From c9a6cecde282a909f4591a8c72b693a059d075f8 Mon Sep 17 00:00:00 2001
From: Daniel Bergman <danielrbergman@gmail.com>
Date: Wed, 15 Jan 2025 13:41:14 -0500
Subject: [PATCH 1/4] more robust macro to check for windows

---
 modules/PhysiCell_settings.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/PhysiCell_settings.cpp b/modules/PhysiCell_settings.cpp
index d4a25698e..ad4be5f84 100644
--- a/modules/PhysiCell_settings.cpp
+++ b/modules/PhysiCell_settings.cpp
@@ -349,7 +349,7 @@ bool create_directories(const std::string &path)
 
 bool create_directory(const std::string &path)
 {
-#if defined(__MINGW32__) || defined(__MINGW64__)
+#if defined(_WIN32)
 	bool success = mkdir(path.c_str()) == 0;
 #else
 	bool success = mkdir(path.c_str(), 0755) == 0;

From eb5e511381c69424fda571cd93c70e5226a79625 Mon Sep 17 00:00:00 2001
From: Heber Lima da Rocha <heberonly@gmail.com>
Date: Fri, 31 Jan 2025 16:04:15 -0500
Subject: [PATCH 2/4] first commit

---
 Makefile                      |  323 +-----
 config/PhysiCell_settings.xml | 2009 +++++++++++++++++++++++++++++++--
 config/cell_rules.csv         |    0
 config/cells.csv              |    1 +
 custom_modules/custom.cpp     |  214 ++++
 custom_modules/custom.h       |   92 ++
 main.cpp                      |  254 +++++
 7 files changed, 2512 insertions(+), 381 deletions(-)
 create mode 100644 config/cell_rules.csv
 create mode 100644 config/cells.csv
 create mode 100644 custom_modules/custom.cpp
 create mode 100644 custom_modules/custom.h
 create mode 100644 main.cpp

diff --git a/Makefile b/Makefile
index 5d256d1c3..7aa7d18d2 100644
--- a/Makefile
+++ b/Makefile
@@ -11,11 +11,24 @@ ifdef PHYSICELL_CPP
 	CC := $(PHYSICELL_CPP)
 endif
 
+ifndef STATIC_OPENMP
+	STATIC_OPENMP = -fopenmp
+endif
+
 ARCH := native # best auto-tuning
 # ARCH := core2 # a reasonably safe default for most CPUs since 2007
 # ARCH := corei7
+# ARCH := corei7-avx # earlier i7 
 # ARCH := core-avx-i # i7 ivy bridge or newer 
 # ARCH := core-avx2 # i7 with Haswell or newer
+# ARCH := nehalem
+# ARCH := westmere
+# ARCH := sandybridge # circa 2011
+# ARCH := ivybridge   # circa 2012
+# ARCH := haswell     # circa 2013
+# ARCH := broadwell   # circa 2014
+# ARCH := skylake     # circa 2015
+# ARCH := bonnell
 # ARCH := silvermont
 # ARCH := skylake-avx512
 # ARCH := nocona #64-bit pentium 4 or later 
@@ -35,7 +48,9 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+CFLAGS_LINK := $(shell echo $(CFLAGS) | sed -e "s/-fopenmp//g")
+COMPILE_COMMAND := $(CC) $(CFLAGS)  $(EXTRA_FLAGS)
+LINK_COMMAND := $(CC) $(CFLAGS_LINK) $(EXTRA_FLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -49,284 +64,27 @@ PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
 
 # put your custom objects here (they should be in the custom_modules directory)
 
-PhysiCell_custom_module_OBJECTS := .o
+PhysiCell_custom_module_OBJECTS := custom.o
 
 pugixml_OBJECTS := pugixml.o
 
 PhysiCell_OBJECTS := $(BioFVM_OBJECTS)  $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_OBJECTS)
 ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS)
 
-EXAMPLES := ./examples/PhysiCell_test_mechanics_1.cpp ./examples/PhysiCell_test_mechanics_2.cpp \
- ./examples/PhysiCell_test_DCIS.cpp ./examples/PhysiCell_test_HDS.cpp \
- ./examples/PhysiCell_test_cell_cycle.cpp ./examples/PhysiCell_test_volume.cpp 
+# compile the project 
+
+all: main.cpp $(ALL_OBJECTS)
+	$(COMPILE_COMMAND) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp 
+	make name
 
-all: 
-	make heterogeneity-sample
-	make 
+static: main.cpp $(ALL_OBJECTS) $(MaBoSS)
+	$(LINK_COMMAND) $(INC) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp $(LIB) -static-libgcc -static-libstdc++ $(STATIC_OPENMP)
 
 name:
 	@echo ""
 	@echo "Executable name is" $(PROGRAM_NAME)
 	@echo ""
 
-# sample projects 	
-list-projects:
-	@echo "Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample"
-	@echo "                 celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample"
-	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample custom-division-sample"
-	@echo "                 asymmetric-division-sample immune-function-sample episode-sample"
-	@echo ""
-	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
-	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
-	@echo ""
-	
-template:
-	cp -r ./sample_projects/template/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/template/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/template/Makefile .
-	cp -r ./sample_projects/template/config/* ./config 
-	
-# sample projects 
-
-# ---- non-intracellular projects 
-biorobots-sample:
-	cp ./sample_projects/biorobots/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/biorobots/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/biorobots/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/biorobots/config/* ./config/
-	
-cancer-biorobots-sample:
-	cp ./sample_projects/cancer_biorobots/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/cancer_biorobots/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/cancer_biorobots/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/cancer_biorobots/config/* ./config/
-	
-cancer-immune-sample:
-	cp ./sample_projects/cancer_immune/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/cancer_immune/main-cancer_immune_3D.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/cancer_immune/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/cancer_immune/config/* ./config/
-
-celltypes3-sample:
-	cp ./sample_projects/celltypes3/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/celltypes3/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/celltypes3/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/celltypes3/config/* ./config/	
-	
-heterogeneity-sample:
-	cp ./sample_projects/heterogeneity/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/heterogeneity/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/heterogeneity/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/heterogeneity/config/* ./config/
-	
-pred-prey-farmer:
-	cp ./sample_projects/pred_prey_farmer/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/pred_prey_farmer/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/pred_prey_farmer/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/pred_prey_farmer/config/* ./config/	
-	
-virus-macrophage-sample:
-	cp ./sample_projects/virus_macrophage/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/virus_macrophage/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/virus_macrophage/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/virus_macrophage/config/* ./config/
-	
-worm-sample:
-	cp ./sample_projects/worm/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/worm/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/worm/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/worm/config/* ./config/
-	
-interaction-sample:
-	cp ./sample_projects/interactions/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/interactions/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/interactions/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/interactions/config/* ./config/
-
-mechano-sample:
-	cp ./sample_projects/mechano/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/mechano/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/mechano/Makefile .
-	cp ./sample_projects/mechano/config/* ./config/
-
-rules-sample:
-	cp ./sample_projects/rules_sample/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/rules_sample/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/rules_sample/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/rules_sample/config/* ./config/
-
-physimess-sample:
-	cp ./sample_projects/physimess/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/physimess/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/physimess/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp -r ./sample_projects/physimess/config/* ./config/
-
-custom-division-sample:
-	cp -r ./sample_projects/custom_division/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/custom_division/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/custom_division/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp -r ./sample_projects/custom_division/config/* ./config/
-
-asymmetric-division-sample:
-	cp -r ./sample_projects/asymmetric_division/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/asymmetric_division/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/asymmetric_division/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp -r ./sample_projects/asymmetric_division/config/* ./config/
-
-immune-function-sample:
-	cp -r ./sample_projects/immune_function/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/immune_function/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/immune_function/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp -r ./sample_projects/immune_function/config/* ./config/
-
-episode-sample:
-	cp -r ./sample_projects/episode/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/episode/main.cpp ./main.cpp
-	cp Makefile Makefile-backup
-	cp ./sample_projects/episode/Makefile .
-	cp -r ./sample_projects/episode/config/* ./config
-
-# ---- intracellular projects 
-ode-energy-sample:
-	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects_intracellular/ode/ode_energy/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects_intracellular/ode/ode_energy/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects_intracellular/ode/ode_energy/config/* ./config/	
-
-physiboss-cell-lines-sample:
-	cp ./sample_projects_intracellular/boolean/physiboss_cell_lines/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects_intracellular/boolean/physiboss_cell_lines/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects_intracellular/boolean/physiboss_cell_lines/config/* ./config/
-
-physiboss-tutorial:
-	cp ./sample_projects_intracellular/boolean/tutorial/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects_intracellular/boolean/tutorial/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects_intracellular/boolean/tutorial/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp -r ./sample_projects_intracellular/boolean/tutorial/config/* ./config/
-
-physiboss-tutorial-invasion:
-	cp ./sample_projects_intracellular/boolean/cancer_invasion/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects_intracellular/boolean/cancer_invasion/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects_intracellular/boolean/cancer_invasion/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp -r ./sample_projects_intracellular/boolean/cancer_invasion/config/* ./config/
-
-ecoli-acetic-switch-sample:
-	cp ./sample_projects_intracellular/fba/ecoli_acetic_switch/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects_intracellular/fba/ecoli_acetic_switch/main_ecoli_acetic_switch.cpp ./main.cpp
-	cp Makefile Makefile-backup
-	cp ./sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile ./
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
-	cp ./sample_projects_intracellular/fba/ecoli_acetic_switch/config/* ./config/
-
-cancer-metabolism-sample:
-	cp ./sample_projects_intracellular/fba/cancer_metabolism/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects_intracellular/fba/cancer_metabolism/main.cpp ./main.cpp
-	cp Makefile Makefile-backup
-	cp ./sample_projects_intracellular/fba/cancer_metabolism/Makefile ./
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
-	cp ./sample_projects_intracellular/fba/cancer_metabolism/config/* ./config/
-
-template_BM:
-	cp ./sample_projects_intracellular/boolean/template_BM/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects_intracellular/boolean/template_BM/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects_intracellular/boolean/template_BM/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp -r ./sample_projects_intracellular/boolean/template_BM/config/* ./config/
-	mkdir ./scripts/
-	cp ./sample_projects_intracellular/boolean/template_BM/scripts/* ./scripts/
-
-# early examples for convergence testing 
-
-physicell_test_mech1: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp 
-	$(COMPILE_COMMAND) -o test_mech1 $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp
-
-physicell_test_mech2: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_2.cpp 
-	$(COMPILE_COMMAND) -o test_mech2 $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_2.cpp
-	
-physicell_test_DCIS: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_DCIS.cpp 
-	$(COMPILE_COMMAND) -o test_DCIS $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_DCIS.cpp
-
-physicell_test_HDS: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_HDS.cpp 
-	$(COMPILE_COMMAND) -o test_HDS $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_HDS.cpp
-
-physicell_test_cell_cycle: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_cell_cycle.cpp 
-	$(COMPILE_COMMAND) -o test_cycle $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_cell_cycle.cpp
-
-PhysiCell_test_volume: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_volume.cpp 
-	$(COMPILE_COMMAND) -o test_volume $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_volume.cpp
-	
-examples: $(PhysiCell_OBJECTS) 
-	$(COMPILE_COMMAND) -o ./examples/test_mech1 ./examples/PhysiCell_test_mechanics_1.cpp $(PhysiCell_OBJECTS)
-	$(COMPILE_COMMAND) -o ./examples/test_mech2 ./examples/PhysiCell_test_mechanics_2.cpp $(PhysiCell_OBJECTS)
-	$(COMPILE_COMMAND) -o ./examples/test_DCIS ./examples/PhysiCell_test_DCIS.cpp $(PhysiCell_OBJECTS)
-	$(COMPILE_COMMAND) -o ./examples/test_HDS ./examples/PhysiCell_test_HDS.cpp $(PhysiCell_OBJECTS)
-	$(COMPILE_COMMAND) -o ./examples/test_cycle ./examples/PhysiCell_test_cell_cycle.cpp $(PhysiCell_OBJECTS)
-	$(COMPILE_COMMAND) -o ./examples/test_volume ./examples/PhysiCell_test_volume.cpp $(PhysiCell_OBJECTS)
-
 # PhysiCell core components	
 
 PhysiCell_phenotype.o: ./core/PhysiCell_phenotype.cpp
@@ -355,7 +113,7 @@ PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
 	
 PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
-
+	
 PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.cpp 
 
@@ -404,34 +162,37 @@ PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp
 
 PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
 	$(COMPILE_COMMAND) -c ./modules/PhysiCell_various_outputs.cpp
-	
+
 PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
 	$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
 	
 PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
-	$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp	
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp
 	
 PhysiCell_basic_signaling.o: ./core/PhysiCell_basic_signaling.cpp
-	$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp 
-
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp 	
+	
 PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
 	$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp 
-
+	
 # user-defined PhysiCell modules
 
+custom.o: ./custom_modules/custom.cpp 
+	$(COMPILE_COMMAND) -c ./custom_modules/custom.cpp
+
 # cleanup
 
 reset:
-	rm -f *.cpp PhysiCell_cell.o
+	rm -f *.cpp 
 	cp ./sample_projects/Makefile-default Makefile 
-	rm -rf ./custom_modules/*
+	rm -f ./custom_modules/*
 	touch ./custom_modules/empty.txt 
 	touch ALL_CITATIONS.txt 
 	touch ./core/PhysiCell_cell.cpp
 	rm ALL_CITATIONS.txt 
 	cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml 
 	touch ./config/empty.csv
-	rm ./config/*.csv	
+	rm -f ./config/*.csv
 	
 clean:
 	rm -f *.o
@@ -441,9 +202,9 @@ data-cleanup:
 	rm -rf ./output
 	mkdir ./output
 	touch ./output/empty.txt
-
+	
 # archival 
-
+	
 checkpoint: 
 	zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* 
 	
@@ -528,15 +289,15 @@ save:
 	cp main.cpp ./user_projects/$(PROJ)
 	cp Makefile ./user_projects/$(PROJ)
 	cp VERSION.txt ./user_projects/$(PROJ)
-	cp -r ./config/* ./user_projects/$(PROJ)/config
-	cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
+	cp ./config/* ./user_projects/$(PROJ)/config
+	cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
 
 load: 
 	echo "Loading project from $(PROJ) ... "
 	cp ./user_projects/$(PROJ)/main.cpp .
 	cp ./user_projects/$(PROJ)/Makefile .
-	cp -r ./user_projects/$(PROJ)/config/* ./config/ 
-	cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
+	cp ./user_projects/$(PROJ)/config/* ./config/ 
+	cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
 
 pack:
 	@echo " "
diff --git a/config/PhysiCell_settings.xml b/config/PhysiCell_settings.xml
index e3cd03b4a..72970bf80 100644
--- a/config/PhysiCell_settings.xml
+++ b/config/PhysiCell_settings.xml
@@ -14,7 +14,7 @@
     </domain>
 
