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‎CITATION.txt‎

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@@ -1,7 +1,7 @@
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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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4-
We implemented and solved the model using PhysiCell (Version 1.5.0) [1].
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We implemented and solved the model using PhysiCell (Version 1.5.1) [1].
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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-
@@ -11,7 +11,7 @@ We implemented and solved the model using PhysiCell (Version 1.5.0) [1].
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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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We implemented and solved the model using PhysiCell (Version 1.5.0) [1],
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We implemented and solved the model using PhysiCell (Version 1.5.1) [1],
1515
with BioFVM [2] to solve the transport equations.
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[1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin,

‎Makefile-backup‎

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VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
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PROGRAM_NAME := project
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CC := g++
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# CC := g++-mp-7 # typical macports compiler name
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# CC := g++-7 # typical homebrew compiler name
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# Check for environment definitions of compiler
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# e.g., on CC = g++-7 on OSX
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ifdef PHYSICELL_CPP
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CC := $(PHYSICELL_CPP)
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endif
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ARCH := native # best auto-tuning
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# ARCH := core2 # a reasonably safe default for most CPUs since 2007
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# ARCH := corei7
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# ARCH := corei7-avx # earlier i7
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# ARCH := core-avx-i # i7 ivy bridge or newer
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# ARCH := core-avx2 # i7 with Haswell or newer
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# ARCH := nehalem
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# ARCH := westmere
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# ARCH := sandybridge # circa 2011
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# ARCH := ivybridge # circa 2012
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# ARCH := haswell # circa 2013
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# ARCH := broadwell # circa 2014
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# ARCH := skylake # circa 2015
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# ARCH := bonnell
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# ARCH := silvermont
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# ARCH := skylake-avx512
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# ARCH := nocona #64-bit pentium 4 or later
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# CFLAGS := -march=$(ARCH) -Ofast -s -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
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CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
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COMPILE_COMMAND := $(CC) $(CFLAGS)
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BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
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BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o
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PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
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PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o
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PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
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PhysiCell_pugixml.o PhysiCell_settings.o
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# put your custom objects here (they should be in the custom_modules directory)
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PhysiCell_custom_module_OBJECTS := .o
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pugixml_OBJECTS := pugixml.o
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PhysiCell_OBJECTS := $(BioFVM_OBJECTS) $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_OBJECTS)
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ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS)
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EXAMPLES := ./examples/PhysiCell_test_mechanics_1.cpp ./examples/PhysiCell_test_mechanics_2.cpp \
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./examples/PhysiCell_test_DCIS.cpp ./examples/PhysiCell_test_HDS.cpp \
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./examples/PhysiCell_test_cell_cycle.cpp ./examples/PhysiCell_test_volume.cpp
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all:
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make heterogeneity-sample
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make
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# sample projects
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template2D:
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cp ./sample_projects/template2D/custom_modules/* ./custom_modules/
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touch main.cpp && cp main.cpp main-backup.cpp
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cp ./sample_projects/template2D/main-2D.cpp ./main.cpp
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cp Makefile Makefile-backup
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cp ./sample_projects/template2D/Makefile .
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cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
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cp ./sample_projects/template2D/config/* ./config/
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template3D:
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cp ./sample_projects/template3D/custom_modules/* ./custom_modules/
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touch main.cpp && cp main.cpp main-backup.cpp
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cp ./sample_projects/template3D/main-3D.cpp ./main.cpp
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cp Makefile Makefile-backup
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cp ./sample_projects/template3D/Makefile .
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cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
