBA │ ├── src │ │ ├── FBA_metabolite.cpp │ │ ├── FBA_metabolite.h │ │ ├── FBA_model.cpp │ │ ├── FBA_model.h │ │ ├── FBA_reaction.cpp │ │ ├── FBA_reaction.h │ │ ├── dfba_intracellular.cpp │ │ └── dfba_intracellular.h │ └── test │ │ ├── data │ │ ├── Ecoli_core.xml │ │ └── iSIM.xml │ │ ├── testClp.cpp │ │ ├── testFBA.cpp │ │ ├── testSBML.cpp │ │ └── test_problem.lp └── libRoadrunner │ ├── empty.txt │ └── src │ ├── librr_intracellular.cpp │ └── librr_intracellular.h ├── beta ├── anim_substrate2D.py ├── anim_svg.py ├── anim_svg_cycle.py ├── cell_tracks.py ├── download_binary.py ├── empty.txt ├── fba_packages.json ├── get_physicell.py ├── get_studio.py ├── new_cell_def.xml ├── params_biorobots.txt ├── params_run.py ├── params_run.txt ├── plot_cells.py ├── plot_data.py ├── pyMCDS.py ├── setup_coin_clp.py ├── setup_fba.py ├── setup_libroadrunner.py ├── setup_windows_dep.py ├── test_build_samples.sh ├── test_diff_svg.py ├── test_diffs_svg.py ├── test_plot_svgs_montage.py ├── test_run_sample.py ├── test_run_samples.py ├── update_Makefiles.py ├── vis_tab.py └── vis_tab_cells_only.py ├── changes.md ├── config └── PhysiCell_settings.xml ├── core ├── PhysiCell.h ├── PhysiCell_basic_signaling.cpp ├── PhysiCell_basic_signaling.h ├── PhysiCell_cell.cpp ├── PhysiCell_cell.h ├── PhysiCell_cell_container.cpp ├── PhysiCell_cell_container.h ├── PhysiCell_constants.cpp ├── PhysiCell_constants.h ├── PhysiCell_custom.cpp ├── PhysiCell_custom.h ├── PhysiCell_digital_cell_line.cpp ├── PhysiCell_digital_cell_line.h ├── PhysiCell_phenotype.cpp ├── PhysiCell_phenotype.h ├── PhysiCell_rules.cpp ├── PhysiCell_rules.h ├── PhysiCell_signal_behavior.cpp ├── PhysiCell_signal_behavior.h ├── PhysiCell_standard_models.cpp ├── PhysiCell_standard_models.h ├── PhysiCell_utilities.cpp └── PhysiCell_utilities.h ├── custom_modules └── empty.txt ├── documentation-deprecated ├── PhysiCell_tutorial(old).pdf ├── PhysiCell_tutorial(old).tex ├── Quickstart.md ├── User_Guide.log ├── User_Guide.pdf ├── User_Guide.synctex.gz ├── User_Guide.tex ├── images │ ├── ParaView_clip_planes.png │ ├── ParaView_clipping_histo.png │ ├── PhysiCell_ParaView_quickstart.png │ ├── Tutorial1_fig1.eps │ ├── Tutorial1_fig1.png │ ├── Tutorial1_fig2.eps │ ├── Tutorial1_fig2.png │ ├── Tutorial2_fig1.eps │ ├── Tutorial2_fig1.png │ ├── Tutorial3_fig1.eps │ ├── Tutorial3_fig1.png │ ├── anaconda_add_to_path_med.png │ ├── cancer_immune_seq4x1_small.png │ ├── cancer_immune_snapshot00000574_small.png │ ├── duct_structure.png │ ├── duct_structure.pptx │ ├── mingw64_env_var_path.png │ ├── plot_cells_gui_biorobots_med.png │ ├── plot_cells_gui_biorobots_small.png │ ├── sample_colormap.eps │ ├── sample_colormap.png │ ├── sample_contour.eps │ ├── sample_contour.png │ ├── sample_surface.eps │ └── sample_surface.png ├── math │ ├── substrate-internalization-equations.log │ ├── substrate-internalization-equations.pdf │ ├── substrate-internalization-equations.synctex.gz │ └── substrate-internalization-equations.tex ├── matlab │ ├── Cytometry_exact.m │ ├── Cytometry_separated_exact.m │ ├── Ki67_basic_exact.m │ ├── Ki67_exact.m │ ├── Live_exact.m │ ├── tune_Ki67_advanced.m │ ├── tune_Ki67_basic.m │ ├── tune_cytometry.m │ ├── tune_cytometry_separated.m │ └── tune_death_in_live_model.m ├── readme.txt └── references.bib ├── examples ├── PhysiCell_test_DCIS.cpp ├── PhysiCell_test_HDS.cpp ├── PhysiCell_test_cell_cycle.cpp ├── PhysiCell_test_mechanics_1.cpp ├── PhysiCell_test_mechanics_2.cpp └── PhysiCell_test_volume.cpp ├── licenses ├── BioFVM.txt ├── MaBoSS.txt ├── PhysiCell.txt └── pugixml.txt ├── matlab ├── composite_cutaway_plot.m ├── cross_section_colormap.m ├── cross_section_contour.m ├── cross_section_surface.m ├── my_immune_plot.m ├── plot_microenvironment.m ├── read_MultiCellDS_xml.m ├── read_MultiCellDS_xml_old.m ├── read_microenvironment.m ├── set_MCDS_constants.m ├── simple_cutaway_plot.m └── simple_plot.m ├── modules ├── PhysiCell_MultiCellDS.cpp ├── PhysiCell_MultiCellDS.h ├── PhysiCell_POV.cpp ├── PhysiCell_POV.h ├── PhysiCell_SVG.cpp ├── PhysiCell_SVG.h ├── PhysiCell_geometry.cpp ├── PhysiCell_geometry.h ├── PhysiCell_pathology.cpp ├── PhysiCell_pathology.h ├── PhysiCell_pugixml.cpp ├── PhysiCell_pugixml.h ├── PhysiCell_settings.cpp ├── PhysiCell_settings.h ├── PhysiCell_standard_modules.h ├── PhysiCell_various_outputs.cpp └── PhysiCell_various_outputs.h ├── output └── empty.txt ├── povray ├── footer.inc ├── header-2D.inc ├── header-front-view.inc ├── header.inc ├── header_3D_cornerview.inc ├── header_front_view_no_box.inc └── header_with_clipping_plane.inc ├── protocols ├── adding new signals or behaviors.md └── new release protocol.txt ├── sample_projects ├── Makefile-default ├── asymmetric_division │ ├── Makefile │ ├── config │ │ ├── PhysiCell_settings.xml │ │ ├── cell_rules.csv │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ └── main.cpp ├── biorobots │ ├── Makefile │ ├── VERSION.txt │ ├── config │ │ ├── PhysiCell_settings.xml │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ └── main.cpp ├── cancer_biorobots │ ├── Makefile │ ├── VERSION.txt │ ├── config │ │ ├── PhysiCell_settings.xml │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ ├── custom.h │ │ └── empty.txt │ └── main.cpp ├── cancer_immune │ ├── Makefile │ ├── config │ │ └── PhysiCell_settings.xml │ ├── custom_modules │ │ ├── cancer_immune_3D.cpp │ │ └── cancer_immune_3D.h │ ├── main-cancer_immune_3D.cpp │ └── scripts │ │ ├── CI_POV_writer.cpp │ │ ├── CI_script.cpp │ │ ├── minutes_to_label.m │ │ ├── my_immune_plot.m │ │ └── temp_labeling_script.m ├── celltypes3 │ ├── Makefile │ ├── config │ │ └── PhysiCell_settings.xml │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ ├── main.cpp │ └── scripts │ │ └── empty.txt ├── custom_division │ ├── Makefile │ ├── config │ │ ├── PhysiCell_settings.xml │ │ ├── cell_rules.csv │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ └── main.cpp ├── episode │ ├── Makefile │ ├── README.txt │ ├── config │ │ ├── PhysiCell_settings.xml │ │ ├── cell_rules.csv │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ ├── main.cpp │ └── scripts │ │ └── empty.txt ├── heterogeneity │ ├── Makefile │ ├── VERSION.txt │ ├── config │ │ ├── PhysiCell_settings.xml │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ ├── custom.h │ │ └── empty.txt │ └── main.cpp ├── immune_function │ ├── Makefile │ ├── VERSION.txt │ ├── config │ │ ├── PhysiCell_settings.xml │ │ ├── cell_rules.csv │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ └── main.cpp ├── interactions │ ├── Makefile │ ├── config │ │ ├── PhysiCell_settings.xml │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ ├── main.cpp │ └── scripts │ │ └── empty.txt ├── mechano │ ├── Makefile │ ├── config │ │ ├── PhysiCell_settings.xml │ │ ├── cells-double-membrane.csv │ │ ├── cells-shell.csv │ │ ├── cells-single-membrane.csv │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ ├── custom.h │ │ └── empty.txt │ └── main.cpp ├── physimess │ ├── Makefile │ ├── config │ │ ├── Cell_Fibre_Mechanics │ │ │ ├── fibre_maze.csv │ │ │ ├── hinge.csv │ │ │ ├── mymodel_fibremaze.xml │ │ │ ├── mymodel_hinge.xml │ │ │ ├── mymodel_pushing.xml │ │ │ ├── mymodel_rotating.xml │ │ │ └── snowplough.csv │ │ ├── Fibre_Crosslinks │ │ │ ├── fibre_crosslink_test.csv │ │ │ ├── fibre_crosslink_test_extended.csv │ │ │ ├── mymodel_extended_fibre_crosslink_test.xml │ │ │ └── mymodel_simple_fibre_crosslink_test.xml │ │ ├── Fibre_Degradation │ │ │ ├── cells_and_fibres.csv │ │ │ ├── cells_and_fibres_attractant.csv │ │ │ ├── mymodel_fibre_degradation.xml │ │ │ └── mymodel_matrix_degradation.xml │ │ ├── Fibre_Initialisation │ │ │ ├── initialfibres.csv │ │ │ ├── mymodel_initialisation.xml │ │ │ └── mymodel_initialisation_maze.xml │ │ ├── Neighbours_in_voxels │ │ │ ├── mymodel_neighbours.xml │ │ │ └── neighbourstest.csv │ │ └── PhysiCell_settings.xml │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ └── main.cpp ├── pred_prey_farmer │ ├── Makefile │ ├── config │ │ ├── PhysiCell_settings.xml │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ ├── main.cpp │ └── scripts │ │ └── empty.txt ├── rules_sample │ ├── Makefile │ ├── VERSION.txt │ ├── config │ │ ├── PhysiCell_settings.xml │ │ ├── cell_rules.csv │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ ├── custom.h │ │ └── empty.txt │ └── main.cpp ├── template │ ├── Makefile │ ├── config │ │ ├── PhysiCell_settings.xml │ │ ├── cell_rules.csv │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ ├── main.cpp │ └── scripts │ │ └── empty.txt ├── virus_macrophage │ ├── Makefile │ ├── config │ │ ├── PhysiCell_settings.xml │ │ └── cells.csv │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ ├── main.cpp │ └── scripts │ │ └── empty.txt └── worm │ ├── Makefile │ ├── config │ ├── PhysiCell_settings.xml │ └── cells.csv │ ├── custom_modules │ ├── custom.cpp │ └── custom.h │ ├── main.cpp │ └── scripts │ └── empty.txt ├── sample_projects_intracellular ├── boolean │ ├── cancer_invasion │ │ ├── Makefile │ │ ├── config │ │ │ ├── PhysiCell_settings.xml │ │ │ ├── PhysiCell_settings_2D.xml │ │ │ ├── PhysiCell_settings_2D_cluster_migration.xml │ │ │ ├── PhysiCell_settings_2D_p63_ki.xml │ │ │ ├── PhysiCell_settings_2D_single_cell_migration.xml │ │ │ ├── PhysiCell_settings_2D_trail_migration.xml │ │ │ ├── PhysiCell_settings_3D.xml │ │ │ ├── boolean_network │ │ │ │ ├── intracellular_model.bnd │ │ │ │ └── intracellular_model.cfg │ │ │ └── cells.csv │ │ ├── custom_modules │ │ │ ├── custom.cpp │ │ │ ├── custom.h │ │ │ ├── custom_main.cpp │ │ │ └── custom_main.h │ │ ├── main.cpp │ │ └── scripts │ │ │ ├── PhysiBoSS_animate.pvsm │ │ │ ├── params │ │ │ ├── cell_phases_dict.json │ │ │ └── phases_grouping_dict.json │ │ │ ├── paraview_vis.pvsm │ │ │ ├── paraview_vis_clipped.pvsm │ │ │ ├── plot_time_course.py │ │ │ ├── plot_tumor.py │ │ │ ├── pyMCDS_cells.py │ │ │ └── summarize_simulation.py │ ├── physiboss_cell_lines │ │ ├── Makefile │ │ ├── VERSION.txt │ │ ├── config │ │ │ ├── PhysiCell_settings.xml │ │ │ ├── cells.csv │ │ │ ├── model.cfg │ │ │ ├── model_0.bnd │ │ │ └── model_1.bnd │ │ ├── custom_modules │ │ │ ├── custom.cpp │ │ │ └── custom.h │ │ ├── main.cpp │ │ └── scripts │ │ │ └── empty.txt │ ├── template_BM │ │ ├── Makefile │ │ ├── config │ │ │ ├── PhysiCell_settings.xml │ │ │ ├── cell_rules.csv │ │ │ └── cells.csv │ │ ├── custom_modules │ │ │ ├── custom.cpp │ │ │ └── custom.h │ │ ├── main.cpp │ │ └── scripts │ │ │ └── empty.txt │ └── tutorial │ │ ├── Makefile │ │ ├── README.md │ │ ├── config │ │ ├── cell_cycle │ │ │ ├── PhysiCell_settings.xml │ │ │ ├── PhysiCell_settings_foxo3_knockout.xml │ │ │ ├── PhysiCell_settings_foxo3_knockout_notebook.xml │ │ │ ├── PhysiCell_settings_notebook.xml │ │ │ ├── PhysiCell_settings_p110_knockin.xml │ │ │ ├── PhysiCell_settings_p110_knockin_notebook.xml │ │ │ ├── PhysiCell_settings_plk1_knockout.xml │ │ │ ├── PhysiCell_settings_plk1_knockout_notebook.xml │ │ │ ├── boolean_network │ │ │ │ ├── intracellular_model.bnd │ │ │ │ └── intracellular_model.cfg │ │ │ ├── cell_rules.csv │ │ │ ├── cells.csv │ │ │ └── more_cells.csv │ │ ├── differentiation │ │ │ ├── PhysiCell_settings.xml │ │ │ ├── PhysiCell_settings_FOXP3_2_lower.xml │ │ │ ├── PhysiCell_settings_FOXP3_2_mutant.xml │ │ │ ├── PhysiCell_settings_NFKB_lower.xml │ │ │ ├── PhysiCell_settings_NFKB_mutant.xml │ │ │ ├── boolean_network │ │ │ │ ├── dendritic_cells.bnd │ │ │ │ ├── dendritic_cells.cfg │ │ │ │ ├── tcell_corral.bnd │ │ │ │ └── tcell_corral.cfg │ │ │ ├── cells.csv │ │ │ └── rules.csv │ │ └── simple_tnf │ │ │ ├── 0_Initial.xml │ │ │ ├── 1_Long_TNF.xml │ │ │ ├── 1_Long_TNF_stochastic_time.xml │ │ │ ├── 2_Short_TNF.xml │ │ │ ├── 3_Necrotic_core.xml │ │ │ ├── 4_Mutants.xml │ │ │ ├── boolean_network │ │ │ ├── cellfate.bnd │ │ │ ├── cellfate.cfg │ │ │ ├── cellfate_with_oxygen.bnd │ │ │ └── cellfate_with_oxygen.cfg │ │ │ ├── cell_rules.csv │ │ │ ├── cells.csv │ │ │ └── cells_mutant.csv │ │ ├── custom_modules │ │ ├── custom.cpp │ │ └── custom.h │ │ ├── main.cpp │ │ └── scripts │ │ ├── CellFate_Analysis.ipynb │ │ ├── Cell_cycle_analysis.ipynb │ │ ├── Cell_cycle_boolean_analysis.ipynb │ │ ├── Corral_analysis.ipynb │ │ ├── README.md │ │ ├── environment.yml │ │ ├── pyMCDS_cells.py │ │ └── tools.py ├── fba │ ├── cancer_metabolism │ │ ├── ALL_CITATIONS.txt │ │ ├── Make-windows │ │ ├── Makefile │ │ ├── config │ │ │ ├── PhysiCell_settings.xml │ │ │ └── iSIM.xml │ │ ├── custom_modules │ │ │ ├── cancer_metabolism.cpp │ │ │ ├── cancer_metabolism.h │ │ │ └── empty.txt │ │ ├── main.cpp │ │ └── scripts │ │ │ └── empty.txt │ └── ecoli_acetic_switch │ │ ├── ALL_CITATIONS.txt │ │ ├── Makefile │ │ ├── PhysiCell_settings.xml │ │ ├── config │ │ ├── Ecoli_core.xml │ │ └── PhysiCell_settings.xml │ │ ├── custom_modules │ │ ├── ecoli_acetic_switch.cpp │ │ ├── ecoli_acetic_switch.h │ │ └── empty.txt │ │ ├── main_ecoli_acetic_switch.cpp │ │ └── scripts │ │ └── empty.txt └── ode │ └── ode_energy │ ├── Makefile │ ├── config │ ├── PhysiCell_settings.xml │ ├── Toy_Metabolic_Model.cps │ ├── Toy_Metabolic_Model.xml │ ├── plotMicroenv.m │ └── plot_intracellular.m │ ├── custom_modules │ ├── custom.cpp │ ├── custom.h │ └── empty.txt │ └── main.cpp ├── tests ├── cases │ ├── output_heterogeneity-sample │ │ ├── snapshot00000000.svg │ │ └── snapshot00000001.svg │ ├── output_interaction-sample │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ ├── snapshot00000002.svg │ │ └── snapshot00000003.svg │ ├── output_mechano-sample │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ └── snapshot00000002.svg │ ├── output_physiboss-cell-lines-sample │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ ├── snapshot00000002.svg │ │ ├── snapshot00000003.svg │ │ ├── snapshot00000004.svg │ │ ├── snapshot00000005.svg │ │ ├── snapshot00000006.svg │ │ ├── snapshot00000007.svg │ │ ├── snapshot00000008.svg │ │ ├── snapshot00000009.svg │ │ ├── snapshot00000010.svg │ │ ├── snapshot00000011.svg │ │ └── snapshot00000012.svg │ ├── output_physiboss-tutorial │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ ├── snapshot00000002.svg │ │ ├── snapshot00000003.svg │ │ ├── snapshot00000004.svg │ │ ├── snapshot00000005.svg │ │ ├── snapshot00000006.svg │ │ ├── snapshot00000007.svg │ │ ├── snapshot00000008.svg │ │ ├── snapshot00000009.svg │ │ ├── snapshot00000010.svg │ │ ├── snapshot00000011.svg │ │ ├── snapshot00000012.svg │ │ ├── snapshot00000013.svg │ │ ├── snapshot00000014.svg │ │ ├── snapshot00000015.svg │ │ ├── snapshot00000016.svg │ │ ├── snapshot00000017.svg │ │ ├── snapshot00000018.svg │ │ ├── snapshot00000019.svg │ │ ├── snapshot00000020.svg │ │ ├── snapshot00000021.svg │ │ ├── snapshot00000022.svg │ │ ├── snapshot00000023.svg │ │ ├── snapshot00000024.svg │ │ ├── snapshot00000025.svg │ │ ├── snapshot00000026.svg │ │ ├── snapshot00000027.svg │ │ ├── snapshot00000028.svg │ │ ├── snapshot00000029.svg │ │ ├── snapshot00000030.svg │ │ ├── snapshot00000031.svg │ │ ├── snapshot00000032.svg │ │ ├── snapshot00000033.svg │ │ ├── snapshot00000034.svg │ │ ├── snapshot00000035.svg │ │ ├── snapshot00000036.svg │ │ ├── snapshot00000037.svg │ │ ├── snapshot00000038.svg │ │ ├── snapshot00000039.svg │ │ ├── snapshot00000040.svg │ │ ├── snapshot00000041.svg │ │ ├── snapshot00000042.svg │ │ ├── snapshot00000043.svg │ │ ├── snapshot00000044.svg │ │ ├── snapshot00000045.svg │ │ ├── snapshot00000046.svg │ │ ├── snapshot00000047.svg │ │ ├── snapshot00000048.svg │ │ ├── snapshot00000049.svg │ │ └── snapshot00000050.svg │ ├── output_physimess-sample │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ ├── snapshot00000002.svg │ │ ├── snapshot00000003.svg │ │ ├── snapshot00000004.svg │ │ ├── snapshot00000005.svg │ │ ├── snapshot00000006.svg │ │ ├── snapshot00000007.svg │ │ ├── snapshot00000008.svg │ │ ├── snapshot00000009.svg │ │ ├── snapshot00000010.svg │ │ ├── snapshot00000011.svg │ │ ├── snapshot00000012.svg │ │ ├── snapshot00000013.svg │ │ ├── snapshot00000014.svg │ │ ├── snapshot00000015.svg │ │ ├── snapshot00000016.svg │ │ ├── snapshot00000017.svg │ │ ├── snapshot00000018.svg │ │ ├── snapshot00000019.svg │ │ ├── snapshot00000020.svg │ │ ├── snapshot00000021.svg │ │ ├── snapshot00000022.svg │ │ ├── snapshot00000023.svg │ │ └── snapshot00000024.svg │ ├── output_rules-sample │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ └── snapshot00000002.svg │ ├── output_template │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ └── snapshot00000002.svg │ ├── output_template_BM │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ └── snapshot00000002.svg │ ├── output_virus-macrophage-sample │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ ├── snapshot00000002.svg │ │ ├── snapshot00000003.svg │ │ ├── snapshot00000004.svg │ │ ├── snapshot00000005.svg │ │ ├── snapshot00000006.svg │ │ ├── snapshot00000007.svg │ │ ├── snapshot00000008.svg │ │ ├── snapshot00000009.svg │ │ ├── snapshot00000010.svg │ │ ├── snapshot00000011.svg │ │ └── snapshot00000012.svg │ └── output_worm-sample │ │ ├── snapshot00000000.svg │ │ ├── snapshot00000001.svg │ │ ├── snapshot00000002.svg │ │ ├── snapshot00000003.svg │ │ ├── snapshot00000004.svg │ │ ├── snapshot00000005.svg │ │ ├── snapshot00000006.svg │ │ ├── snapshot00000007.svg │ │ ├── snapshot00000008.svg │ │ ├── snapshot00000009.svg │ │ ├── snapshot00000010.svg │ │ ├── snapshot00000011.svg │ │ ├── snapshot00000012.svg │ │ ├── snapshot00000013.svg │ │ ├── snapshot00000014.svg │ │ ├── snapshot00000015.svg │ │ ├── snapshot00000016.svg │ │ ├── snapshot00000017.svg │ │ ├── snapshot00000018.svg │ │ ├── snapshot00000019.svg │ │ ├── snapshot00000020.svg │ │ ├── snapshot00000021.svg │ │ ├── snapshot00000022.svg │ │ ├── snapshot00000023.svg │ │ ├── snapshot00000024.svg │ │ ├── snapshot00000025.svg │ │ ├── snapshot00000026.svg │ │ ├── snapshot00000027.svg │ │ ├── snapshot00000028.svg │ │ ├── snapshot00000029.svg │ │ ├── snapshot00000030.svg │ │ ├── snapshot00000031.svg │ │ ├── snapshot00000032.svg │ │ ├── snapshot00000033.svg │ │ ├── snapshot00000034.svg │ │ ├── snapshot00000035.svg │ │ ├── snapshot00000036.svg │ │ ├── snapshot00000037.svg │ │ ├── snapshot00000038.svg │ │ ├── snapshot00000039.svg │ │ └── snapshot00000040.svg ├── system │ ├── README.md │ ├── config_hetero_1core.xml │ └── output_heterogenity │ │ └── final_1core_240min.svg ├── timing │ ├── Makefile │ ├── README.md │ └── main.cpp └── unit │ ├── Makefile │ ├── README.md │ └── main.cpp ├── unit_tests ├── cell_definition │ ├── Makefile │ ├── test_cell_def0.cpp │ ├── test_cell_def1.cpp │ └── test_cell_def2.cpp ├── custom_DCs_2substrates │ ├── Makefile │ ├── 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