     <overall>
-        <max_time units="min">14400</max_time>
+        <max_time units="min">2880</max_time>
         <time_units>min</time_units>
         <space_units>micron</space_units>
         <dt_diffusion units="min">0.01</dt_diffusion>
@@ -35,6 +35,12 @@
         <SVG>
             <interval units="min">60</interval>
             <enable>true</enable>
+            <plot_substrate enabled="false" limits="true">
+                <substrate>debris</substrate>
+                <colormap>YlOrRd</colormap>
+                <min_conc>0</min_conc>
+                <max_conc>1</max_conc>
+            </plot_substrate>
         </SVG>
         <legacy_data>
             <enable>false</enable>
@@ -44,29 +50,15 @@
     <options>
         <legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
+        <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
+        <random_seed>0</random_seed>
     </options>
 
     <microenvironment_setup>
-        <variable name="oxygen" units="dimensionless" ID="0">
+        <variable name="debris" units="dimensionless" ID="0">
             <physical_parameter_set>
                 <diffusion_coefficient units="micron^2/min">100000.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.1</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="mmHg">38</initial_condition>
-            <Dirichlet_boundary_condition units="mmHg" enabled="True">0</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="True">38</boundary_value>
-                <boundary_value ID="xmax" enabled="True">10</boundary_value>
-                <boundary_value ID="ymin" enabled="True">10</boundary_value>
-                <boundary_value ID="ymax" enabled="True">38</boundary_value>
-                <boundary_value ID="zmin" enabled="False">0</boundary_value>
-                <boundary_value ID="zmax" enabled="False">0</boundary_value>
-            </Dirichlet_options>
-        </variable>
-        <variable name="necrotic debris" units="dimensionless" ID="1">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">10</diffusion_coefficient>
-                <decay_rate units="1/min">.1</decay_rate>
+                <decay_rate units="1/min">10</decay_rate>
             </physical_parameter_set>
             <initial_condition units="mmHg">0</initial_condition>
             <Dirichlet_boundary_condition units="mmHg" enabled="False">0</Dirichlet_boundary_condition>
@@ -79,20 +71,132 @@
                 <boundary_value ID="zmax" enabled="False">0</boundary_value>
             </Dirichlet_options>
         </variable>
-        <variable name="apoptotic debris" units="dimensionless" ID="2">
+        <variable name="cxc3cl1" units="dimensionless" ID="1">
             <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">10</diffusion_coefficient>
-                <decay_rate units="1/min">0.1</decay_rate>
+                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.0</decay_rate>
             </physical_parameter_set>
-            <initial_condition units="mmHg">0</initial_condition>
-            <Dirichlet_boundary_condition units="mmHg" enabled="False">0</Dirichlet_boundary_condition>
+            <initial_condition units="dimensionless">0.0</initial_condition>
+            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
             <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False">0</boundary_value>
-                <boundary_value ID="xmax" enabled="False">0</boundary_value>
-                <boundary_value ID="ymin" enabled="False">0</boundary_value>
-                <boundary_value ID="ymax" enabled="False">0</boundary_value>
-                <boundary_value ID="zmin" enabled="False">0</boundary_value>
-                <boundary_value ID="zmax" enabled="False">0</boundary_value>
+                <boundary_value ID="xmin" enabled="False" />
+                <boundary_value ID="xmax" enabled="False" />
+                <boundary_value ID="ymin" enabled="False" />
+                <boundary_value ID="ymax" enabled="False" />
+                <boundary_value ID="zmin" enabled="False" />
+                <boundary_value ID="zmax" enabled="False" />
+            </Dirichlet_options>
+        </variable>
+        <variable name="egf" units="dimensionless" ID="2">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.0</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="dimensionless">0.0</initial_condition>
+            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="False" />
+                <boundary_value ID="xmax" enabled="False" />
+                <boundary_value ID="ymin" enabled="False" />
+                <boundary_value ID="ymax" enabled="False" />
+                <boundary_value ID="zmin" enabled="False" />
+                <boundary_value ID="zmax" enabled="False" />
+            </Dirichlet_options>
+        </variable>
+        <variable name="ifng" units="dimensionless" ID="3">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.0</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="dimensionless">0.0</initial_condition>
+            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="False" />
+                <boundary_value ID="xmax" enabled="False" />
+                <boundary_value ID="ymin" enabled="False" />
+                <boundary_value ID="ymax" enabled="False" />
+                <boundary_value ID="zmin" enabled="False" />
+                <boundary_value ID="zmax" enabled="False" />
+            </Dirichlet_options>
+        </variable>
+        <variable name="il2" units="dimensionless" ID="4">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.0</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="dimensionless">0.0</initial_condition>
+            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="False" />
+                <boundary_value ID="xmax" enabled="False" />
+                <boundary_value ID="ymin" enabled="False" />
+                <boundary_value ID="ymax" enabled="False" />
+                <boundary_value ID="zmin" enabled="False" />
+                <boundary_value ID="zmax" enabled="False" />
+            </Dirichlet_options>
+        </variable>
+        <variable name="il4" units="dimensionless" ID="5">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.0</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="dimensionless">0.0</initial_condition>
+            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="False" />
+                <boundary_value ID="xmax" enabled="False" />
+                <boundary_value ID="ymin" enabled="False" />
+                <boundary_value ID="ymax" enabled="False" />
+                <boundary_value ID="zmin" enabled="False" />
+                <boundary_value ID="zmax" enabled="False" />
+            </Dirichlet_options>
+        </variable>
+        <variable name="il6" units="dimensionless" ID="6">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.0</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="dimensionless">0.0</initial_condition>
+            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="False" />
+                <boundary_value ID="xmax" enabled="False" />
+                <boundary_value ID="ymin" enabled="False" />
+                <boundary_value ID="ymax" enabled="False" />
+                <boundary_value ID="zmin" enabled="False" />
+                <boundary_value ID="zmax" enabled="False" />
+            </Dirichlet_options>
+        </variable>
+        <variable name="il10" units="dimensionless" ID="7">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.0</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="dimensionless">0.0</initial_condition>
+            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="False" />
+                <boundary_value ID="xmax" enabled="False" />
+                <boundary_value ID="ymin" enabled="False" />
+                <boundary_value ID="ymax" enabled="False" />
+                <boundary_value ID="zmin" enabled="False" />
+                <boundary_value ID="zmax" enabled="False" />
+            </Dirichlet_options>
+        </variable>
+        <variable name="il12" units="dimensionless" ID="8">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.0</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="dimensionless">0.0</initial_condition>
+            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="False" />
+                <boundary_value ID="xmax" enabled="False" />
+                <boundary_value ID="ymin" enabled="False" />
+                <boundary_value ID="ymax" enabled="False" />
+                <boundary_value ID="zmin" enabled="False" />
+                <boundary_value ID="zmax" enabled="False" />
             </Dirichlet_options>
         </variable>
         <options>
@@ -108,19 +212,31 @@
     </microenvironment_setup>
 
