add immune_test_2024 to Makefiles as immune-function-sample

MathCancer · Oct 28, 2024 · 7bf8434 · 7bf8434
1 parent a37ee57
commit 7bf8434
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Showing 11 changed files with 21 additions and 3 deletions.
diff --git a/Makefile b/Makefile
@@ -74,7 +74,7 @@ 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"
+	@echo "					asymmetric-division-sample immune-function-sample"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
@@ -216,6 +216,15 @@ asymmetric-division-sample:
 	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/
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/

diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default
@@ -74,7 +74,7 @@ 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"
+	@echo "					asymmetric-division-sample immune-function-sample"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
@@ -216,6 +216,15 @@ asymmetric-division-sample:
 	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/
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/

diff --git a/sample_projects/immune_test_2024/Makefile → sample_projects/immune_function/Makefile b/sample_projects/immune_test_2024/Makefile → sample_projects/immune_function/Makefile
diff --git a/sample_projects/immune_test_2024/VERSION.txt → sample_projects/immune_function/VERSION.txt b/sample_projects/immune_test_2024/VERSION.txt → sample_projects/immune_function/VERSION.txt
diff --git a/...e_test_2024/config/PhysiCell_settings.xml → ...ne_function/config/PhysiCell_settings.xml b/...e_test_2024/config/PhysiCell_settings.xml → ...ne_function/config/PhysiCell_settings.xml
diff --git a/...ts/immune_test_2024/config/cell_rules.csv → ...cts/immune_function/config/cell_rules.csv b/...ts/immune_test_2024/config/cell_rules.csv → ...cts/immune_function/config/cell_rules.csv
@@ -7,4 +7,4 @@ tumor cell,apoptotic,increases,apoptotic debris secretion,1,0.5,10,1
 tumor cell,necrotic,increases,necrotic debris secretion,1,0.5,10,1
 // tumor cell,doxorubicin,increases,damage rate,1,0.5,4,0
 tumor cell,time,decreases,damage repair rate,0,15,10,0
-fast T cell,damage delivered,increases,transformation to exhausted T cell,...
+fast T cell,damage delivered,increases,transform to exhausted T cell,0.01,30.0,8,0
diff --git a/...rojects/immune_test_2024/config/cells.csv → ...projects/immune_function/config/cells.csv b/...rojects/immune_test_2024/config/cells.csv → ...projects/immune_function/config/cells.csv
diff --git a/...mmune_test_2024/custom_modules/custom.cpp → ...immune_function/custom_modules/custom.cpp b/...mmune_test_2024/custom_modules/custom.cpp → ...immune_function/custom_modules/custom.cpp
diff --git a/.../immune_test_2024/custom_modules/custom.h → ...s/immune_function/custom_modules/custom.h b/.../immune_test_2024/custom_modules/custom.h → ...s/immune_function/custom_modules/custom.h
diff --git a/sample_projects/immune_test_2024/main.cpp → sample_projects/immune_function/main.cpp b/sample_projects/immune_test_2024/main.cpp → sample_projects/immune_function/main.cpp
diff --git a/sample_projects/immune_test_2024/custom_modules/empty.txt b/sample_projects/immune_test_2024/custom_modules/empty.txt