├── .github ├── contributing.md ├── issue_template.md └── workflows │ └── repo-stats.yml ├── Docker ├── Dockerfile ├── README.md └── docking.sh ├── Doxyfile ├── LICENSE ├── Licenses ├── BioFVM.txt ├── MaBoSS.txt ├── PhysiBoSS.txt └── PhysiCell.txt ├── MaBoSS-env-2.0 ├── .gitignore ├── LICENSE ├── MaBoSS.env ├── README ├── bindings │ └── python │ │ ├── maboss-ori.py │ │ ├── maboss │ │ ├── __init__.py │ │ ├── atexit.py │ │ ├── comm.py │ │ ├── result.py │ │ └── simul.py │ │ └── test_maboss.py ├── check-requirements.sh ├── conda │ └── maboss │ │ ├── build.sh │ │ └── meta.yaml ├── containers │ ├── docker │ │ └── Dockerfile │ └── singularity │ │ └── Singularity ├── docker-compose.yml ├── engine │ ├── README │ ├── binaries │ │ ├── linux-x86 │ │ │ └── MaBoSS │ │ ├── macos-x86 │ │ │ └── MaBoSS │ │ └── win-x86 │ │ │ └── MaBoSS.exe │ ├── doc │ │ ├── DescriptionOutputFile.pdf │ │ ├── MaBoSS-RefCard.pdf │ │ ├── Makefile │ │ ├── README │ │ ├── basic-network.bnd │ │ ├── basic-network.cfg │ │ ├── maboss-refcard.xml │ │ └── params.xsl │ ├── examples │ │ ├── Cell_cycle │ │ │ ├── README │ │ │ ├── cellcycle.bnd │ │ │ ├── cellcycle_ds_out_probtraj.csv │ │ │ ├── cellcycle_ds_out_probtraj.ods │ │ │ ├── cellcycle_ds_out_run.txt │ │ │ ├── cellcycle_ds_out_statdist.csv │ │ │ ├── cellcycle_out_probtraj.csv │ │ │ ├── cellcycle_out_probtraj.ods │ │ │ ├── cellcycle_out_run.txt │ │ │ ├── cellcycle_out_statdist.csv │ │ │ ├── cellcycle_runcfg-thread_1.cfg │ │ │ ├── cellcycle_runcfg-thread_12.cfg │ │ │ ├── cellcycle_runcfg-thread_6.cfg │ │ │ ├── cellcycle_runcfg-thread_6b.cfg │ │ │ ├── cellcycle_runcfg.cfg │ │ │ └── cellcycle_var.vd │ │ ├── Exact_matlab_test_ex2 │ │ │ ├── Aact.m │ │ │ ├── Ainact.m │ │ │ ├── Essai.m │ │ │ ├── README │ │ │ ├── StochExactSim.m │ │ │ ├── entropy.m │ │ │ ├── example2_matlab.bnd │ │ │ ├── example2_matlab_config.cfg │ │ │ └── matlab.mat │ │ ├── Paper_examples │ │ │ ├── .RData │ │ │ ├── .Rhistory │ │ │ ├── Four_cycle.bnd │ │ │ ├── Four_cycle_probtraj.csv │ │ │ ├── Four_cycle_probtraj_FastEscape.csv │ │ │ ├── Four_cycle_probtraj_SlowEscape.csv │ │ │ ├── Four_cycle_run.cfg │ │ │ ├── Four_cycle_run.txt │ │ │ ├── Four_cycle_statdist.csv │ │ │ ├── p53_Mdm2.bnd │ │ │ ├── p53_Mdm2_PseudOsc_probtraj.csv │ │ │ ├── p53_Mdm2_PseudOsc_run.txt │ │ │ ├── p53_Mdm2_PseudOsc_statdist.csv │ │ │ ├── p53_Mdm2_probtraj.csv │ │ │ ├── p53_Mdm2_run.txt │ │ │ ├── p53_Mdm2_runcfg.cfg │ │ │ ├── p53_Mdm2_runcfg_PseudOsc.cfg │ │ │ └── p53_Mdm2_statdist.csv │ │ ├── ToyModel │ │ │ ├── Four_cycle.bnd │ │ │ ├── Four_cycle_FEscape.cfg │ │ │ ├── Four_cycle_SEscape.cfg │ │ │ ├── Four_cycle_SEscape_long.cfg │ │ │ └── README │ │ ├── cellcycle.bnd │ │ ├── cellcycle_runcfg.cfg │ │ ├── cellcycle_var.vd │ │ ├── ewing │ │ │ ├── ewing_full.bnd │ │ │ └── ewing_full.cfg │ │ ├── ex1.bnd │ │ ├── example.bnd │ │ ├── example2.bnd │ │ ├── example3.bnd │ │ ├── full_example.bnd │ │ ├── gs_example2.bnd │ │ ├── gs_var2b.vd │ │ ├── p53_Mdm2.bnd │ │ ├── p53_Mdm2 │ │ │ ├── README │ │ │ ├── p53_Mdm2.bnd │ │ │ ├── p53_Mdm2_run.txt │ │ │ └── p53_Mdm2_runcfg.cfg │ │ ├── p53_Mdm2_runcfg.cfg │ │ ├── p53_Mdm2_var.vd │ │ ├── rateTr │ │ │ ├── regulatorygraph_rateTr.bnd │ │ │ └── wildtype_rateTr.cfg │ │ ├── var.vd │ │ ├── var1.vd │ │ ├── var2a.vd │ │ ├── var2b.vd │ │ ├── var3a.vd │ │ ├── var3b.vd │ │ ├── var3c.vd │ │ └── var3d.vd │ ├── src │ │ ├── BooleanGrammar.cc │ │ ├── BooleanGrammar.h │ │ ├── BooleanGrammar.l │ │ ├── BooleanGrammar.output │ │ ├── BooleanGrammar.tab.c │ │ ├── BooleanGrammar.y │ │ ├── BooleanNetwork.cc │ │ ├── BooleanNetwork.h │ │ ├── BuiltinFunctions.cc │ │ ├── Client.cc │ │ ├── Client.h │ │ ├── Cumulator.cc │ │ ├── Cumulator.h │ │ ├── DataStreamer.cc │ │ ├── DataStreamer.h │ │ ├── EnsembleEngine.cc │ │ ├── EnsembleEngine.h │ │ ├── Function.cc │ │ ├── Function.h │ │ ├── LogicalExprGen.cc │ │ ├── MaBEstEngine.cc │ │ ├── MaBEstEngine.h │ │ ├── MaBoSS-client.cc │ │ ├── MaBoSS-server.cc │ │ ├── MaBoSS.cc │ │ ├── Makefile │ │ ├── Makefile.maboss │ │ ├── ProbaDist.cc │ │ ├── ProbaDist.h │ │ ├── Probe.h │ │ ├── RPC.cc │ │ ├── RPC.h │ │ ├── RandomGenerator.h │ │ ├── RunConfig.cc │ │ ├── RunConfig.h │ │ ├── RunConfigGrammar.cc │ │ ├── RunConfigGrammar.l │ │ ├── RunConfigGrammar.output │ │ ├── RunConfigGrammar.tab.c │ │ ├── RunConfigGrammar.y │ │ ├── Server.cc │ │ ├── Server.h │ │ ├── Utils.cc │ │ ├── Utils.h │ │ ├── depend.mk │ │ ├── init-config.sh │ │ ├── lex.CTBNDL.cc │ │ ├── lex.RC.cc │ │ ├── libMaBoSS.a │ │ ├── maboss-config.h │ │ └── user_func.cc │ └── tests │ │ ├── ExampleTraj4FP │ │ ├── ToyMod4FP.bnd │ │ ├── ToyMod4FP.cfg │ │ ├── ToyMod4FP_fp.csv │ │ ├── ToyMod4FP_probtraj.csv │ │ ├── ToyMod4FP_run.txt │ │ ├── ToyMod4FP_statdist.csv │ │ └── ToyMod4FP_traj.txt │ │ ├── cellcycle.bnd │ │ ├── cellcycle_runcfg-thread_1.cfg │ │ ├── cellcycle_runcfg-thread_6.cfg │ │ ├── cellcycle_runcfg.cfg │ │ ├── refer │ │ ├── Cell_cycle_thread_1_probtraj.csv │ │ ├── Cell_cycle_thread_1_run.txt │ │ ├── Cell_cycle_thread_1_statdist.csv │ │ ├── Cell_cycle_thread_6_probtraj.csv │ │ ├── Cell_cycle_thread_6_run.txt │ │ └── Cell_cycle_thread_6_statdist.csv │ │ ├── share.sh │ │ └── test-cellcycle.sh ├── make-package.sh ├── tools │ ├── .nfs0000000161deadc200000053 │ ├── MBSS_DrugSim.py │ ├── MBSS_FormatTable.pl │ ├── MBSS_InitCondFromTrajectory.pl │ ├── MBSS_MultipleSim.py │ ├── MBSS_MutBnd.pl │ ├── MBSS_MutBndCfg.pl │ ├── MBSS_PieChart.py │ ├── MBSS_PrepareProjectFile.pm │ ├── MBSS_PrepareProjectFile.sh │ ├── MBSS_PrepareProjectFilePieChart.py │ ├── MBSS_PrepareProjectFileTrajectoryFig.py │ ├── MBSS_SensitivityAnalysis.pl │ ├── MBSS_TrajectoryFig.py │ ├── UpPMaBoSS │ └── doc │ │ ├── Description_DrugSim.docx │ │ ├── Description_DrugSim.pdf │ │ ├── Description_FormatTable.pdf │ │ ├── Description_FormatTable.tex │ │ ├── Description_InitCondFromTraj.pdf │ │ ├── Description_InitCondFromTraj.tex │ │ ├── Description_InitCondFromTrajectory.pdf │ │ ├── Description_InitCondFromTrajectory.tex │ │ ├── Description_MultipleSim.pdf │ │ ├── Description_MultipleSim.tex │ │ ├── Description_MutBndCfg.pdf │ │ ├── Description_MutBndCfg.tex │ │ ├── Description_PieChart.pdf │ │ ├── Description_PieChart.tex │ │ ├── Description_PrepareProjectFile.pdf │ │ ├── Description_PrepareProjectFile.tex │ │ ├── Description_ProjectPrepFile.pdf │ │ ├── Description_ProjectPrepFile.tex │ │ ├── Description_SensitivityAnalysis.pdf │ │ ├── Description_SensitivityAnalysis.tex │ │ ├── Description_TrajFig.pdf │ │ ├── Description_TrajFig.tex │ │ ├── Description_TrajectoryFig.pdf │ │ ├── Description_TrajectoryFig.tex │ │ ├── README_DrugSim.txt │ │ ├── README_FormatTable.txt │ │ ├── README_InitCondFromTrajectory.txt │ │ ├── README_MultipleSim.txt │ │ ├── README_MutBndCfg.txt │ │ ├── README_PieChart.txt │ │ ├── README_PrepareProjectFile.txt │ │ ├── README_SensitivityAnalysis.txt │ │ └── README_TrajectoryFig.txt └── tutorial │ ├── MaBoSS-2.0 │ ├── Example.pmbss │ ├── ExampleProfile.txt │ ├── Example_DrugSim.txt │ ├── TutorialMaBoSS_2_0.docx │ ├── TutorialMaBoSS_2_0.pdf │ ├── example.bnd │ ├── example.cfg │ └── example.zginml │ └── SBMLQual │ ├── SBMLQual_Tutorial.pdf │ ├── SBMLQual_Tutorial.ppt │ ├── chaouiya_maboss.bnd │ └── chaouiya_maboss.cfg ├── Makefile ├── README.md ├── bin └── .gitignore ├── doc ├── html │ └── .gitignore ├── imgs │ ├── example_cell_sorting.png │ ├── example_cells_with_ECM.png │ ├── example_hello_world.png │ ├── example_mutants.png │ ├── example_spheroid_visu.png │ ├── folders.png │ ├── hello.png │ ├── paraview.png │ ├── paraviewing_step1.png │ ├── paraviewing_step2.png │ ├── paraviewing_step3.png │ ├── physiboss_plot_example.svg │ └── simulation.png └── wiki │ ├── Example_Cell_Sorting.md │ ├── Example_Cells_With_ECM.md │ ├── Example_Hello_World.md │ ├── Example_Mutants.md │ ├── Example_Mutants_paper.md │ ├── Example_Spheroid_TNF.md │ ├── Home.md │ ├── Installation.md │ ├── Parameters.md │ ├── Paraviewing.md │ ├── PhysiBoSS_CreateInitTxtFile.md │ ├── PhysiBoSS_Plot.md │ ├── README.md │ └── _Footer.md ├── examples ├── Letort_et_al_2018 │ ├── fig2 │ │ ├── BN │ │ │ ├── bn_conf.cfg │ │ │ └── bn_nodes.bnd │ │ ├── fig2A_left │ │ │ ├── init.txt │ │ │ ├── microutput │ │ │ │ └── .gitignore │ │ │ ├── output │ │ │ │ └── .gitignore │ │ │ └── parameters.xml │ │ ├── fig2A_right │ │ │ ├── ecm.txt │ │ │ ├── init.txt │ │ │ ├── microutput │ │ │ │ └── .gitignore │ │ │ ├── output │ │ │ │ └── .gitignore │ │ │ └── parameters.xml │ │ ├── fig2B_left │ │ │ ├── init.txt │ │ │ ├── microutput │ │ │ │ └── .gitignore │ │ │ ├── output │ │ │ │ └── .gitignore │ │ │ └── parameters.xml │ │ └── fig2B_right │ │ │ ├── init.txt │ │ │ ├── microutput │ │ │ └── .gitignore │ │ │ ├── output │ │ │ └── .gitignore │ │ │ └── parameters.xml │ ├── fig3 │ │ ├── BN │ │ │ ├── bn_conf.cfg │ │ │ └── bn_nodes.bnd │ │ └── run0 │ │ │ ├── init.txt │ │ │ ├── microutput │ │ │ └── .gitignore │ │ │ ├── output │ │ │ └── .gitignore │ │ │ └── parameters.xml │ ├── fig4 │ │ ├── BN │ │ │ ├── bn_conf.cfg │ │ │ └── bn_nodes.bnd │ │ ├── notnf │ │ │ ├── init.txt │ │ │ └── parameters.xml │ │ └── tnf_pulse │ │ │ ├── init.txt │ │ │ └── parameters.xml │ └── fig5 │ │ ├── BN │ │ ├── bn_conf.cfg │ │ └── bn_nodes.bnd │ │ ├── mutant_IKK_cFLIP_nooxygen │ │ ├── init.txt │ │ └── parameters.xml │ │ └── mutant_IKK_cFLIP_oxygen │ │ ├── init.txt │ │ └── parameters.xml ├── example_Hello_World │ ├── BN │ │ ├── bn_conf.cfg │ │ └── bn_nodes.bnd │ ├── run0 │ │ ├── init.txt │ │ ├── microutput │ │ │ └── .gitignore │ │ ├── output │ │ │ └── .gitignore │ │ └── parameters.xml │ └── run1 │ │ ├── init.txt │ │ ├── microutput │ │ └── .gitignore │ │ ├── output │ │ └── .gitignore │ │ └── parameters.xml ├── example_cells_with_ECM │ ├── BN │ │ ├── bn_conf.cfg │ │ └── bn_nodes.bnd │ └── run0 │ │ ├── ecm.txt │ │ ├── init.txt │ │ ├── microutput │ │ └── .gitignore │ │ ├── output │ │ └── .gitignore │ │ └── parameters.xml ├── example_mutants │ ├── BN │ │ ├── bn_conf.cfg │ │ └── bn_nodes.bnd │ ├── init_mutant.xml │ ├── run0 │ │ ├── init.txt │ │ ├── microutput │ │ │ └── .gitignore │ │ ├── output │ │ │ └── .gitignore │ │ └── parameters.xml │ └── run1 │ │ ├── init.txt │ │ ├── microutput │ │ └── .gitignore │ │ ├── output │ │ └── .gitignore │ │ └── parameters.xml ├── example_sorting │ ├── run0 │ │ ├── init.txt │ │ ├── microutput │ │ │ └── .gitignore │ │ ├── output │ │ │ └── .gitignore │ │ └── parameters.xml │ └── run1 │ │ ├── init.txt │ │ ├── microutput │ │ └── .gitignore │ │ ├── output │ │ └── .gitignore │ │ └── parameters.xml └── example_spheroid_TNF │ ├── BN │ ├── bn_conf.cfg │ └── bn_nodes.bnd │ ├── init_spheroid.xml │ └── run0 │ ├── init.txt │ ├── microutput │ └── .gitignore │ ├── output │ └── .gitignore │ └── parameters.xml ├── paraview_files ├── example_cell_sorting.pvsm ├── example_hello_world.pvsm ├── example_mutant.pvsm ├── example_spheroid_TNF.pvsm ├── sphere_quarter.pvsm └── withECM.pvsm ├── scripts ├── postsimu │ ├── Analyze.py │ ├── Functions_Plot.py │ ├── Phases.py │ └── Utils.py └── presimu │ ├── prepareInitialFileFromBinary.R │ ├── prepare_onefolder.sh │ ├── prepare_runs.sh │ └── templating.py └── src ├── BioFVM ├── BioFVM.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 ├── base ├── readXML.cpp ├── readXML.h ├── utilities.cpp ├── utilities.h ├── vector3d.cpp ├── vector3d.h ├── writeSVG.cpp └── writeSVG.h ├── core ├── PhysiCell_constants.h ├── cell.cpp ├── cell.h ├── cell_container.cpp ├── cell_container.h ├── cell_cycle.cpp ├── cell_cycle.h ├── cell_cycle_classic.cpp ├── cell_cycle_classic.h ├── cell_cycle_network.cpp ├── cell_cycle_network.h ├── cell_line.cpp ├── cell_line.h ├── cell_phenotype.cpp ├── cell_phenotype.h ├── cell_volume.cpp ├── cell_volume.h ├── doSVG.cpp ├── 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