     <cell_definitions>
-        <cell_definition name="malignant epithelial" ID="0">
+        <cell_definition name="neoplastic epithelial" ID="0">
             <phenotype>
-                <cycle code="5" name="live">
-                    <phase_transition_rates units="1/min">
-                        <rate start_index="0" end_index="0" fixed_duration="false">0.000</rate>
-                    </phase_transition_rates>
+                <cycle code="2" name="flow cytometry">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="false">245.32200</duration>
+                        <duration index="1" fixed_duration="false">555.78600</duration>
+                        <duration index="2" fixed_duration="false">584.89200</duration>
+                    </phase_durations>
+                    <standard_asymmetric_division enabled="False">
+                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">1.0</asymmetric_division_probability>
+                    </standard_asymmetric_division>
                 </cycle>
                 <death>
                     <model code="100" name="apoptosis">
                         <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_durations units="min">
-                            <duration index="0" fixed_duration="true">516</duration>
-                        </phase_durations>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
+                        </phase_transition_rates>
                         <parameters>
                             <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
                             <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
@@ -131,17 +247,17 @@
                         </parameters>
                     </model>
                     <model code="101" name="necrosis">
-                        <death_rate units="1/min">2.80E-03</death_rate>
-                        <phase_durations units="min">
-                            <duration index="0" fixed_duration="true">0</duration>
-                            <duration index="1" fixed_duration="true">86400</duration>
-                        </phase_durations>
+                        <death_rate units="1/min">0.0</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
+                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
+                        </phase_transition_rates>
                         <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-2</unlysed_fluid_change_rate>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
                             <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-3</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">0</calcification_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">7e-05</calcification_rate>
                             <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
                         </parameters>
                     </model>
@@ -153,119 +269,1812 @@
                     <fluid_change_rate units="1/min">0.05</fluid_change_rate>
                     <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
                     <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0</calcified_fraction>
-                    <calcification_rate units="1/min">0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
+                    <calcification_rate units="1/min">0.0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
                 </volume>
                 <mechanics>
                     <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
                     <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
                     <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
                     <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="malignant epithelial">1</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
                     </cell_adhesion_affinities>
                     <options>
                         <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
                         <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
                     </options>
-                    <cell_BM_adhesion_strength units="micron/min">4.0</cell_BM_adhesion_strength>
-                    <cell_BM_repulsion_strength units="micron/min">10.0</cell_BM_repulsion_strength>
                     <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                     <attachment_rate units="1/min">0.0</attachment_rate>
                     <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
                 </mechanics>
                 <motility>
-                    <speed units="micron/min">1</speed>
-                    <persistence_time units="min">1</persistence_time>
-                    <migration_bias units="dimensionless">.5</migration_bias>
+                    <speed units="micron/min">1.0</speed>
+                    <persistence_time units="min">1.0</persistence_time>
+                    <migration_bias units="dimensionless">0.0</migration_bias>
                     <options>
                         <enabled>false</enabled>
                         <use_2D>true</use_2D>
                         <chemotaxis>
                             <enabled>false</enabled>
-                            <substrate>oxygen</substrate>
+                            <substrate>debris</substrate>
                             <direction>1</direction>
                         </chemotaxis>
                         <advanced_chemotaxis>
                             <enabled>false</enabled>
                             <normalize_each_gradient>false</normalize_each_gradient>
                             <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="necrotic debris">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="apoptotic debris">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
                             </chemotactic_sensitivities>
                         </advanced_chemotaxis>
                     </options>
                 </motility>
                 <secretion>
-                    <substrate name="oxygen">
-                        <secretion_rate units="1/min">0</secretion_rate>
-                        <secretion_target units="substrate density">1</secretion_target>
-                        <uptake_rate units="1/min">10</uptake_rate>
-                        <net_export_rate units="total substrate/min">0</net_export_rate>
+                    <substrate name="debris">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="cxc3cl1">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="egf">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
                     </substrate>
-                    <substrate name="necrotic debris">
+                    <substrate name="ifng">
                         <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1</secretion_target>
+                        <secretion_target units="substrate density">1.0</secretion_target>
                         <uptake_rate units="1/min">0.0</uptake_rate>
                         <net_export_rate units="total substrate/min">0.0</net_export_rate>
                     </substrate>
-                    <substrate name="apoptotic debris">
+                    <substrate name="il2">
                         <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1</secretion_target>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il4">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il6">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il10">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il12">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
                         <uptake_rate units="1/min">0.0</uptake_rate>
                         <net_export_rate units="total substrate/min">0.0</net_export_rate>
                     </substrate>
                 </secretion>
                 <cell_interactions>
-                    <dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
+                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
+                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
                     <live_phagocytosis_rates>
-                        <phagocytosis_rate name="malignant epithelial" units="1/min">0</phagocytosis_rate>
-                        <phagocytosis_rate name="default" units="1/min">0</phagocytosis_rate>
+                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
                     </live_phagocytosis_rates>
                     <attack_rates>
-                        <attack_rate name="malignant epithelial" units="1/min">0</attack_rate>
-                        <attack_rate name="default" units="1/min">0</attack_rate>
+                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
+                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
+                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
                     </attack_rates>
-                    <damage_rate units="1/min">1</damage_rate>
+                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
                     <fusion_rates>
-                        <fusion_rate name="malignant epithelial" units="1/min">0</fusion_rate>
-                        <fusion_rate name="default" units="1/min">0</fusion_rate>
+                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
                     </fusion_rates>
                 </cell_interactions>
                 <cell_transformations>
                     <transformation_rates>
-                        <transformation_rate name="malignant epithelial" units="1/min">0</transformation_rate>
-                        <transformation_rate name="default" units="1/min">0</transformation_rate>
+                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
                     </transformation_rates>
                 </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
             </phenotype>
             <custom_data>
                 <sample conserved="false" units="dimensionless" description="">1.0</sample>
             </custom_data>
+            <initial_parameter_distributions enabled="false">
+                <distribution enabled="false" type="Log10Normal" check_base="true">
+                    <behavior>Volume</behavior>
+                    <mu>4</mu>
+                    <sigma>2</sigma>
+                    <upper_bound>100000</upper_bound>
+                </distribution>
+                <distribution enabled="false" type="LogUniform" check_base="true">
+                    <behavior>apoptosis</behavior>
+                    <min>1e-6</min>
+                    <max>1e-2</max>
+                </distribution>
+            </initial_parameter_distributions>
         </cell_definition>
-    </cell_definitions>
-
-    <initial_conditions>
-        <cell_positions type="csv" enabled="true">
-            <folder>./config</folder>
-            <filename>cells.csv</filename>
-        </cell_positions>
-    </initial_conditions>
-
-    <cell_rules>
-        <rulesets>
-            <ruleset protocol="CBHG" version="3.0" format="csv" enabled="true">
-                <folder>./config</folder>
-                <filename>cell_rules_v2.csv</filename>
-            </ruleset>
-        </rulesets>
-        <settings />
-    </cell_rules>
-
+        <cell_definition name="monocyte" ID="1">
+            <phenotype>
+                <cycle code="2" name="flow cytometry">
+                    <phase_transition_rates units="1/min">
+                        <rate start_index="0" end_index="1" fixed_duration="false">0</rate>
+                        <rate start_index="1" end_index="2" fixed_duration="false">0.00208</rate>
+                        <rate start_index="2" end_index="0" fixed_duration="false">0.00333</rate>
+                    </phase_transition_rates>
+                    <standard_asymmetric_division enabled="False">
+                        <asymmetric_division_probability name="monocyte" units="dimensionless">1.0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
+                    </standard_asymmetric_division>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">5.31667e-05</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">0</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                    <model code="101" name="necrosis">
+                        <death_rate units="1/min">0.0</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
+                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">7e-05</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                </death>
+                <volume>
+                    <total units="micron^3">2494</total>
+                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
+                    <nuclear units="micron^3">540</nuclear>
+                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
+                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
+                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
+                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
+                    <calcification_rate units="1/min">0.0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
+                </volume>
+                <mechanics>
+                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
+                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
+                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
+                    <cell_adhesion_affinities>
+                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
+                    </cell_adhesion_affinities>
+                    <options>
+                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
+                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
+                    </options>
+                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
+                    <attachment_rate units="1/min">0.0</attachment_rate>
+                    <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
+                </mechanics>
+                <motility>
+                    <speed units="micron/min">1.0</speed>
+                    <persistence_time units="min">1.0</persistence_time>
+                    <migration_bias units="dimensionless">0.0</migration_bias>
+                    <options>
+                        <enabled>true</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>false</enabled>
+                            <substrate>debris</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>false</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="debris">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="cxc3cl1">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="egf">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="ifng">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il2">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il4">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il6">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il10">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il12">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
+                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
+                    <live_phagocytosis_rates>
+                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
+                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
+                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
+                    </attack_rates>
+                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+                    <fusion_rates>
+                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
+            </phenotype>
+            <custom_data>
+                <sample conserved="false" units="dimensionless" description="">0.0</sample>
+            </custom_data>
+            <initial_parameter_distributions enabled="false">
+          </initial_parameter_distributions>
+        </cell_definition>
+        <cell_definition name="mac_cadm1" ID="2">
+            <phenotype>
+                <cycle code="2" name="flow cytometry">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="false">308.64198</duration>
+                        <duration index="1" fixed_duration="false">480.76923</duration>
+                        <duration index="2" fixed_duration="false">300.30030</duration>
+                    </phase_durations>
+                    <standard_asymmetric_division enabled="False">
+                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">1.0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
+                    </standard_asymmetric_division>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">5.31667e-05</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">0</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                    <model code="101" name="necrosis">
+                        <death_rate units="1/min">0.0</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
+                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">7e-05</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                </death>
+                <volume>
+                    <total units="micron^3">2494</total>
+                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
+                    <nuclear units="micron^3">540</nuclear>
+                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
+                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
+                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
+                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
+                    <calcification_rate units="1/min">0.0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
+                </volume>
+                <mechanics>
+                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
+                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
+                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
+                    <cell_adhesion_affinities>
+                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
+                    </cell_adhesion_affinities>
+                    <options>
+                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
+                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
+                    </options>
+                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
+                    <attachment_rate units="1/min">0.0</attachment_rate>
+                    <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
+                </mechanics>
+                <motility>
+                    <speed units="micron/min">1.0</speed>
+                    <persistence_time units="min">1.0</persistence_time>
+                    <migration_bias units="dimensionless">0.0</migration_bias>
+                    <options>
+                        <enabled>true</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>false</enabled>
+                            <substrate>debris</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>true</enabled>
+                            <normalize_each_gradient>true</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="debris">1.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="cxc3cl1">1.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="debris">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="cxc3cl1">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="egf">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="ifng">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il2">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il4">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il6">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il10">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il12">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
+                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
+                    <live_phagocytosis_rates>
+                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
+                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
+                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
+                    </attack_rates>
+                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+                    <fusion_rates>
+                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
+            </phenotype>
+            <custom_data>
+                <sample conserved="false" units="dimensionless" description="">0.0</sample>
+            </custom_data>
+            <initial_parameter_distributions enabled="false">
+          </initial_parameter_distributions>
+        </cell_definition>
+        <cell_definition name="mac_folr2" ID="3">
+            <phenotype>
+                <cycle code="2" name="flow cytometry">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="false">308.64198</duration>
+                        <duration index="1" fixed_duration="false">480.76923</duration>
+                        <duration index="2" fixed_duration="false">300.30030</duration>
+                    </phase_durations>
+                    <standard_asymmetric_division enabled="False">
+                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">1.0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
+                    </standard_asymmetric_division>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">5.31667e-05</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">0</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                    <model code="101" name="necrosis">
+                        <death_rate units="1/min">0.0</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
+                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">7e-05</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                </death>
+                <volume>
+                    <total units="micron^3">2494</total>
+                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
+                    <nuclear units="micron^3">540</nuclear>
+                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
+                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
+                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
+                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
+                    <calcification_rate units="1/min">0.0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
+                </volume>
+                <mechanics>
+                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
+                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
+                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
+                    <cell_adhesion_affinities>
+                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
+                    </cell_adhesion_affinities>
+                    <options>
+                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
+                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
+                    </options>
+                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
+                    <attachment_rate units="1/min">0.0</attachment_rate>
+                    <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
+                </mechanics>
+                <motility>
+                    <speed units="micron/min">1.0</speed>
+                    <persistence_time units="min">1.0</persistence_time>
+                    <migration_bias units="dimensionless">0.5</migration_bias>
+                    <options>
+                        <enabled>true</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>false</enabled>
+                            <substrate>debris</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>true</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="debris">1.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="debris">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="cxc3cl1">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="egf">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="ifng">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il2">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il4">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il6">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il10">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il12">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
+                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
+                    <live_phagocytosis_rates>
+                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
+                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
+                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
+                    </attack_rates>
+                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+                    <fusion_rates>
+                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
+            </phenotype>
+            <custom_data>
+                <sample conserved="false" units="dimensionless" description="">0.0</sample>
+            </custom_data>
+            <initial_parameter_distributions enabled="false">
+          </initial_parameter_distributions>
+        </cell_definition>
+        <cell_definition name="mac_other" ID="4">
+            <phenotype>
+                <cycle code="2" name="flow cytometry">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="false">308.64198</duration>
+                        <duration index="1" fixed_duration="false">480.76923</duration>
+                        <duration index="2" fixed_duration="false">300.30030</duration>
+                    </phase_durations>
+                    <standard_asymmetric_division enabled="False">
+                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_other" units="dimensionless">1.0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
+                    </standard_asymmetric_division>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">5.31667e-05</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">0</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                    <model code="101" name="necrosis">
+                        <death_rate units="1/min">0.0</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
+                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">7e-05</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                </death>
+                <volume>
+                    <total units="micron^3">2494</total>
+                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
+                    <nuclear units="micron^3">540</nuclear>
+                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
+                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
+                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
+                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
+                    <calcification_rate units="1/min">0.0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
+                </volume>
+                <mechanics>
+                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
+                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
+                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
+                    <cell_adhesion_affinities>
+                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
+                    </cell_adhesion_affinities>
+                    <options>
+                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
+                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
+                    </options>
+                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
+                    <attachment_rate units="1/min">0.0</attachment_rate>
+                    <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
+                </mechanics>
+                <motility>
+                    <speed units="micron/min">1.0</speed>
+                    <persistence_time units="min">1.0</persistence_time>
+                    <migration_bias units="dimensionless">0.7</migration_bias>
+                    <options>
+                        <enabled>true</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>false</enabled>
+                            <substrate>debris</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>true</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="debris">1.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="debris">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="cxc3cl1">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="egf">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="ifng">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il2">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il4">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il6">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il10">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il12">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
+                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
+                    <live_phagocytosis_rates>
+                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
+                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
+                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
+                    </attack_rates>
+                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+                    <fusion_rates>
+                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
+            </phenotype>
+            <custom_data>
+                <sample conserved="false" units="dimensionless" description="">0.0</sample>
+            </custom_data>
+            <initial_parameter_distributions enabled="false">
+          </initial_parameter_distributions>
+        </cell_definition>
+        <cell_definition name="dendritic" ID="5">
+            <phenotype>
+                <cycle code="2" name="flow cytometry">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="false">308.64198</duration>
+                        <duration index="1" fixed_duration="false">480.76923</duration>
+                        <duration index="2" fixed_duration="false">300.30030</duration>
+                    </phase_durations>
+                    <standard_asymmetric_division enabled="False">
+                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="dendritic" units="dimensionless">1.0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
+                    </standard_asymmetric_division>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">5.31667e-05</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">0</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                    <model code="101" name="necrosis">
+                        <death_rate units="1/min">0.0</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
+                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">7e-05</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                </death>
+                <volume>
+                    <total units="micron^3">2494</total>
+                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
+                    <nuclear units="micron^3">540</nuclear>
+                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
+                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
+                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
+                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
+                    <calcification_rate units="1/min">0.0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
+                </volume>
+                <mechanics>
+                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
+                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
+                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
+                    <cell_adhesion_affinities>
+                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
+                    </cell_adhesion_affinities>
+                    <options>
+                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
+                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
+                    </options>
+                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
+                    <attachment_rate units="1/min">0.0</attachment_rate>
+                    <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
+                </mechanics>
+                <motility>
+                    <speed units="micron/min">1.0</speed>
+                    <persistence_time units="min">1.0</persistence_time>
+                    <migration_bias units="dimensionless">0.0</migration_bias>
+                    <options>
+                        <enabled>false</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>false</enabled>
+                            <substrate>debris</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>false</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="debris">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="cxc3cl1">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="egf">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="ifng">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il2">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il4">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il6">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il10">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il12">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
+                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
+                    <live_phagocytosis_rates>
+                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
+                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
+                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
+                    </attack_rates>
+                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+                    <fusion_rates>
+                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
+            </phenotype>
+            <custom_data>
+                <sample conserved="false" units="dimensionless" description="">0.0</sample>
+            </custom_data>
+            <initial_parameter_distributions enabled="false">
+          </initial_parameter_distributions>
+        </cell_definition>
+        <cell_definition name="t_cd4" ID="6">
+            <phenotype>
+                <cycle code="2" name="flow cytometry">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="false">308.64198</duration>
+                        <duration index="1" fixed_duration="false">480.76923</duration>
+                        <duration index="2" fixed_duration="false">300.30030</duration>
+                    </phase_durations>
+                    <standard_asymmetric_division enabled="False">
+                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd4" units="dimensionless">1.0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
+                    </standard_asymmetric_division>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">5.31667e-05</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">0</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                    <model code="101" name="necrosis">
+                        <death_rate units="1/min">0.0</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
+                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">7e-05</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                </death>
+                <volume>
+                    <total units="micron^3">2494</total>
+                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
+                    <nuclear units="micron^3">540</nuclear>
+                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
+                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
+                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
+                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
+                    <calcification_rate units="1/min">0.0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
+                </volume>
+                <mechanics>
+                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
+                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
+                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
+                    <cell_adhesion_affinities>
+                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
+                    </cell_adhesion_affinities>
+                    <options>
+                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
+                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
+                    </options>
+                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
+                    <attachment_rate units="1/min">0.0</attachment_rate>
+                    <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
+                </mechanics>
+                <motility>
+                    <speed units="micron/min">1.0</speed>
+                    <persistence_time units="min">1.0</persistence_time>
+                    <migration_bias units="dimensionless">0.0</migration_bias>
+                    <options>
+                        <enabled>true</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>false</enabled>
+                            <substrate>debris</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>false</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="debris">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="cxc3cl1">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="egf">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="ifng">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il2">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il4">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il6">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il10">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il12">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
+                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
+                    <live_phagocytosis_rates>
+                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
+                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
+                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
+                    </attack_rates>
+                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+                    <fusion_rates>
+                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
+            </phenotype>
+            <custom_data>
+                <sample conserved="false" units="dimensionless" description="">0.0</sample>
+            </custom_data>
+            <initial_parameter_distributions enabled="false">
+          </initial_parameter_distributions>
+        </cell_definition>
+        <cell_definition name="t_cd8" ID="7">
+            <phenotype>
+                <cycle code="2" name="flow cytometry">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="false">308.64198</duration>
+                        <duration index="1" fixed_duration="false">480.76923</duration>
+                        <duration index="2" fixed_duration="false">300.30030</duration>
+                    </phase_durations>
+                    <standard_asymmetric_division enabled="False">
+                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="t_cd8" units="dimensionless">1.0</asymmetric_division_probability>
+                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
+                    </standard_asymmetric_division>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">5.31667e-05</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">0</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                    <model code="101" name="necrosis">
+                        <death_rate units="1/min">0.0</death_rate>
+                        <phase_transition_rates units="1/min">
+                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
+                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
+                        </phase_transition_rates>
+                        <parameters>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">7e-05</calcification_rate>
+                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
+                        </parameters>
+                    </model>
+                </death>
+                <volume>
+                    <total units="micron^3">2494</total>
+                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
+                    <nuclear units="micron^3">540</nuclear>
+                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
+                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
+                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
+                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
+                    <calcification_rate units="1/min">0.0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
+                </volume>
+                <mechanics>
+                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
+                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
+                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
+                    <cell_adhesion_affinities>
+                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
+                    </cell_adhesion_affinities>
+                    <options>
+                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
+                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
+                    </options>
+                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
+                    <attachment_rate units="1/min">0.0</attachment_rate>
+                    <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
+                </mechanics>
+                <motility>
+                    <speed units="micron/min">1.0</speed>
+                    <persistence_time units="min">1.0</persistence_time>
+                    <migration_bias units="dimensionless">0.0</migration_bias>
+                    <options>
+                        <enabled>true</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>false</enabled>
+                            <substrate>debris</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>false</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="debris">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="cxc3cl1">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="egf">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="ifng">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il2">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il4">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il6">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il10">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                    <substrate name="il12">
+                        <secretion_rate units="1/min">0.0</secretion_rate>
+                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <uptake_rate units="1/min">0.0</uptake_rate>
+                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
+                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
+                    <live_phagocytosis_rates>
+                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
+                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
+                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
+                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
+                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
+                    </attack_rates>
+                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+                    <fusion_rates>
+                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
+            </phenotype>
+            <custom_data>
+                <sample conserved="false" units="dimensionless" description="">0.0</sample>
+            </custom_data>
+            <initial_parameter_distributions enabled="false">
+          </initial_parameter_distributions>
+        </cell_definition>
+    </cell_definitions>
+
+    <initial_conditions>
+        <cell_positions type="csv" enabled="false">
+            <folder>./config</folder>
+            <filename>cells.csv</filename>
+        </cell_positions>
+    </initial_conditions>
+
+    <cell_rules>
+        <rulesets>
+            <ruleset protocol="CBHG" version="3.0" format="csv" enabled="false">
+                <folder>./config</folder>
+                <filename>cell_rules.csv</filename>
+            </ruleset>
+        </rulesets>
+        <settings />
+    </cell_rules>
 