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cp ./sample_projects/template3D/config/* ./config/
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# sample projects
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biorobots-sample:
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cp ./sample_projects/biorobots/custom_modules/* ./custom_modules/
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touch main.cpp && cp main.cpp main-backup.cpp
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cp ./sample_projects/biorobots/main-biorobots.cpp ./main.cpp
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cp Makefile Makefile-backup
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cp ./sample_projects/biorobots/Makefile .
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cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
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cp ./sample_projects/biorobots/config/* ./config/
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cancer-biorobots-sample:
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cp ./sample_projects/cancer_biorobots/custom_modules/* ./custom_modules/
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touch main.cpp && cp main.cpp main-backup.cpp
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cp ./sample_projects/cancer_biorobots/main-cancer_biorobots.cpp ./main.cpp
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cp Makefile Makefile-backup
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cp ./sample_projects/cancer_biorobots/Makefile .
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cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
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cp ./sample_projects/cancer_biorobots/config/* ./config/
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heterogeneity-sample:
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cp ./sample_projects/heterogeneity/custom_modules/* ./custom_modules/
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touch main.cpp && cp main.cpp main-backup.cpp
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cp ./sample_projects/heterogeneity/main-heterogeneity.cpp ./main.cpp
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cp Makefile Makefile-backup
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cp ./sample_projects/heterogeneity/Makefile .
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cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
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cp ./sample_projects/heterogeneity/config/* ./config/
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cancer-immune-sample:
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cp ./sample_projects/cancer_immune/custom_modules/* ./custom_modules/
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touch main.cpp && cp main.cpp main-backup.cpp
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cp ./sample_projects/cancer_immune/main-cancer_immune_3D.cpp ./main.cpp
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cp Makefile Makefile-backup
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cp ./sample_projects/cancer_immune/Makefile .
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cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
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cp ./sample_projects/cancer_immune/config/* ./config/
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virus-macrophage-sample:
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cp ./sample_projects/virus_macrophage/custom_modules/* ./custom_modules/
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touch main.cpp && cp main.cpp main-backup.cpp
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cp ./sample_projects/virus_macrophage/main-virus_macrophage.cpp ./main.cpp
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cp Makefile Makefile-backup
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cp ./sample_projects/virus_macrophage/Makefile .
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cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
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cp ./sample_projects/virus_macrophage/config/* ./config/
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beta-testing:
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cp ./sample_projects/beta_testing/custom_modules/* ./custom_modules/
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touch main.cpp && cp main.cpp main-backup.cpp
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cp ./sample_projects/beta_testing/main-beta.cpp ./main.cpp
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cp Makefile Makefile-backup
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cp ./sample_projects/beta_testing/Makefile .
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cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
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cp ./sample_projects/beta_testing/config/* ./config/
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# early examples for convergence testing
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physicell_test_mech1: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp
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$(COMPILE_COMMAND) -o test_mech1 $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp
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physicell_test_mech2: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_2.cpp
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$(COMPILE_COMMAND) -o test_mech2 $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_2.cpp
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physicell_test_DCIS: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_DCIS.cpp
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$(COMPILE_COMMAND) -o test_DCIS $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_DCIS.cpp
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physicell_test_HDS: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_HDS.cpp
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$(COMPILE_COMMAND) -o test_HDS $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_HDS.cpp
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physicell_test_cell_cycle: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_cell_cycle.cpp
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$(COMPILE_COMMAND) -o test_cycle $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_cell_cycle.cpp
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PhysiCell_test_volume: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_volume.cpp
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$(COMPILE_COMMAND) -o test_volume $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_volume.cpp
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examples: $(PhysiCell_OBJECTS)
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$(COMPILE_COMMAND) -o ./examples/test_mech1 ./examples/PhysiCell_test_mechanics_1.cpp $(PhysiCell_OBJECTS)
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$(COMPILE_COMMAND) -o ./examples/test_mech2 ./examples/PhysiCell_test_mechanics_2.cpp $(PhysiCell_OBJECTS)