     <user_parameters>
-        <random_seed type="int" units="dimensionless" description="">0</random_seed>
-        <number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">0</number_of_cells>
+        <number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">12</number_of_cells>
     </user_parameters>
 </PhysiCell_settings>
\ No newline at end of file
diff --git a/config/cell_rules.csv b/config/cell_rules.csv
new file mode 100644
index 000000000..e69de29bb
diff --git a/config/cells.csv b/config/cells.csv
new file mode 100644
index 000000000..734bdc767
--- /dev/null
+++ b/config/cells.csv
@@ -0,0 +1 @@
+0,0,0,0
\ No newline at end of file
diff --git a/custom_modules/custom.cpp b/custom_modules/custom.cpp
new file mode 100644
index 000000000..59b23bd93
--- /dev/null
+++ b/custom_modules/custom.cpp
@@ -0,0 +1,214 @@
+/*
+###############################################################################
+# 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) 2015-2021, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include "./custom.h"
+
+void create_cell_types( void )
+{
+	// set the random seed 
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
+	
+	/* 
+	   Put any modifications to default cell definition here if you 
+	   want to have "inherited" by other cell types. 
+	   
+	   This is a good place to set default functions. 
+	*/ 
+	
+	initialize_default_cell_definition(); 
+	cell_defaults.phenotype.secretion.sync_to_microenvironment( &microenvironment ); 
+	
+	cell_defaults.functions.volume_update_function = standard_volume_update_function;
+	cell_defaults.functions.update_velocity = standard_update_cell_velocity;
+
+	cell_defaults.functions.update_migration_bias = NULL; 
+	cell_defaults.functions.update_phenotype = NULL; // update_cell_and_death_parameters_O2_based; 
+	cell_defaults.functions.custom_cell_rule = NULL; 
+	cell_defaults.functions.contact_function = NULL; 
+	
+	cell_defaults.functions.add_cell_basement_membrane_interactions = NULL; 
+	cell_defaults.functions.calculate_distance_to_membrane = NULL; 
+	
+	/*
+	   This parses the cell definitions in the XML config file. 
+	*/
+	
+	initialize_cell_definitions_from_pugixml(); 
+
+	/*
+	   This builds the map of cell definitions and summarizes the setup. 
+	*/
+		
+	build_cell_definitions_maps(); 
+
+	/*
+	   This intializes cell signal and response dictionaries 
+	*/
+
+	setup_signal_behavior_dictionaries(); 	
+
+	/*
+       Cell rule definitions 
+	*/
+
+	setup_cell_rules(); 
+
+	/* 
+	   Put any modifications to individual cell definitions here. 
+	   
+	   This is a good place to set custom functions. 
+	*/ 
+	
+	cell_defaults.functions.update_phenotype = phenotype_function; 
+	cell_defaults.functions.custom_cell_rule = custom_function; 
+	cell_defaults.functions.contact_function = contact_function; 
+	
+	/*
+	   This builds the map of cell definitions and summarizes the setup. 
+	*/
+		
+	display_cell_definitions( std::cout ); 
+	
+	return; 
+}
+
+void setup_microenvironment( void )
+{
+	// set domain parameters 
+	
+	// put any custom code to set non-homogeneous initial conditions or 
+	// extra Dirichlet nodes here. 
+	
+	// initialize BioFVM 
+	
+	initialize_microenvironment(); 	
+	
+	return; 
+}
+
+void setup_tissue( void )
+{
+	double Xmin = microenvironment.mesh.bounding_box[0]; 
+	double Ymin = microenvironment.mesh.bounding_box[1]; 
+	double Zmin = microenvironment.mesh.bounding_box[2]; 
+
+	double Xmax = microenvironment.mesh.bounding_box[3]; 
+	double Ymax = microenvironment.mesh.bounding_box[4]; 
+	double Zmax = microenvironment.mesh.bounding_box[5]; 
+	
+	if( default_microenvironment_options.simulate_2D == true )
+	{
+		Zmin = 0.0; 
+		Zmax = 0.0; 
+	}
+	
+	double Xrange = Xmax - Xmin; 
+	double Yrange = Ymax - Ymin; 
+	double Zrange = Zmax - Zmin; 
+	
+	// create some of each type of cell 
+	
+	Cell* pC;
+	
+	for( int k=0; k < cell_definitions_by_index.size() ; k++ )
+	{
+		Cell_Definition* pCD = cell_definitions_by_index[k]; 
+		std::cout << "Placing cells of type " << pCD->name << " ... " << std::endl; 
+		for( int n = 0 ; n < parameters.ints("number_of_cells") ; n++ )
+		{
+			std::vector<double> position = {0,0,0}; 
+			position[0] = Xmin + UniformRandom()*Xrange; 
+			position[1] = Ymin + UniformRandom()*Yrange; 
+			position[2] = Zmin + UniformRandom()*Zrange; 
+			
+			pC = create_cell( *pCD ); 
+			pC->assign_position( position );
+		}
+	}
+	std::cout << std::endl; 
+	
+	// load cells from your CSV file (if enabled)
+	load_cells_from_pugixml();
+	set_parameters_from_distributions();
+	
+	return; 
+}
+
+std::vector<std::string> my_coloring_function( Cell* pCell )
+{ return paint_by_number_cell_coloring(pCell); }
+
+void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt )
+{ return; }
+
+void custom_function( Cell* pCell, Phenotype& phenotype , double dt )
+{ return; } 
+
+void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt )
+{ return; } 
\ No newline at end of file
diff --git a/custom_modules/custom.h b/custom_modules/custom.h
new file mode 100644
index 000000000..0e6df8d02
--- /dev/null
+++ b/custom_modules/custom.h
@@ -0,0 +1,92 @@
+/*
+###############################################################################
+# 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) 2015-2021, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include "../core/PhysiCell.h"
+#include "../modules/PhysiCell_standard_modules.h" 
+
+using namespace BioFVM; 
+using namespace PhysiCell;
+
+// setup functions to help us along 
+
+void create_cell_types( void );
+void setup_tissue( void ); 
+
+// set up the BioFVM microenvironment 
+void setup_microenvironment( void ); 
+
+// custom pathology coloring function 
+
+std::vector<std::string> my_coloring_function( Cell* );
+
+// custom functions can go here 
+
+void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt );
+void custom_function( Cell* pCell, Phenotype& phenotype , double dt );
+
+void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt ); 
+
diff --git a/main.cpp b/main.cpp
new file mode 100644
index 000000000..bf6e65d15
--- /dev/null
+++ b/main.cpp
@@ -0,0 +1,254 @@
+/*
+###############################################################################
+# 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) 2015-2022, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include <cstdio>
+#include <cstdlib>
+#include <iostream>
+#include <ctime>
+#include <cmath>
+#include <omp.h>
+#include <fstream>
+
+#include "./core/PhysiCell.h"
+#include "./modules/PhysiCell_standard_modules.h" 
+
+// put custom code modules here! 
+
+#include "./custom_modules/custom.h" 
+	
+using namespace BioFVM;
+using namespace PhysiCell;
+
+int main( int argc, char* argv[] )
+{
+	// load and parse settings file(s)
+	
+	bool XML_status = false; 
+	char copy_command [1024]; 
+	if( argc > 1 )
+	{
+		XML_status = load_PhysiCell_config_file( argv[1] ); 
+		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+	}
+	else
+	{
+		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
+		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
+	}
+	if( !XML_status )
+	{ exit(-1); }
+	
+	// copy config file to output directry 
+	system( copy_command ); 
+	
+	// OpenMP setup
+	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
+	
+	// time setup 
+	std::string time_units = "min"; 
+
+	/* Microenvironment setup */ 
+	
+	setup_microenvironment(); // modify this in the custom code 
+	
+	/* PhysiCell setup */ 
+ 	
+	// set mechanics voxel size, and match the data structure to BioFVM
+	double mechanics_voxel_size = 30; 
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	
+	/* Users typically start modifying here. START USERMODS */ 
+	
+	create_cell_types();
+	
+	setup_tissue();
+
+	/* Users typically stop modifying here. END USERMODS */ 
+	
+	// set MultiCellDS save options 
+
+	set_save_biofvm_mesh_as_matlab( true ); 
+	set_save_biofvm_data_as_matlab( true ); 
+	set_save_biofvm_cell_data( true ); 
+	set_save_biofvm_cell_data_as_custom_matlab( true );
+	
+	// save a simulation snapshot 
+	
+	char filename[1024];
+	sprintf( filename , "%s/initial" , PhysiCell_settings.folder.c_str() ); 
+	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+	
+	// save a quick SVG cross section through z = 0, after setting its 
+	// length bar to 200 microns 
+
+	PhysiCell_SVG_options.length_bar = 200; 
+
+	// for simplicity, set a pathology coloring function 
+	
+	std::vector<std::string> (*cell_coloring_function)(Cell*) = my_coloring_function;
+	std::string (*substrate_coloring_function)(double, double, double) = paint_by_density_percentage;
+
+	sprintf( filename , "%s/initial.svg" , PhysiCell_settings.folder.c_str() ); 
+	SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function );
+	
+	sprintf( filename , "%s/legend.svg" , PhysiCell_settings.folder.c_str() ); 
+	create_plot_legend( filename , cell_coloring_function ); 
+	
+	display_citations(); 
+	
+	// set the performance timers 
+
+	BioFVM::RUNTIME_TIC();
+	BioFVM::TIC();
+	
+	std::ofstream report_file;
+	if( PhysiCell_settings.enable_legacy_saves == true )
+	{	
+		sprintf( filename , "%s/simulation_report.txt" , PhysiCell_settings.folder.c_str() ); 
+		
+		report_file.open(filename); 	// create the data log file 
+		report_file<<"simulated time\tnum cells\tnum division\tnum death\twall time"<<std::endl;
+	}
+	
+	// main loop 
+	
+	try 
+	{		
+		while( PhysiCell_globals.current_time < PhysiCell_settings.max_time + 0.1*diffusion_dt )
+		{
+			// save data if it's time. 
+			if( PhysiCell_globals.current_time > PhysiCell_globals.next_full_save_time - 0.5 * diffusion_dt )
+			{
+				display_simulation_status( std::cout ); 
+				if( PhysiCell_settings.enable_legacy_saves == true )
+				{	
+					log_output( PhysiCell_globals.current_time , PhysiCell_globals.full_output_index, microenvironment, report_file);
+				}
+				
+				if( PhysiCell_settings.enable_full_saves == true )
+				{	
+					sprintf( filename , "%s/output%08u" , PhysiCell_settings.folder.c_str(),  PhysiCell_globals.full_output_index ); 
+					
+					save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+				}
+				
+				PhysiCell_globals.full_output_index++; 
+				PhysiCell_globals.next_full_save_time += PhysiCell_settings.full_save_interval;
+			}
+			
+			// save SVG plot if it's time
+			if( PhysiCell_globals.current_time > PhysiCell_globals.next_SVG_save_time - 0.5 * diffusion_dt )
+			{
+				if( PhysiCell_settings.enable_SVG_saves == true )
+				{	
+					sprintf( filename , "%s/snapshot%08u.svg" , PhysiCell_settings.folder.c_str() , PhysiCell_globals.SVG_output_index );
+					SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
+
+					PhysiCell_globals.SVG_output_index++; 
+					PhysiCell_globals.next_SVG_save_time  += PhysiCell_settings.SVG_save_interval;
+				}
+			}
+
+			// update the microenvironment
+			microenvironment.simulate_diffusion_decay( diffusion_dt );
+			
+			// run PhysiCell 
+			((Cell_Container *)microenvironment.agent_container)->update_all_cells( PhysiCell_globals.current_time );
+			
+			/*
+			  Custom add-ons could potentially go here. 
+			*/
+			
+			PhysiCell_globals.current_time += diffusion_dt;
+		}
+		
+		if( PhysiCell_settings.enable_legacy_saves == true )
+		{			
+			log_output(PhysiCell_globals.current_time, PhysiCell_globals.full_output_index, microenvironment, report_file);
+			report_file.close();
+		}
+	}
+	catch( const std::exception& e )
+	{ // reference to the base of a polymorphic object
+		std::cout << e.what(); // information from length_error printed
+	}
+	
+	// save a final simulation snapshot 
+	
+	sprintf( filename , "%s/final" , PhysiCell_settings.folder.c_str() ); 
+	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+	
+	sprintf( filename , "%s/final.svg" , PhysiCell_settings.folder.c_str() );
+	SVG_plot(filename, microenvironment, 0.0, PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
+
+	// timer 
+	
+	std::cout << std::endl << "Total simulation runtime: " << std::endl; 
+	BioFVM::display_stopwatch_value( std::cout , BioFVM::runtime_stopwatch_value() ); 
+
+	return 0; 
+}

From 69a23dbe7eaac4f41dc9548ad85072eff7921a03 Mon Sep 17 00:00:00 2001
From: Daniel Bergman <danielrbergman@gmail.com>
Date: Fri, 31 Jan 2025 16:33:08 -0500
Subject: [PATCH 3/4] revert back to 1.14.2 state (but different hash)

---
 Makefile                      |  323 +++++-
 config/PhysiCell_settings.xml | 1979 ++-------------------------------
 config/cell_rules.csv         |    0
 config/cells.csv              |    1 -
 custom_modules/custom.cpp     |  214 ----
 custom_modules/custom.h       |   92 --
 main.cpp                      |  254 -----
 7 files changed, 366 insertions(+), 2497 deletions(-)
 delete mode 100644 config/cell_rules.csv
 delete mode 100644 config/cells.csv
 delete mode 100644 custom_modules/custom.cpp
 delete mode 100644 custom_modules/custom.h
 delete mode 100644 main.cpp

diff --git a/Makefile b/Makefile
index 7aa7d18d2..5d256d1c3 100644
--- a/Makefile
+++ b/Makefile
@@ -11,24 +11,11 @@ ifdef PHYSICELL_CPP
 	CC := $(PHYSICELL_CPP)
 endif
 
-ifndef STATIC_OPENMP
-	STATIC_OPENMP = -fopenmp
-endif
-
 ARCH := native # best auto-tuning
 # ARCH := core2 # a reasonably safe default for most CPUs since 2007
 # ARCH := corei7
-# ARCH := corei7-avx # earlier i7 
 # ARCH := core-avx-i # i7 ivy bridge or newer 
 # ARCH := core-avx2 # i7 with Haswell or newer
-# ARCH := nehalem
-# ARCH := westmere
-# ARCH := sandybridge # circa 2011
-# ARCH := ivybridge   # circa 2012
-# ARCH := haswell     # circa 2013
-# ARCH := broadwell   # circa 2014
-# ARCH := skylake     # circa 2015
-# ARCH := bonnell
 # ARCH := silvermont
 # ARCH := skylake-avx512
 # ARCH := nocona #64-bit pentium 4 or later 
@@ -48,9 +35,7 @@ else
 	endif
 endif
 
-CFLAGS_LINK := $(shell echo $(CFLAGS) | sed -e "s/-fopenmp//g")
-COMPILE_COMMAND := $(CC) $(CFLAGS)  $(EXTRA_FLAGS)
-LINK_COMMAND := $(CC) $(CFLAGS_LINK) $(EXTRA_FLAGS)
+COMPILE_COMMAND := $(CC) $(CFLAGS) 
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -64,27 +49,284 @@ PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
 
 # put your custom objects here (they should be in the custom_modules directory)
 
-PhysiCell_custom_module_OBJECTS := custom.o
+PhysiCell_custom_module_OBJECTS := .o
 
 pugixml_OBJECTS := pugixml.o
 
 PhysiCell_OBJECTS := $(BioFVM_OBJECTS)  $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_OBJECTS)
 ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS)
 
-# compile the project 
-
-all: main.cpp $(ALL_OBJECTS)
-	$(COMPILE_COMMAND) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp 
-	make name
+EXAMPLES := ./examples/PhysiCell_test_mechanics_1.cpp ./examples/PhysiCell_test_mechanics_2.cpp \
+ ./examples/PhysiCell_test_DCIS.cpp ./examples/PhysiCell_test_HDS.cpp \
+ ./examples/PhysiCell_test_cell_cycle.cpp ./examples/PhysiCell_test_volume.cpp 
 
-static: main.cpp $(ALL_OBJECTS) $(MaBoSS)
-	$(LINK_COMMAND) $(INC) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp $(LIB) -static-libgcc -static-libstdc++ $(STATIC_OPENMP)
+all: 
+	make heterogeneity-sample
+	make 
 
 name:
 	@echo ""
 	@echo "Executable name is" $(PROGRAM_NAME)
 	@echo ""
 
+# sample projects 	
+list-projects:
+	@echo "Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample"
+	@echo "                 celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample"
+	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample custom-division-sample"
+	@echo "                 asymmetric-division-sample immune-function-sample episode-sample"
+	@echo ""
+	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
+	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
+	@echo ""
+	
+template:
+	cp -r ./sample_projects/template/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/template/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/template/Makefile .
+	cp -r ./sample_projects/template/config/* ./config 
+	
+# sample projects 
+
+# ---- non-intracellular projects 
+biorobots-sample:
+	cp ./sample_projects/biorobots/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/biorobots/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/biorobots/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/biorobots/config/* ./config/
+	
+cancer-biorobots-sample:
+	cp ./sample_projects/cancer_biorobots/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/cancer_biorobots/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/cancer_biorobots/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/cancer_biorobots/config/* ./config/
+	
+cancer-immune-sample:
+	cp ./sample_projects/cancer_immune/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/cancer_immune/main-cancer_immune_3D.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/cancer_immune/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/cancer_immune/config/* ./config/
+
+celltypes3-sample:
+	cp ./sample_projects/celltypes3/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/celltypes3/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/celltypes3/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/celltypes3/config/* ./config/	
+	
+heterogeneity-sample:
+	cp ./sample_projects/heterogeneity/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/heterogeneity/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/heterogeneity/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/heterogeneity/config/* ./config/
+	
+pred-prey-farmer:
+	cp ./sample_projects/pred_prey_farmer/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/pred_prey_farmer/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/pred_prey_farmer/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/pred_prey_farmer/config/* ./config/	
+	
+virus-macrophage-sample:
+	cp ./sample_projects/virus_macrophage/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/virus_macrophage/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/virus_macrophage/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/virus_macrophage/config/* ./config/
+	
+worm-sample:
+	cp ./sample_projects/worm/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/worm/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/worm/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/worm/config/* ./config/
+	
+interaction-sample:
+	cp ./sample_projects/interactions/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/interactions/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/interactions/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/interactions/config/* ./config/
+
+mechano-sample:
+	cp ./sample_projects/mechano/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/mechano/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/mechano/Makefile .
+	cp ./sample_projects/mechano/config/* ./config/
+
+rules-sample:
+	cp ./sample_projects/rules_sample/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/rules_sample/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/rules_sample/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/rules_sample/config/* ./config/
+
+physimess-sample:
+	cp ./sample_projects/physimess/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/physimess/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/physimess/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/physimess/config/* ./config/
+
+custom-division-sample:
+	cp -r ./sample_projects/custom_division/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/custom_division/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/custom_division/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/custom_division/config/* ./config/
+
+asymmetric-division-sample:
+	cp -r ./sample_projects/asymmetric_division/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/asymmetric_division/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/asymmetric_division/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/asymmetric_division/config/* ./config/
+
+immune-function-sample:
+	cp -r ./sample_projects/immune_function/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/immune_function/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/immune_function/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/immune_function/config/* ./config/
+
+episode-sample:
+	cp -r ./sample_projects/episode/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/episode/main.cpp ./main.cpp
+	cp Makefile Makefile-backup
+	cp ./sample_projects/episode/Makefile .
+	cp -r ./sample_projects/episode/config/* ./config
+
+# ---- intracellular projects 
+ode-energy-sample:
+	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects_intracellular/ode/ode_energy/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects_intracellular/ode/ode_energy/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects_intracellular/ode/ode_energy/config/* ./config/	
+
+physiboss-cell-lines-sample:
+	cp ./sample_projects_intracellular/boolean/physiboss_cell_lines/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects_intracellular/boolean/physiboss_cell_lines/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects_intracellular/boolean/physiboss_cell_lines/config/* ./config/
+
+physiboss-tutorial:
+	cp ./sample_projects_intracellular/boolean/tutorial/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects_intracellular/boolean/tutorial/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects_intracellular/boolean/tutorial/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects_intracellular/boolean/tutorial/config/* ./config/
+
+physiboss-tutorial-invasion:
+	cp ./sample_projects_intracellular/boolean/cancer_invasion/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects_intracellular/boolean/cancer_invasion/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects_intracellular/boolean/cancer_invasion/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects_intracellular/boolean/cancer_invasion/config/* ./config/
+
+ecoli-acetic-switch-sample:
+	cp ./sample_projects_intracellular/fba/ecoli_acetic_switch/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects_intracellular/fba/ecoli_acetic_switch/main_ecoli_acetic_switch.cpp ./main.cpp
+	cp Makefile Makefile-backup
+	cp ./sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile ./
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
+	cp ./sample_projects_intracellular/fba/ecoli_acetic_switch/config/* ./config/
+
+cancer-metabolism-sample:
+	cp ./sample_projects_intracellular/fba/cancer_metabolism/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects_intracellular/fba/cancer_metabolism/main.cpp ./main.cpp
+	cp Makefile Makefile-backup
+	cp ./sample_projects_intracellular/fba/cancer_metabolism/Makefile ./
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
+	cp ./sample_projects_intracellular/fba/cancer_metabolism/config/* ./config/
+
+template_BM:
+	cp ./sample_projects_intracellular/boolean/template_BM/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects_intracellular/boolean/template_BM/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects_intracellular/boolean/template_BM/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects_intracellular/boolean/template_BM/config/* ./config/
+	mkdir ./scripts/
+	cp ./sample_projects_intracellular/boolean/template_BM/scripts/* ./scripts/
+
+# early examples for convergence testing 
+
+physicell_test_mech1: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp 
+	$(COMPILE_COMMAND) -o test_mech1 $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp
+
+physicell_test_mech2: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_2.cpp 
+	$(COMPILE_COMMAND) -o test_mech2 $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_2.cpp
+	
+physicell_test_DCIS: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_DCIS.cpp 
+	$(COMPILE_COMMAND) -o test_DCIS $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_DCIS.cpp
+
+physicell_test_HDS: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_HDS.cpp 
+	$(COMPILE_COMMAND) -o test_HDS $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_HDS.cpp
+
+physicell_test_cell_cycle: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_cell_cycle.cpp 
+	$(COMPILE_COMMAND) -o test_cycle $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_cell_cycle.cpp
+
+PhysiCell_test_volume: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_volume.cpp 
+	$(COMPILE_COMMAND) -o test_volume $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_volume.cpp
+	
+examples: $(PhysiCell_OBJECTS) 
+	$(COMPILE_COMMAND) -o ./examples/test_mech1 ./examples/PhysiCell_test_mechanics_1.cpp $(PhysiCell_OBJECTS)
+	$(COMPILE_COMMAND) -o ./examples/test_mech2 ./examples/PhysiCell_test_mechanics_2.cpp $(PhysiCell_OBJECTS)
+	$(COMPILE_COMMAND) -o ./examples/test_DCIS ./examples/PhysiCell_test_DCIS.cpp $(PhysiCell_OBJECTS)
+	$(COMPILE_COMMAND) -o ./examples/test_HDS ./examples/PhysiCell_test_HDS.cpp $(PhysiCell_OBJECTS)
+	$(COMPILE_COMMAND) -o ./examples/test_cycle ./examples/PhysiCell_test_cell_cycle.cpp $(PhysiCell_OBJECTS)
+	$(COMPILE_COMMAND) -o ./examples/test_volume ./examples/PhysiCell_test_volume.cpp $(PhysiCell_OBJECTS)
+
 # PhysiCell core components	
 
 PhysiCell_phenotype.o: ./core/PhysiCell_phenotype.cpp
@@ -113,7 +355,7 @@ PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
 	
 PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
-	
+
 PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.cpp 
 
@@ -162,37 +404,34 @@ PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp
 
 PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
 	$(COMPILE_COMMAND) -c ./modules/PhysiCell_various_outputs.cpp
-
+	
 PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
 	$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
 	
 PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
-	$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp	
 	
 PhysiCell_basic_signaling.o: ./core/PhysiCell_basic_signaling.cpp
-	$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp 	
-	
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp 
+
 PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
 	$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp 
-	
-# user-defined PhysiCell modules
 
-custom.o: ./custom_modules/custom.cpp 
-	$(COMPILE_COMMAND) -c ./custom_modules/custom.cpp
+# user-defined PhysiCell modules
 
 # cleanup
 
 reset:
-	rm -f *.cpp 
+	rm -f *.cpp PhysiCell_cell.o
 	cp ./sample_projects/Makefile-default Makefile 
-	rm -f ./custom_modules/*
+	rm -rf ./custom_modules/*
 	touch ./custom_modules/empty.txt 
 	touch ALL_CITATIONS.txt 
 	touch ./core/PhysiCell_cell.cpp
 	rm ALL_CITATIONS.txt 
 	cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml 
 	touch ./config/empty.csv
-	rm -f ./config/*.csv
+	rm ./config/*.csv	
 	
 clean:
 	rm -f *.o
@@ -202,9 +441,9 @@ data-cleanup:
 	rm -rf ./output
 	mkdir ./output
 	touch ./output/empty.txt
-	
+
 # archival 
-	
+
 checkpoint: 
 	zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* 
 	
@@ -289,15 +528,15 @@ save:
 	cp main.cpp ./user_projects/$(PROJ)
 	cp Makefile ./user_projects/$(PROJ)
 	cp VERSION.txt ./user_projects/$(PROJ)
-	cp ./config/* ./user_projects/$(PROJ)/config
-	cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
+	cp -r ./config/* ./user_projects/$(PROJ)/config
+	cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
 
 load: 
 	echo "Loading project from $(PROJ) ... "
 	cp ./user_projects/$(PROJ)/main.cpp .
 	cp ./user_projects/$(PROJ)/Makefile .
-	cp ./user_projects/$(PROJ)/config/* ./config/ 
-	cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
+	cp -r ./user_projects/$(PROJ)/config/* ./config/ 
+	cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
 
 pack:
 	@echo " "
diff --git a/config/PhysiCell_settings.xml b/config/PhysiCell_settings.xml
index 72970bf80..e3cd03b4a 100644
--- a/config/PhysiCell_settings.xml
+++ b/config/PhysiCell_settings.xml
@@ -14,7 +14,7 @@
     </domain>
 
     <overall>
-        <max_time units="min">2880</max_time>
+        <max_time units="min">14400</max_time>
         <time_units>min</time_units>
         <space_units>micron</space_units>
         <dt_diffusion units="min">0.01</dt_diffusion>
@@ -35,12 +35,6 @@
         <SVG>
             <interval units="min">60</interval>
             <enable>true</enable>
-            <plot_substrate enabled="false" limits="true">
-                <substrate>debris</substrate>
-                <colormap>YlOrRd</colormap>
-                <min_conc>0</min_conc>
-                <max_conc>1</max_conc>
-            </plot_substrate>
         </SVG>
         <legacy_data>
             <enable>false</enable>
@@ -50,15 +44,29 @@
     <options>
         <legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
-        <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
-        <random_seed>0</random_seed>
     </options>
 
     <microenvironment_setup>
-        <variable name="debris" units="dimensionless" ID="0">
+        <variable name="oxygen" units="dimensionless" ID="0">
             <physical_parameter_set>
                 <diffusion_coefficient units="micron^2/min">100000.0</diffusion_coefficient>
-                <decay_rate units="1/min">10</decay_rate>
+                <decay_rate units="1/min">0.1</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="mmHg">38</initial_condition>
+            <Dirichlet_boundary_condition units="mmHg" enabled="True">0</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="True">38</boundary_value>
+                <boundary_value ID="xmax" enabled="True">10</boundary_value>
+                <boundary_value ID="ymin" enabled="True">10</boundary_value>
+                <boundary_value ID="ymax" enabled="True">38</boundary_value>
+                <boundary_value ID="zmin" enabled="False">0</boundary_value>
+                <boundary_value ID="zmax" enabled="False">0</boundary_value>
+            </Dirichlet_options>
+        </variable>
+        <variable name="necrotic debris" units="dimensionless" ID="1">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">10</diffusion_coefficient>
+                <decay_rate units="1/min">.1</decay_rate>
             </physical_parameter_set>
             <initial_condition units="mmHg">0</initial_condition>
             <Dirichlet_boundary_condition units="mmHg" enabled="False">0</Dirichlet_boundary_condition>
@@ -71,132 +79,20 @@
                 <boundary_value ID="zmax" enabled="False">0</boundary_value>
             </Dirichlet_options>
         </variable>
-        <variable name="cxc3cl1" units="dimensionless" ID="1">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.0</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="dimensionless">0.0</initial_condition>
-            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False" />
-                <boundary_value ID="xmax" enabled="False" />
-                <boundary_value ID="ymin" enabled="False" />
-                <boundary_value ID="ymax" enabled="False" />
-                <boundary_value ID="zmin" enabled="False" />
-                <boundary_value ID="zmax" enabled="False" />
-            </Dirichlet_options>
-        </variable>
-        <variable name="egf" units="dimensionless" ID="2">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.0</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="dimensionless">0.0</initial_condition>
-            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False" />
-                <boundary_value ID="xmax" enabled="False" />
-                <boundary_value ID="ymin" enabled="False" />
-                <boundary_value ID="ymax" enabled="False" />
-                <boundary_value ID="zmin" enabled="False" />
-                <boundary_value ID="zmax" enabled="False" />
-            </Dirichlet_options>
-        </variable>
-        <variable name="ifng" units="dimensionless" ID="3">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.0</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="dimensionless">0.0</initial_condition>
-            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False" />
-                <boundary_value ID="xmax" enabled="False" />
-                <boundary_value ID="ymin" enabled="False" />
-                <boundary_value ID="ymax" enabled="False" />
-                <boundary_value ID="zmin" enabled="False" />
-                <boundary_value ID="zmax" enabled="False" />
-            </Dirichlet_options>
-        </variable>
-        <variable name="il2" units="dimensionless" ID="4">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.0</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="dimensionless">0.0</initial_condition>
-            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False" />
-                <boundary_value ID="xmax" enabled="False" />
-                <boundary_value ID="ymin" enabled="False" />
-                <boundary_value ID="ymax" enabled="False" />
-                <boundary_value ID="zmin" enabled="False" />
-                <boundary_value ID="zmax" enabled="False" />
-            </Dirichlet_options>
-        </variable>
-        <variable name="il4" units="dimensionless" ID="5">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.0</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="dimensionless">0.0</initial_condition>
-            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False" />
-                <boundary_value ID="xmax" enabled="False" />
-                <boundary_value ID="ymin" enabled="False" />
-                <boundary_value ID="ymax" enabled="False" />
-                <boundary_value ID="zmin" enabled="False" />
-                <boundary_value ID="zmax" enabled="False" />
-            </Dirichlet_options>
-        </variable>
-        <variable name="il6" units="dimensionless" ID="6">
+        <variable name="apoptotic debris" units="dimensionless" ID="2">
             <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.0</decay_rate>
+                <diffusion_coefficient units="micron^2/min">10</diffusion_coefficient>
+                <decay_rate units="1/min">0.1</decay_rate>
             </physical_parameter_set>
-            <initial_condition units="dimensionless">0.0</initial_condition>
-            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False" />
-                <boundary_value ID="xmax" enabled="False" />
-                <boundary_value ID="ymin" enabled="False" />
-                <boundary_value ID="ymax" enabled="False" />
-                <boundary_value ID="zmin" enabled="False" />
-                <boundary_value ID="zmax" enabled="False" />
-            </Dirichlet_options>
-        </variable>
-        <variable name="il10" units="dimensionless" ID="7">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.0</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="dimensionless">0.0</initial_condition>
-            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False" />
-                <boundary_value ID="xmax" enabled="False" />
-                <boundary_value ID="ymin" enabled="False" />
-                <boundary_value ID="ymax" enabled="False" />
-                <boundary_value ID="zmin" enabled="False" />
-                <boundary_value ID="zmax" enabled="False" />
-            </Dirichlet_options>
-        </variable>
-        <variable name="il12" units="dimensionless" ID="8">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">0.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.0</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="dimensionless">0.0</initial_condition>
-            <Dirichlet_boundary_condition units="dimensionless" enabled="False">0.0</Dirichlet_boundary_condition>
+            <initial_condition units="mmHg">0</initial_condition>
+            <Dirichlet_boundary_condition units="mmHg" enabled="False">0</Dirichlet_boundary_condition>
             <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="False" />
-                <boundary_value ID="xmax" enabled="False" />
-                <boundary_value ID="ymin" enabled="False" />
-                <boundary_value ID="ymax" enabled="False" />
-                <boundary_value ID="zmin" enabled="False" />
-                <boundary_value ID="zmax" enabled="False" />
+                <boundary_value ID="xmin" enabled="False">0</boundary_value>
+                <boundary_value ID="xmax" enabled="False">0</boundary_value>
+                <boundary_value ID="ymin" enabled="False">0</boundary_value>
+                <boundary_value ID="ymax" enabled="False">0</boundary_value>
+                <boundary_value ID="zmin" enabled="False">0</boundary_value>
+                <boundary_value ID="zmax" enabled="False">0</boundary_value>
             </Dirichlet_options>
         </variable>
         <options>
@@ -212,271 +108,19 @@
     </microenvironment_setup>
 