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$(COMPILE_COMMAND) -o ./examples/test_DCIS ./examples/PhysiCell_test_DCIS.cpp $(PhysiCell_OBJECTS)
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$(COMPILE_COMMAND) -o ./examples/test_HDS ./examples/PhysiCell_test_HDS.cpp $(PhysiCell_OBJECTS)
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$(COMPILE_COMMAND) -o ./examples/test_cycle ./examples/PhysiCell_test_cell_cycle.cpp $(PhysiCell_OBJECTS)
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$(COMPILE_COMMAND) -o ./examples/test_volume ./examples/PhysiCell_test_volume.cpp $(PhysiCell_OBJECTS)
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# PhysiCell core components
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PhysiCell_phenotype.o: ./core/PhysiCell_phenotype.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_phenotype.cpp
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PhysiCell_digital_cell_line.o: ./core/PhysiCell_digital_cell_line.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_digital_cell_line.cpp
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PhysiCell_cell.o: ./core/PhysiCell_cell.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_cell.cpp
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PhysiCell_cell_container.o: ./core/PhysiCell_cell_container.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_cell_container.cpp
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PhysiCell_standard_models.o: ./core/PhysiCell_standard_models.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_standard_models.cpp
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PhysiCell_utilities.o: ./core/PhysiCell_utilities.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_utilities.cpp
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PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp
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# BioFVM core components (needed by PhysiCell)
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BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_vector.cpp
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BioFVM_agent_container.o: ./BioFVM/BioFVM_agent_container.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_agent_container.cpp
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BioFVM_mesh.o: ./BioFVM/BioFVM_mesh.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_mesh.cpp
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BioFVM_microenvironment.o: ./BioFVM/BioFVM_microenvironment.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_microenvironment.cpp
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BioFVM_solvers.o: ./BioFVM/BioFVM_solvers.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_solvers.cpp
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BioFVM_utilities.o: ./BioFVM/BioFVM_utilities.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_utilities.cpp
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BioFVM_basic_agent.o: ./BioFVM/BioFVM_basic_agent.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_basic_agent.cpp
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BioFVM_matlab.o: ./BioFVM/BioFVM_matlab.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_matlab.cpp
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BioFVM_MultiCellDS.o: ./BioFVM/BioFVM_MultiCellDS.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_MultiCellDS.cpp
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pugixml.o: ./BioFVM/pugixml.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/pugixml.cpp
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# standard PhysiCell modules
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PhysiCell_SVG.o: ./modules/PhysiCell_SVG.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_SVG.cpp
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PhysiCell_pathology.o: ./modules/PhysiCell_pathology.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_pathology.cpp
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PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_MultiCellDS.cpp
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PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_various_outputs.cpp
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PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
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PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp
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# user-defined PhysiCell modules
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# cleanup
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reset:
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rm -f *.cpp
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cp ./sample_projects/Makefile-default Makefile
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rm -f ./custom_modules/*
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touch ./custom_modules/empty.txt
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touch ALL_CITATIONS.txt
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rm ALL_CITATIONS.txt
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cp ./config/PhysiCell_settings_default.xml ./config/PhysiCell_settings.xml
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touch ./output/empty.txt
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clean:
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rm -f *.o
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rm -f $(PROGRAM_NAME)*
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data-cleanup:
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rm -f *.mat
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rm -f *.xml
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rm -f *.svg
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rm -f ./output/*
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touch ./output/empty.txt
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# archival
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zip:
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zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
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cp latest.zip $$(date +%b_%d_%Y_%H%M).zip
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cp latest.zip VERSION_$(VERSION).zip
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mv *.zip archives/
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tar:
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tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
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cp latest.tar $$(date +%b_%d_%Y_%H%M).tar
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cp latest.tar VERSION_$(VERSION).tar
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mv *.tar archives/
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unzip:
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cp ./archives/latest.zip .
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unzip latest.zip
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untar:
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cp ./archives/latest.tar .
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tar -xzf latest.tar