     <cell_definitions>
-        <cell_definition name="neoplastic epithelial" ID="0">
-            <phenotype>
-                <cycle code="2" name="flow cytometry">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">245.32200</duration>
-                        <duration index="1" fixed_duration="false">555.78600</duration>
-                        <duration index="2" fixed_duration="false">584.89200</duration>
-                    </phase_durations>
-                    <standard_asymmetric_division enabled="False">
-                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">1.0</asymmetric_division_probability>
-                    </standard_asymmetric_division>
-                </cycle>
-                <death>
-                    <model code="100" name="apoptosis">
-                        <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">0</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                    <model code="101" name="necrosis">
-                        <death_rate units="1/min">0.0</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
-                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">7e-05</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                </death>
-                <volume>
-                    <total units="micron^3">2494</total>
-                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
-                    <nuclear units="micron^3">540</nuclear>
-                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
-                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
-                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
-                    <calcification_rate units="1/min">0.0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
-                </volume>
-                <mechanics>
-                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
-                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
-                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
-                    <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
-                    </cell_adhesion_affinities>
-                    <options>
-                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
-                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
-                    </options>
-                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
-                    <attachment_rate units="1/min">0.0</attachment_rate>
-                    <detachment_rate units="1/min">0.0</detachment_rate>
-                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
-                </mechanics>
-                <motility>
-                    <speed units="micron/min">1.0</speed>
-                    <persistence_time units="min">1.0</persistence_time>
-                    <migration_bias units="dimensionless">0.0</migration_bias>
-                    <options>
-                        <enabled>false</enabled>
-                        <use_2D>true</use_2D>
-                        <chemotaxis>
-                            <enabled>false</enabled>
-                            <substrate>debris</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>false</enabled>
-                            <normalize_each_gradient>false</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="debris">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="cxc3cl1">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="egf">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="ifng">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il2">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il4">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il6">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il10">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il12">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                </secretion>
-                <cell_interactions>
-                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
-                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
-                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
-                    <live_phagocytosis_rates>
-                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
-                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
-                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
-                    </attack_rates>
-                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
-                    <attack_duration units="min">0.1</attack_duration>
-                    <fusion_rates>
-                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
-                    </transformation_rates>
-                </cell_transformations>
-                <cell_integrity>
-                    <damage_rate units="1/min">0.0</damage_rate>
-                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
-                </cell_integrity>
-            </phenotype>
-            <custom_data>
-                <sample conserved="false" units="dimensionless" description="">1.0</sample>
-            </custom_data>
-            <initial_parameter_distributions enabled="false">
-                <distribution enabled="false" type="Log10Normal" check_base="true">
-                    <behavior>Volume</behavior>
-                    <mu>4</mu>
-                    <sigma>2</sigma>
-                    <upper_bound>100000</upper_bound>
-                </distribution>
-                <distribution enabled="false" type="LogUniform" check_base="true">
-                    <behavior>apoptosis</behavior>
-                    <min>1e-6</min>
-                    <max>1e-2</max>
-                </distribution>
-            </initial_parameter_distributions>
-        </cell_definition>
-        <cell_definition name="monocyte" ID="1">
+        <cell_definition name="malignant epithelial" ID="0">
             <phenotype>
-                <cycle code="2" name="flow cytometry">
+                <cycle code="5" name="live">
                     <phase_transition_rates units="1/min">
-                        <rate start_index="0" end_index="1" fixed_duration="false">0</rate>
-                        <rate start_index="1" end_index="2" fixed_duration="false">0.00208</rate>
-                        <rate start_index="2" end_index="0" fixed_duration="false">0.00333</rate>
+                        <rate start_index="0" end_index="0" fixed_duration="false">0.000</rate>
                     </phase_transition_rates>
-                    <standard_asymmetric_division enabled="False">
-                        <asymmetric_division_probability name="monocyte" units="dimensionless">1.0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
-                    </standard_asymmetric_division>
                 </cycle>
                 <death>
                     <model code="100" name="apoptosis">
                         <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
-                        </phase_transition_rates>
+                        <phase_durations units="min">
+                            <duration index="0" fixed_duration="true">516</duration>
+                        </phase_durations>
                         <parameters>
                             <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
                             <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
@@ -487,17 +131,17 @@
                         </parameters>
                     </model>
                     <model code="101" name="necrosis">
-                        <death_rate units="1/min">0.0</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
-                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
-                        </phase_transition_rates>
+                        <death_rate units="1/min">2.80E-03</death_rate>
+                        <phase_durations units="min">
+                            <duration index="0" fixed_duration="true">0</duration>
+                            <duration index="1" fixed_duration="true">86400</duration>
+                        </phase_durations>
                         <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
+                            <unlysed_fluid_change_rate units="1/min">1.11667e-2</unlysed_fluid_change_rate>
                             <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">7e-05</calcification_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-3</nuclear_biomass_change_rate>
+                            <calcification_rate units="1/min">0</calcification_rate>
                             <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
                         </parameters>
                     </model>
@@ -509,1556 +153,101 @@
                     <fluid_change_rate units="1/min">0.05</fluid_change_rate>
                     <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
                     <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
-                    <calcification_rate units="1/min">0.0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
+                    <calcified_fraction units="dimensionless">0</calcified_fraction>
+                    <calcification_rate units="1/min">0</calcification_rate>
+                    <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
                 </volume>
                 <mechanics>
                     <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
                     <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
                     <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
                     <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="malignant epithelial">1</cell_adhesion_affinity>
                     </cell_adhesion_affinities>
                     <options>
                         <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
                         <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
                     </options>
+                    <cell_BM_adhesion_strength units="micron/min">4.0</cell_BM_adhesion_strength>
+                    <cell_BM_repulsion_strength units="micron/min">10.0</cell_BM_repulsion_strength>
                     <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                     <attachment_rate units="1/min">0.0</attachment_rate>
                     <detachment_rate units="1/min">0.0</detachment_rate>
-                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
                 </mechanics>
                 <motility>
-                    <speed units="micron/min">1.0</speed>
-                    <persistence_time units="min">1.0</persistence_time>
-                    <migration_bias units="dimensionless">0.0</migration_bias>
+                    <speed units="micron/min">1</speed>
+                    <persistence_time units="min">1</persistence_time>
+                    <migration_bias units="dimensionless">.5</migration_bias>
                     <options>
-                        <enabled>true</enabled>
+                        <enabled>false</enabled>
                         <use_2D>true</use_2D>
                         <chemotaxis>
                             <enabled>false</enabled>
-                            <substrate>debris</substrate>
+                            <substrate>oxygen</substrate>
                             <direction>1</direction>
                         </chemotaxis>
                         <advanced_chemotaxis>
                             <enabled>false</enabled>
                             <normalize_each_gradient>false</normalize_each_gradient>
                             <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="necrotic debris">0.0</chemotactic_sensitivity>
+                                <chemotactic_sensitivity substrate="apoptotic debris">0.0</chemotactic_sensitivity>
                             </chemotactic_sensitivities>
                         </advanced_chemotaxis>
                     </options>
                 </motility>
                 <secretion>
-                    <substrate name="debris">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="cxc3cl1">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="egf">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="ifng">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il2">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il4">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il6">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
+                    <substrate name="oxygen">
+                        <secretion_rate units="1/min">0</secretion_rate>
+                        <secretion_target units="substrate density">1</secretion_target>
+                        <uptake_rate units="1/min">10</uptake_rate>
+                        <net_export_rate units="total substrate/min">0</net_export_rate>
                     </substrate>
-                    <substrate name="il10">
+                    <substrate name="necrotic debris">
                         <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <secretion_target units="substrate density">1</secretion_target>
                         <uptake_rate units="1/min">0.0</uptake_rate>
                         <net_export_rate units="total substrate/min">0.0</net_export_rate>
                     </substrate>
-                    <substrate name="il12">
+                    <substrate name="apoptotic debris">
                         <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
+                        <secretion_target units="substrate density">1</secretion_target>
                         <uptake_rate units="1/min">0.0</uptake_rate>
                         <net_export_rate units="total substrate/min">0.0</net_export_rate>
                     </substrate>
                 </secretion>
                 <cell_interactions>
-                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
-                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
-                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
+                    <dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
                     <live_phagocytosis_rates>
-                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
+                        <phagocytosis_rate name="malignant epithelial" units="1/min">0</phagocytosis_rate>
+                        <phagocytosis_rate name="default" units="1/min">0</phagocytosis_rate>
                     </live_phagocytosis_rates>
                     <attack_rates>
-                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
-                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
-                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
+                        <attack_rate name="malignant epithelial" units="1/min">0</attack_rate>
+                        <attack_rate name="default" units="1/min">0</attack_rate>
                     </attack_rates>
-                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
-                    <attack_duration units="min">0.1</attack_duration>
+                    <damage_rate units="1/min">1</damage_rate>
                     <fusion_rates>
-                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="malignant epithelial" units="1/min">0</fusion_rate>
+                        <fusion_rate name="default" units="1/min">0</fusion_rate>
                     </fusion_rates>
                 </cell_interactions>
                 <cell_transformations>
                     <transformation_rates>
-                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="malignant epithelial" units="1/min">0</transformation_rate>
+                        <transformation_rate name="default" units="1/min">0</transformation_rate>
                     </transformation_rates>
                 </cell_transformations>
-                <cell_integrity>
-                    <damage_rate units="1/min">0.0</damage_rate>
-                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
-                </cell_integrity>
             </phenotype>
             <custom_data>
-                <sample conserved="false" units="dimensionless" description="">0.0</sample>
+                <sample conserved="false" units="dimensionless" description="">1.0</sample>
             </custom_data>
-            <initial_parameter_distributions enabled="false">
-          </initial_parameter_distributions>
-        </cell_definition>
-        <cell_definition name="mac_cadm1" ID="2">
-            <phenotype>
-                <cycle code="2" name="flow cytometry">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">308.64198</duration>
-                        <duration index="1" fixed_duration="false">480.76923</duration>
-                        <duration index="2" fixed_duration="false">300.30030</duration>
-                    </phase_durations>
-                    <standard_asymmetric_division enabled="False">
-                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">1.0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
-                    </standard_asymmetric_division>
-                </cycle>
-                <death>
-                    <model code="100" name="apoptosis">
-                        <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">0</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                    <model code="101" name="necrosis">
-                        <death_rate units="1/min">0.0</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
-                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">7e-05</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                </death>
-                <volume>
-                    <total units="micron^3">2494</total>
-                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
-                    <nuclear units="micron^3">540</nuclear>
-                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
-                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
-                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
-                    <calcification_rate units="1/min">0.0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
-                </volume>
-                <mechanics>
-                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
-                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
-                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
-                    <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
-                    </cell_adhesion_affinities>
-                    <options>
-                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
-                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
-                    </options>
-                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
-                    <attachment_rate units="1/min">0.0</attachment_rate>
-                    <detachment_rate units="1/min">0.0</detachment_rate>
-                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
-                </mechanics>
-                <motility>
-                    <speed units="micron/min">1.0</speed>
-                    <persistence_time units="min">1.0</persistence_time>
-                    <migration_bias units="dimensionless">0.0</migration_bias>
-                    <options>
-                        <enabled>true</enabled>
-                        <use_2D>true</use_2D>
-                        <chemotaxis>
-                            <enabled>false</enabled>
-                            <substrate>debris</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>true</enabled>
-                            <normalize_each_gradient>true</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="debris">1.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="cxc3cl1">1.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="debris">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="cxc3cl1">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="egf">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="ifng">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il2">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il4">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il6">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il10">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il12">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                </secretion>
-                <cell_interactions>
-                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
-                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
-                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
-                    <live_phagocytosis_rates>
-                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
-                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
-                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
-                    </attack_rates>
-                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
-                    <attack_duration units="min">0.1</attack_duration>
-                    <fusion_rates>
-                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
-                    </transformation_rates>
-                </cell_transformations>
-                <cell_integrity>
-                    <damage_rate units="1/min">0.0</damage_rate>
-                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
-                </cell_integrity>
-            </phenotype>
-            <custom_data>
-                <sample conserved="false" units="dimensionless" description="">0.0</sample>
-            </custom_data>
-            <initial_parameter_distributions enabled="false">
-          </initial_parameter_distributions>
-        </cell_definition>
-        <cell_definition name="mac_folr2" ID="3">
-            <phenotype>
-                <cycle code="2" name="flow cytometry">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">308.64198</duration>
-                        <duration index="1" fixed_duration="false">480.76923</duration>
-                        <duration index="2" fixed_duration="false">300.30030</duration>
-                    </phase_durations>
-                    <standard_asymmetric_division enabled="False">
-                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">1.0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
-                    </standard_asymmetric_division>
-                </cycle>
-                <death>
-                    <model code="100" name="apoptosis">
-                        <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">0</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                    <model code="101" name="necrosis">
-                        <death_rate units="1/min">0.0</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
-                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">7e-05</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                </death>
-                <volume>
-                    <total units="micron^3">2494</total>
-                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
-                    <nuclear units="micron^3">540</nuclear>
-                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
-                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
-                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
-                    <calcification_rate units="1/min">0.0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
-                </volume>
-                <mechanics>
-                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
-                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
-                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
-                    <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
-                    </cell_adhesion_affinities>
-                    <options>
-                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
-                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
-                    </options>
-                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
-                    <attachment_rate units="1/min">0.0</attachment_rate>
-                    <detachment_rate units="1/min">0.0</detachment_rate>
-                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
-                </mechanics>
-                <motility>
-                    <speed units="micron/min">1.0</speed>
-                    <persistence_time units="min">1.0</persistence_time>
-                    <migration_bias units="dimensionless">0.5</migration_bias>
-                    <options>
-                        <enabled>true</enabled>
-                        <use_2D>true</use_2D>
-                        <chemotaxis>
-                            <enabled>false</enabled>
-                            <substrate>debris</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>true</enabled>
-                            <normalize_each_gradient>false</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="debris">1.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="debris">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="cxc3cl1">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="egf">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="ifng">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il2">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il4">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il6">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il10">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il12">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                </secretion>
-                <cell_interactions>
-                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
-                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
-                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
-                    <live_phagocytosis_rates>
-                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
-                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
-                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
-                    </attack_rates>
-                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
-                    <attack_duration units="min">0.1</attack_duration>
-                    <fusion_rates>
-                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
-                    </transformation_rates>
-                </cell_transformations>
-                <cell_integrity>
-                    <damage_rate units="1/min">0.0</damage_rate>
-                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
-                </cell_integrity>
-            </phenotype>
-            <custom_data>
-                <sample conserved="false" units="dimensionless" description="">0.0</sample>
-            </custom_data>
-            <initial_parameter_distributions enabled="false">
-          </initial_parameter_distributions>
-        </cell_definition>
-        <cell_definition name="mac_other" ID="4">
-            <phenotype>
-                <cycle code="2" name="flow cytometry">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">308.64198</duration>
-                        <duration index="1" fixed_duration="false">480.76923</duration>
-                        <duration index="2" fixed_duration="false">300.30030</duration>
-                    </phase_durations>
-                    <standard_asymmetric_division enabled="False">
-                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_other" units="dimensionless">1.0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
-                    </standard_asymmetric_division>
-                </cycle>
-                <death>
-                    <model code="100" name="apoptosis">
-                        <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">0</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                    <model code="101" name="necrosis">
-                        <death_rate units="1/min">0.0</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
-                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">7e-05</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                </death>
-                <volume>
-                    <total units="micron^3">2494</total>
-                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
-                    <nuclear units="micron^3">540</nuclear>
-                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
-                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
-                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
-                    <calcification_rate units="1/min">0.0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
-                </volume>
-                <mechanics>
-                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
-                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
-                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
-                    <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
-                    </cell_adhesion_affinities>
-                    <options>
-                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
-                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
-                    </options>
-                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
-                    <attachment_rate units="1/min">0.0</attachment_rate>
-                    <detachment_rate units="1/min">0.0</detachment_rate>
-                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
-                </mechanics>
-                <motility>
-                    <speed units="micron/min">1.0</speed>
-                    <persistence_time units="min">1.0</persistence_time>
-                    <migration_bias units="dimensionless">0.7</migration_bias>
-                    <options>
-                        <enabled>true</enabled>
-                        <use_2D>true</use_2D>
-                        <chemotaxis>
-                            <enabled>false</enabled>
-                            <substrate>debris</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>true</enabled>
-                            <normalize_each_gradient>false</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="debris">1.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="debris">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="cxc3cl1">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="egf">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="ifng">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il2">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il4">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il6">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il10">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il12">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                </secretion>
-                <cell_interactions>
-                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
-                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
-                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
-                    <live_phagocytosis_rates>
-                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
-                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
-                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
-                    </attack_rates>
-                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
-                    <attack_duration units="min">0.1</attack_duration>
-                    <fusion_rates>
-                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
-                    </transformation_rates>
-                </cell_transformations>
-                <cell_integrity>
-                    <damage_rate units="1/min">0.0</damage_rate>
-                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
-                </cell_integrity>
-            </phenotype>
-            <custom_data>
-                <sample conserved="false" units="dimensionless" description="">0.0</sample>
-            </custom_data>
-            <initial_parameter_distributions enabled="false">
-          </initial_parameter_distributions>
-        </cell_definition>
-        <cell_definition name="dendritic" ID="5">
-            <phenotype>
-                <cycle code="2" name="flow cytometry">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">308.64198</duration>
-                        <duration index="1" fixed_duration="false">480.76923</duration>
-                        <duration index="2" fixed_duration="false">300.30030</duration>
-                    </phase_durations>
-                    <standard_asymmetric_division enabled="False">
-                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="dendritic" units="dimensionless">1.0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
-                    </standard_asymmetric_division>
-                </cycle>
-                <death>
-                    <model code="100" name="apoptosis">
-                        <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">0</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                    <model code="101" name="necrosis">
-                        <death_rate units="1/min">0.0</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
-                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">7e-05</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                </death>
-                <volume>
-                    <total units="micron^3">2494</total>
-                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
-                    <nuclear units="micron^3">540</nuclear>
-                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
-                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
-                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
-                    <calcification_rate units="1/min">0.0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
-                </volume>
-                <mechanics>
-                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
-                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
-                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
-                    <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
-                    </cell_adhesion_affinities>
-                    <options>
-                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
-                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
-                    </options>
-                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
-                    <attachment_rate units="1/min">0.0</attachment_rate>
-                    <detachment_rate units="1/min">0.0</detachment_rate>
-                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
-                </mechanics>
-                <motility>
-                    <speed units="micron/min">1.0</speed>
-                    <persistence_time units="min">1.0</persistence_time>
-                    <migration_bias units="dimensionless">0.0</migration_bias>
-                    <options>
-                        <enabled>false</enabled>
-                        <use_2D>true</use_2D>
-                        <chemotaxis>
-                            <enabled>false</enabled>
-                            <substrate>debris</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>false</enabled>
-                            <normalize_each_gradient>false</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="debris">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="cxc3cl1">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="egf">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="ifng">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il2">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il4">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il6">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il10">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il12">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                </secretion>
-                <cell_interactions>
-                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
-                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
-                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
-                    <live_phagocytosis_rates>
-                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
-                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
-                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
-                    </attack_rates>
-                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
-                    <attack_duration units="min">0.1</attack_duration>
-                    <fusion_rates>
-                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
-                    </transformation_rates>
-                </cell_transformations>
-                <cell_integrity>
-                    <damage_rate units="1/min">0.0</damage_rate>
-                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
-                </cell_integrity>
-            </phenotype>
-            <custom_data>
-                <sample conserved="false" units="dimensionless" description="">0.0</sample>
-            </custom_data>
-            <initial_parameter_distributions enabled="false">
-          </initial_parameter_distributions>
-        </cell_definition>
-        <cell_definition name="t_cd4" ID="6">
-            <phenotype>
-                <cycle code="2" name="flow cytometry">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">308.64198</duration>
-                        <duration index="1" fixed_duration="false">480.76923</duration>
-                        <duration index="2" fixed_duration="false">300.30030</duration>
-                    </phase_durations>
-                    <standard_asymmetric_division enabled="False">
-                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd4" units="dimensionless">1.0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd8" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
-                    </standard_asymmetric_division>
-                </cycle>
-                <death>
-                    <model code="100" name="apoptosis">
-                        <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">0</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                    <model code="101" name="necrosis">
-                        <death_rate units="1/min">0.0</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
-                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">7e-05</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                </death>
-                <volume>
-                    <total units="micron^3">2494</total>
-                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
-                    <nuclear units="micron^3">540</nuclear>
-                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
-                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
-                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
-                    <calcification_rate units="1/min">0.0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
-                </volume>
-                <mechanics>
-                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
-                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
-                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
-                    <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
-                    </cell_adhesion_affinities>
-                    <options>
-                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
-                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
-                    </options>
-                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
-                    <attachment_rate units="1/min">0.0</attachment_rate>
-                    <detachment_rate units="1/min">0.0</detachment_rate>
-                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
-                </mechanics>
-                <motility>
-                    <speed units="micron/min">1.0</speed>
-                    <persistence_time units="min">1.0</persistence_time>
-                    <migration_bias units="dimensionless">0.0</migration_bias>
-                    <options>
-                        <enabled>true</enabled>
-                        <use_2D>true</use_2D>
-                        <chemotaxis>
-                            <enabled>false</enabled>
-                            <substrate>debris</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>false</enabled>
-                            <normalize_each_gradient>false</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="debris">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="cxc3cl1">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="egf">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="ifng">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il2">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il4">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il6">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il10">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il12">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                </secretion>
-                <cell_interactions>
-                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
-                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
-                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
-                    <live_phagocytosis_rates>
-                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
-                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
-                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
-                    </attack_rates>
-                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
-                    <attack_duration units="min">0.1</attack_duration>
-                    <fusion_rates>
-                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
-                    </transformation_rates>
-                </cell_transformations>
-                <cell_integrity>
-                    <damage_rate units="1/min">0.0</damage_rate>
-                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
-                </cell_integrity>
-            </phenotype>
-            <custom_data>
-                <sample conserved="false" units="dimensionless" description="">0.0</sample>
-            </custom_data>
-            <initial_parameter_distributions enabled="false">
-          </initial_parameter_distributions>
-        </cell_definition>
-        <cell_definition name="t_cd8" ID="7">
-            <phenotype>
-                <cycle code="2" name="flow cytometry">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">308.64198</duration>
-                        <duration index="1" fixed_duration="false">480.76923</duration>
-                        <duration index="2" fixed_duration="false">300.30030</duration>
-                    </phase_durations>
-                    <standard_asymmetric_division enabled="False">
-                        <asymmetric_division_probability name="monocyte" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_cadm1" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_folr2" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="mac_other" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="dendritic" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd4" units="dimensionless">0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="t_cd8" units="dimensionless">1.0</asymmetric_division_probability>
-                        <asymmetric_division_probability name="neoplastic epithelial" units="dimensionless">0</asymmetric_division_probability>
-                    </standard_asymmetric_division>
-                </cycle>
-                <death>
-                    <model code="100" name="apoptosis">
-                        <death_rate units="1/min">5.31667e-05</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">0.001938</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">0</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                    <model code="101" name="necrosis">
-                        <death_rate units="1/min">0.0</death_rate>
-                        <phase_transition_rates units="1/min">
-                            <rate start_index="0" end_index="1" fixed_duration="false">9000000000.0</rate>
-                            <rate start_index="1" end_index="2" fixed_duration="true">1.15741e-05</rate>
-                        </phase_transition_rates>
-                        <parameters>
-                            <unlysed_fluid_change_rate units="1/min">1.11667e-02</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-05</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-4</nuclear_biomass_change_rate>
-                            <calcification_rate units="1/min">7e-05</calcification_rate>
-                            <relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
-                        </parameters>
-                    </model>
-                </death>
-                <volume>
-                    <total units="micron^3">2494</total>
-                    <fluid_fraction units="dimensionless">0.75</fluid_fraction>
-                    <nuclear units="micron^3">540</nuclear>
-                    <fluid_change_rate units="1/min">0.05</fluid_change_rate>
-                    <cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
-                    <nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
-                    <calcified_fraction units="dimensionless">0.0</calcified_fraction>
-                    <calcification_rate units="1/min">0.0</calcification_rate>
-                    <relative_rupture_volume units="dimensionless">2</relative_rupture_volume>
-                </volume>
-                <mechanics>
-                    <cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
-                    <cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
-                    <relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
-                    <cell_adhesion_affinities>
-                        <cell_adhesion_affinity name="monocyte">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_cadm1">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_folr2">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd8">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="t_cd4">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="dendritic">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="mac_other">1.0</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="neoplastic epithelial">1.0</cell_adhesion_affinity>
-                    </cell_adhesion_affinities>
-                    <options>
-                        <set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
-                        <set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
-                    </options>
-                    <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
-                    <attachment_rate units="1/min">0.0</attachment_rate>
-                    <detachment_rate units="1/min">0.0</detachment_rate>
-                    <maximum_number_of_attachments>12</maximum_number_of_attachments>
-                </mechanics>
-                <motility>
-                    <speed units="micron/min">1.0</speed>
-                    <persistence_time units="min">1.0</persistence_time>
-                    <migration_bias units="dimensionless">0.0</migration_bias>
-                    <options>
-                        <enabled>true</enabled>
-                        <use_2D>true</use_2D>
-                        <chemotaxis>
-                            <enabled>false</enabled>
-                            <substrate>debris</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>false</enabled>
-                            <normalize_each_gradient>false</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="debris">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="cxc3cl1">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="egf">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="ifng">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il2">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il4">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il6">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il10">0.0</chemotactic_sensitivity>
-                                <chemotactic_sensitivity substrate="il12">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="debris">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="cxc3cl1">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="egf">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="ifng">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il2">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il4">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il6">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il10">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                    <substrate name="il12">
-                        <secretion_rate units="1/min">0.0</secretion_rate>
-                        <secretion_target units="substrate density">1.0</secretion_target>
-                        <uptake_rate units="1/min">0.0</uptake_rate>
-                        <net_export_rate units="total substrate/min">0.0</net_export_rate>
-                    </substrate>
-                </secretion>
-                <cell_interactions>
-                    <apoptotic_phagocytosis_rate units="1/min">0.0</apoptotic_phagocytosis_rate>
-                    <necrotic_phagocytosis_rate units="1/min">0.0</necrotic_phagocytosis_rate>
-                    <other_dead_phagocytosis_rate units="1/min">0.0</other_dead_phagocytosis_rate>
-                    <live_phagocytosis_rates>
-                        <phagocytosis_rate name="monocyte" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_cadm1" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_folr2" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd8" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="t_cd4" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="dendritic" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="mac_other" units="1/min">0.0</phagocytosis_rate>
-                        <phagocytosis_rate name="neoplastic epithelial" units="1/min">0.0</phagocytosis_rate>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <attack_rate name="monocyte" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_cadm1" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_folr2" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd8" units="1/min">0.0</attack_rate>
-                        <attack_rate name="t_cd4" units="1/min">0.0</attack_rate>
-                        <attack_rate name="dendritic" units="1/min">0.0</attack_rate>
-                        <attack_rate name="mac_other" units="1/min">0.0</attack_rate>
-                        <attack_rate name="neoplastic epithelial" units="1/min">0.0</attack_rate>
-                    </attack_rates>
-                    <attack_damage_rate units="1/min">1.0</attack_damage_rate>
-                    <attack_duration units="min">0.1</attack_duration>
-                    <fusion_rates>
-                        <fusion_rate name="monocyte" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_cadm1" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_folr2" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd8" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="t_cd4" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="dendritic" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="mac_other" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="neoplastic epithelial" units="1/min">0.0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="monocyte" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_cadm1" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_folr2" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd8" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="t_cd4" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="dendritic" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="mac_other" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="neoplastic epithelial" units="1/min">0.0</transformation_rate>
-                    </transformation_rates>
-                </cell_transformations>
-                <cell_integrity>
-                    <damage_rate units="1/min">0.0</damage_rate>
-                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
-                </cell_integrity>
-            </phenotype>
-            <custom_data>
-                <sample conserved="false" units="dimensionless" description="">0.0</sample>
-            </custom_data>
-            <initial_parameter_distributions enabled="false">
-          </initial_parameter_distributions>
         </cell_definition>
     </cell_definitions>
 