‎README.md‎

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# PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems.
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**Version:** 1.5.0
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**Version:** 1.5.1
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**Release date:** 7 June 2019
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@@ -60,68 +60,33 @@ See changes.md for the full change log.
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* * *
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## Release summary:
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This release introduces the ability to track the net internalization of diffusible substrates from the microenvironment, conserving mass with the diffusion-reaction partial differentiatial equations in BioFVM. This is part of longer-term plans to support molecular-scale models (e.g., as encoded by SBML). It also introduces the ability for cells to ingest other cells (and acquire their internalized substrates and volume), the ability for cells to release their internalized substrates back to the microenvironment after death, and a new cell death model (lysis).
65-
66-
To illustrate these new capabilities, this release introduces a new sample project called virus-macrophage-sample. In this project, virus particles diffuse through the microenvironment, are uptaken by cells, replicate within cells, and trigger lytic death after reaching a threshold. Lysed cells release their virus particles to further diffuse through the environment. Macrophages move by random migration, test for contact with cells, and ingest / phagocytose cells based upon their viral load. Macrophages degrade their internalized viral particles.
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68-
This release also added clearer methods to specify the microenvironment initial conditions, and improved documentation.
64+
This minor release fixes bugs in the new virus-macrophage sample project. Users should also consult the reslease notes for 1.5.0.
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7066
**NOTE:** OSX users must now define PHYSICELL_CPP system variable. See the documentation.
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7268
### Major new features and changes:
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74-
+ Added functionality in BioFVM to (optionally) track the total amount of substrates in each cell, based upon tracking uptake and secretion. Note that without additional, user-defined functions to internally create or consume substrate (e.g., synthesizing proteins, or using oxygen in metabolism), this can result in negative internal values (if cells only secrete but no internal creation functions have been set) or unbounded positive values (if cells uptake a substrate but do not consume it). In particular, Basic_Agents (and hence Cells) now have:
75-
++ std::vector<double>* internalized_substrates (tracks internalized substrates)
76-
++ std::vector<double>* fraction_released_at_death (sets the fraction of each substrate that is released at cell death)
77-
++ std::vector<double>* fraction_transferred_when_ingested (sets the fraction of each substrate that is transferred to a predatory cell if the cell is eaten).
78-
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Users should access these via the cell's (new) molecular portion of the phenotype. See below.
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In BioFVM::Microenvironment_Options class, we added:
82-
++ bool track_internalized_substrates_in_each_agent. Set this to true to enable the tracking.
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84-
+ In BioFVM::Microenvironment_Options, we added the ability to set the (uniform) microenvironment initial conditions, via:
85-
++ std::vector<double> initial_condition_vector.
86-
87-
If this has size zero, then BioFVM will use the std::vector<double> Dirichlet_condition_vector as a reasonable guess at initial conditions as in prior versions.
88-
89-
+ We added a new function to Basic_Agent (and hence Cell) to facilitate registering with the microenvironment:
90-
++ void Basic_Agent::register_microenvironment( Microenvironment* microenvironment_in )
91-
92-
This function will ensure that the secretion, uptake, and internalization tracking data structures of the individual cell agent are properly matched to the microenvironment.
93-
94-
+ Added new "Molecular" block to Phenotype, for storing internalized substrates and for eventual inclusion of molecular-scale models (via SBML). The major elements are:
95-
++ std::vector<double> internalized_substrates (tracks internalized substrates)
96-
++ std::vector<double> fraction_released_at_death (sets the fraction of each substrate that is released at cell death)
97-
++ std::vector<double> fraction_transferred_when_ingested (sets the fraction of each substrate that is transferred to a predatory cell if the cell is eaten).
98-
99-
+ Added lyse_cell() to Cell, to allow a cell to immediately be lysed and potentially release its internalized substrates. Lysed cells are removed from the simulation.
100-
101-
+ Added ingest_cell(Cell*) to Cell, to allow a cell to ingest (e.g., phagocytose) another cell, acquire its volume, and also (optionally) acquire its internalized substrates. This should be useful for immunology.
70+
+ None
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### Minor new features and changes:
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105-
+ Added void Microenvironment::update_dirichlet_node( int voxel_index , int substrate_index , double new_value ) based on pc4nanobio changes, which allows you to update a single substrate's dirichlet condition at specific voxel, rather than all of them.
106-
107-
+ Added void sync_to_microenvironment( Microenvironment* pMicroenvironment ) to Phenotype to facilitate syncing the cell's phenotype to the microenvironment (and subsequently calls the functions in phenotype.secretion and phenotype.molecular). This isn't used yet, but perhaps it should be.
74+
+ None
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10976
### Beta features (not fully supported):
11077

11178
+ None
11279

11380
### Bugfixes:
11481

115-
+ Updated BioFVM's operator<< on std::vector<double> so that it doesn't output x="value", y="value", z = "value" for 3-D vectors.
116-
117-
+ Fixed the search for cycle phase indices in the 2D and 3D template projects, to make sure it searches teh flow_cytometry_separated_cycle_model model and not the Ki67_advanced model, as part of the create_cell_types() function in the custom.cpp files.
82+
+ In the virus-macrophage sample project, switch cell death (in epithelial_function) from apoptosis to cell_lysis to demonstrate the new function.
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119-
+ In PhysiCell_standard_models, standard_volume_update_function is now fixed to update phenotype.volume.fluid. (This was not used in any mechanics or other calculations, so it does not affect prior modeling results.)
84+
+ In the virus-macrophage sample project, enable internalized substrate tracking in the setup_microenvironment() function.
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121-
+ Removed repeated parameters (attached_worker_migration_bias, unattached_worker_migration_bias) in the cancer biorobots sample project.
86+
+ In the virus-macrophage sample project, use a slower viral replication rate. (Should take 240 minutes to reach the lysis threshold.)
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123-
+ trigger_death() now works.
124-
88+
+ In the virus-macrophage sample project, switched to a maximum simulation time of 24 hours (1440 minutes).
89+
12590
### Notices for intended changes that may affect backwards compatibility:
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12792
+ We intend to merge Custom_Variable and Custom_Vector_Variable in the very near future.
@@ -155,3 +120,7 @@ This function will ensure that the secretion, uptake, and internalization tracki
155120
+ create an angiogenesis sample project
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157122
+ create a small library of angiogenesis and vascularization codes as an optional standard module in ./modules (but not as a core component)
123+
124+
+ improved plotting options in SVG
125+
126+
* * *

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