     <initial_conditions>
-        <cell_positions type="csv" enabled="false">
+        <cell_positions type="csv" enabled="true">
             <folder>./config</folder>
             <filename>cells.csv</filename>
         </cell_positions>
@@ -2066,15 +255,17 @@
 
     <cell_rules>
         <rulesets>
-            <ruleset protocol="CBHG" version="3.0" format="csv" enabled="false">
+            <ruleset protocol="CBHG" version="3.0" format="csv" enabled="true">
                 <folder>./config</folder>
-                <filename>cell_rules.csv</filename>
+                <filename>cell_rules_v2.csv</filename>
             </ruleset>
         </rulesets>
         <settings />
     </cell_rules>
 
+
     <user_parameters>
-        <number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">12</number_of_cells>
+        <random_seed type="int" units="dimensionless" description="">0</random_seed>
+        <number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">0</number_of_cells>
     </user_parameters>
 </PhysiCell_settings>
\ No newline at end of file
diff --git a/config/cell_rules.csv b/config/cell_rules.csv
deleted file mode 100644
index e69de29bb..000000000
diff --git a/config/cells.csv b/config/cells.csv
deleted file mode 100644
index 734bdc767..000000000
--- a/config/cells.csv
+++ /dev/null
@@ -1 +0,0 @@
-0,0,0,0
\ No newline at end of file
diff --git a/custom_modules/custom.cpp b/custom_modules/custom.cpp
deleted file mode 100644
index 59b23bd93..000000000
--- a/custom_modules/custom.cpp
+++ /dev/null
@@ -1,214 +0,0 @@
-/*
-###############################################################################
-# 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) 2015-2021, 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.                                                 #
-#                                                                             #
-###############################################################################
-*/
-
-#include "./custom.h"
-
-void create_cell_types( void )
-{
-	// set the random seed 
-	if (parameters.ints.find_index("random_seed") != -1)
-	{
-		SeedRandom(parameters.ints("random_seed"));
-	}
-	
-	/* 
-	   Put any modifications to default cell definition here if you 
-	   want to have "inherited" by other cell types. 
-	   
-	   This is a good place to set default functions. 
-	*/ 
-	
-	initialize_default_cell_definition(); 
-	cell_defaults.phenotype.secretion.sync_to_microenvironment( &microenvironment ); 
-	
-	cell_defaults.functions.volume_update_function = standard_volume_update_function;
-	cell_defaults.functions.update_velocity = standard_update_cell_velocity;
-
-	cell_defaults.functions.update_migration_bias = NULL; 
-	cell_defaults.functions.update_phenotype = NULL; // update_cell_and_death_parameters_O2_based; 
-	cell_defaults.functions.custom_cell_rule = NULL; 
-	cell_defaults.functions.contact_function = NULL; 
-	
-	cell_defaults.functions.add_cell_basement_membrane_interactions = NULL; 
-	cell_defaults.functions.calculate_distance_to_membrane = NULL; 
-	
-	/*
-	   This parses the cell definitions in the XML config file. 
-	*/
-	
-	initialize_cell_definitions_from_pugixml(); 
-
-	/*
-	   This builds the map of cell definitions and summarizes the setup. 
-	*/
-		
-	build_cell_definitions_maps(); 
-
-	/*
-	   This intializes cell signal and response dictionaries 
-	*/
-
-	setup_signal_behavior_dictionaries(); 	
-
-	/*
-       Cell rule definitions 
-	*/
-
-	setup_cell_rules(); 
-
-	/* 
-	   Put any modifications to individual cell definitions here. 
-	   
-	   This is a good place to set custom functions. 
-	*/ 
-	
-	cell_defaults.functions.update_phenotype = phenotype_function; 
-	cell_defaults.functions.custom_cell_rule = custom_function; 
-	cell_defaults.functions.contact_function = contact_function; 
-	
-	/*
-	   This builds the map of cell definitions and summarizes the setup. 
-	*/
-		
-	display_cell_definitions( std::cout ); 
-	
-	return; 
-}
-
-void setup_microenvironment( void )
-{
-	// set domain parameters 
-	
-	// put any custom code to set non-homogeneous initial conditions or 
-	// extra Dirichlet nodes here. 
-	
-	// initialize BioFVM 
-	
-	initialize_microenvironment(); 	
-	
-	return; 
-}
-
-void setup_tissue( void )
-{
-	double Xmin = microenvironment.mesh.bounding_box[0]; 
-	double Ymin = microenvironment.mesh.bounding_box[1]; 
-	double Zmin = microenvironment.mesh.bounding_box[2]; 
-
-	double Xmax = microenvironment.mesh.bounding_box[3]; 
-	double Ymax = microenvironment.mesh.bounding_box[4]; 
-	double Zmax = microenvironment.mesh.bounding_box[5]; 
-	
-	if( default_microenvironment_options.simulate_2D == true )
-	{
-		Zmin = 0.0; 
-		Zmax = 0.0; 
-	}
-	
-	double Xrange = Xmax - Xmin; 
-	double Yrange = Ymax - Ymin; 
-	double Zrange = Zmax - Zmin; 
-	
-	// create some of each type of cell 
-	
-	Cell* pC;
-	
-	for( int k=0; k < cell_definitions_by_index.size() ; k++ )
-	{
-		Cell_Definition* pCD = cell_definitions_by_index[k]; 
-		std::cout << "Placing cells of type " << pCD->name << " ... " << std::endl; 
-		for( int n = 0 ; n < parameters.ints("number_of_cells") ; n++ )
-		{
-			std::vector<double> position = {0,0,0}; 
-			position[0] = Xmin + UniformRandom()*Xrange; 
-			position[1] = Ymin + UniformRandom()*Yrange; 
-			position[2] = Zmin + UniformRandom()*Zrange; 
-			
-			pC = create_cell( *pCD ); 
-			pC->assign_position( position );
-		}
-	}
-	std::cout << std::endl; 
-	
-	// load cells from your CSV file (if enabled)
-	load_cells_from_pugixml();
-	set_parameters_from_distributions();
-	
-	return; 
-}
-
-std::vector<std::string> my_coloring_function( Cell* pCell )
-{ return paint_by_number_cell_coloring(pCell); }
-
-void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt )
-{ return; }
-
-void custom_function( Cell* pCell, Phenotype& phenotype , double dt )
-{ return; } 
-
-void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt )
-{ return; } 
\ No newline at end of file
diff --git a/custom_modules/custom.h b/custom_modules/custom.h
deleted file mode 100644
index 0e6df8d02..000000000
--- a/custom_modules/custom.h
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
-###############################################################################
-# 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) 2015-2021, 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.                                                 #
-#                                                                             #
-###############################################################################
-*/
-
-#include "../core/PhysiCell.h"
-#include "../modules/PhysiCell_standard_modules.h" 
-
-using namespace BioFVM; 
-using namespace PhysiCell;
-
-// setup functions to help us along 
-
-void create_cell_types( void );
-void setup_tissue( void ); 
-
-// set up the BioFVM microenvironment 
-void setup_microenvironment( void ); 
-
-// custom pathology coloring function 
-
-std::vector<std::string> my_coloring_function( Cell* );
-
-// custom functions can go here 
-
-void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt );
-void custom_function( Cell* pCell, Phenotype& phenotype , double dt );
-
-void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt ); 
-
diff --git a/main.cpp b/main.cpp
deleted file mode 100644
index bf6e65d15..000000000
--- a/main.cpp
+++ /dev/null
@@ -1,254 +0,0 @@
-/*
-###############################################################################
-# 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) 2015-2022, 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.                                                 #
-#                                                                             #
-###############################################################################
-*/
-
-#include <cstdio>
-#include <cstdlib>
-#include <iostream>
-#include <ctime>
-#include <cmath>
-#include <omp.h>
-#include <fstream>
-
-#include "./core/PhysiCell.h"
-#include "./modules/PhysiCell_standard_modules.h" 
-
-// put custom code modules here! 
-
-#include "./custom_modules/custom.h" 
-	
-using namespace BioFVM;
-using namespace PhysiCell;
-
-int main( int argc, char* argv[] )
-{
-	// load and parse settings file(s)
-	
-	bool XML_status = false; 
-	char copy_command [1024]; 
-	if( argc > 1 )
-	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
-	}
-	else
-	{
-		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
-	}
-	if( !XML_status )
-	{ exit(-1); }
-	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
-	// OpenMP setup
-	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
-	
-	// time setup 
-	std::string time_units = "min"; 
-
-	/* Microenvironment setup */ 
-	
-	setup_microenvironment(); // modify this in the custom code 
-	
-	/* PhysiCell setup */ 
- 	
-	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
-	
-	/* Users typically start modifying here. START USERMODS */ 
-	
-	create_cell_types();
-	
-	setup_tissue();
-
-	/* Users typically stop modifying here. END USERMODS */ 
-	
-	// set MultiCellDS save options 
-
-	set_save_biofvm_mesh_as_matlab( true ); 
-	set_save_biofvm_data_as_matlab( true ); 
-	set_save_biofvm_cell_data( true ); 
-	set_save_biofvm_cell_data_as_custom_matlab( true );
-	
-	// save a simulation snapshot 
-	
-	char filename[1024];
-	sprintf( filename , "%s/initial" , PhysiCell_settings.folder.c_str() ); 
-	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
-	
-	// save a quick SVG cross section through z = 0, after setting its 
-	// length bar to 200 microns 
-
-	PhysiCell_SVG_options.length_bar = 200; 
-
-	// for simplicity, set a pathology coloring function 
-	
-	std::vector<std::string> (*cell_coloring_function)(Cell*) = my_coloring_function;
-	std::string (*substrate_coloring_function)(double, double, double) = paint_by_density_percentage;
-
-	sprintf( filename , "%s/initial.svg" , PhysiCell_settings.folder.c_str() ); 
-	SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function );
-	
-	sprintf( filename , "%s/legend.svg" , PhysiCell_settings.folder.c_str() ); 
-	create_plot_legend( filename , cell_coloring_function ); 
-	
-	display_citations(); 
-	
-	// set the performance timers 
-
-	BioFVM::RUNTIME_TIC();
-	BioFVM::TIC();
-	
-	std::ofstream report_file;
-	if( PhysiCell_settings.enable_legacy_saves == true )
-	{	
-		sprintf( filename , "%s/simulation_report.txt" , PhysiCell_settings.folder.c_str() ); 
-		
-		report_file.open(filename); 	// create the data log file 
-		report_file<<"simulated time\tnum cells\tnum division\tnum death\twall time"<<std::endl;
-	}
-	
-	// main loop 
-	
-	try 
-	{		
-		while( PhysiCell_globals.current_time < PhysiCell_settings.max_time + 0.1*diffusion_dt )
-		{
-			// save data if it's time. 
-			if( PhysiCell_globals.current_time > PhysiCell_globals.next_full_save_time - 0.5 * diffusion_dt )
-			{
-				display_simulation_status( std::cout ); 
-				if( PhysiCell_settings.enable_legacy_saves == true )
-				{	
-					log_output( PhysiCell_globals.current_time , PhysiCell_globals.full_output_index, microenvironment, report_file);
-				}
-				
-				if( PhysiCell_settings.enable_full_saves == true )
-				{	
-					sprintf( filename , "%s/output%08u" , PhysiCell_settings.folder.c_str(),  PhysiCell_globals.full_output_index ); 
-					
-					save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
-				}
-				
-				PhysiCell_globals.full_output_index++; 
-				PhysiCell_globals.next_full_save_time += PhysiCell_settings.full_save_interval;
-			}
-			
-			// save SVG plot if it's time
-			if( PhysiCell_globals.current_time > PhysiCell_globals.next_SVG_save_time - 0.5 * diffusion_dt )
-			{
-				if( PhysiCell_settings.enable_SVG_saves == true )
-				{	
-					sprintf( filename , "%s/snapshot%08u.svg" , PhysiCell_settings.folder.c_str() , PhysiCell_globals.SVG_output_index );
-					SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
-
-					PhysiCell_globals.SVG_output_index++; 
-					PhysiCell_globals.next_SVG_save_time  += PhysiCell_settings.SVG_save_interval;
-				}
-			}
-
-			// update the microenvironment
-			microenvironment.simulate_diffusion_decay( diffusion_dt );
-			
-			// run PhysiCell 
-			((Cell_Container *)microenvironment.agent_container)->update_all_cells( PhysiCell_globals.current_time );
-			
-			/*
-			  Custom add-ons could potentially go here. 
-			*/
-			
-			PhysiCell_globals.current_time += diffusion_dt;
-		}
-		
-		if( PhysiCell_settings.enable_legacy_saves == true )
-		{			
-			log_output(PhysiCell_globals.current_time, PhysiCell_globals.full_output_index, microenvironment, report_file);
-			report_file.close();
-		}
-	}
-	catch( const std::exception& e )
-	{ // reference to the base of a polymorphic object
-		std::cout << e.what(); // information from length_error printed
-	}
-	
-	// save a final simulation snapshot 
-	
-	sprintf( filename , "%s/final" , PhysiCell_settings.folder.c_str() ); 
-	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
-	
-	sprintf( filename , "%s/final.svg" , PhysiCell_settings.folder.c_str() );
-	SVG_plot(filename, microenvironment, 0.0, PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
-
-	// timer 
-	
-	std::cout << std::endl << "Total simulation runtime: " << std::endl; 
-	BioFVM::display_stopwatch_value( std::cout , BioFVM::runtime_stopwatch_value() ); 
-
-	return 0; 
-}

From 474918842f6f558ff4f2889ffcd0f23bd620aa05 Mon Sep 17 00:00:00 2001
From: bue <epbucher@iu.edu>
Date: Fri, 13 Jun 2025 12:28:33 -0400
Subject: [PATCH 4/4] Take warned_rng variable extern to be able to suppress
 the mislead message 'WARNING: Setting the random seed again.' when models in
 consecutive episodes are run.

---
 core/PhysiCell_utilities.cpp     | 6 +++---
 core/PhysiCell_utilities.h       | 5 ++---
 sample_projects/episode/main.cpp | 1 +
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/core/PhysiCell_utilities.cpp b/core/PhysiCell_utilities.cpp
index 91f0cd582..316404856 100644
--- a/core/PhysiCell_utilities.cpp
+++ b/core/PhysiCell_utilities.cpp
@@ -78,18 +78,18 @@ thread_local bool local_pnrg_setup_done = false;
 unsigned int physicell_random_seed = 0; 
 std::vector<unsigned int> physicell_random_seeds; 
 
+bool warned_rng = false;
 void setup_rng( void )
 {
 	static bool setup_done = false;
-	static bool warned = false;
-	if (!warned && setup_done)
+	if (!warned_rng && setup_done)
 	{
 		std::cout << "WARNING: Setting the random seed again." << std::endl
 				  << "\tYou probably have set a user parameter called random_seed." << std::endl
 				  << "\tHere, we will use the random seed set in user parameters." << std::endl	
 				  << "\tHOWEVER, as of PhysiCell 1.14.0, you should set the random seed in the <options><random_seed> element in the config file." << std::endl
 				  << "\tFuture versions of PhysiCell may throw an error here. Kindly remove the user parameter and just use the <options><random_seed> element." << std::endl;
-		warned = true;
+		warned_rng = true;
 	}
 	std::cout << "Setting up RNG with seed " << physicell_random_seed << std::endl;
 
diff --git a/core/PhysiCell_utilities.h b/core/PhysiCell_utilities.h
index 7e4ec1548..199134ef1 100644
--- a/core/PhysiCell_utilities.h
+++ b/core/PhysiCell_utilities.h
@@ -80,9 +80,8 @@
 
 namespace PhysiCell{
 
-
-	extern std::vector<unsigned int> physicell_random_seeds; 
-
+extern std::vector<unsigned int> physicell_random_seeds;
+extern bool warned_rng;
 void setup_rng( void );
 void SeedRandom( unsigned int input );
 void SeedRandom( void );
diff --git a/sample_projects/episode/main.cpp b/sample_projects/episode/main.cpp
index 2f32cb696..f6cf70e11 100644
--- a/sample_projects/episode/main.cpp
+++ b/sample_projects/episode/main.cpp
@@ -160,6 +160,7 @@ int main( int argc, char* argv[] )
 		{
 			// load xml file
 			std::cout << "load setting xml " << settingxml << " ..." << std::endl;
+			warned_rng = true;
 			bool XML_status = false;
 			XML_status = read_PhysiCell_config_file( settingxml );
 			if ( XML_status ) { PhysiCell_settings.read_from_pugixml(); }