First push of prostate project files

Makefile

@@ -1,5 +1,5 @@
 VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
-PROGRAM_NAME := project
+PROGRAM_NAME := prostate
 
 CC := g++
 # CC := g++-mp-7 # typical macports compiler name
@@ -11,16 +11,19 @@ ifdef PHYSICELL_CPP
 	CC := $(PHYSICELL_CPP)
 endif
 
+# prostate model has more than 64 nodes, so we have 
+# to set up this var to the number of nodes
+MABOSS_MAX_NODES = 256
+
 ### MaBoSS configuration 
 # MaBoSS max nodes
 ifndef MABOSS_MAX_NODES
-MABOSS_MAX_NODES = 256
+MABOSS_MAX_NODES = 64
 endif
 
 # MaBoSS directory
 MABOSS_DIR = addons/PhysiBoSS/MaBoSS/engine
 CUR_DIR = $(shell pwd)
-CUSTOM_DIR = sample_projects/Arnau_model/custom_modules
 
 ifneq ($(OS), Windows_NT)
 	LDL_FLAG = -ldl
@@ -58,7 +61,9 @@ ARCH := native # best auto-tuning
 # ARCH := nocona #64-bit pentium 4 or later 
 
 # CFLAGS := -march=$(ARCH) -Ofast -s -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
-CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
+CFLAGS := -g -march=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
+# debug:
+# CFLAGS := -march=$(ARCH) -O0 -ggdb -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
 
 ifeq ($(OS),Windows_NT)
 else
@@ -91,18 +96,21 @@ MaBoSS := ./addons/PhysiBoSS/MaBoSS/engine/src/BooleanNetwork.h
 
 PhysiBoSS_OBJECTS := maboss_network.o maboss_intracellular.o
 
-PhysiCell_custom_module_OBJECTS := custom.o
+PhysiCell_custom_module_OBJECTS := custom.o drug_sensitivity.o boolean_model_interface.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) $(PhysiBoSS_OBJECTS)
+ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS) $(PhysiBoSS_OBJECTS) 
+#$(PhysiBoSS_module_OBJECTS)
 
 # compile the project 
 
 all: main.cpp $(ALL_OBJECTS) $(MaBoSS)
 	$(COMPILE_COMMAND) $(INC) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp $(LIB)
-	make name 
+	@echo ""
+	@echo "check for $(PROGRAM_NAME)"
+	make name
 
 static: main.cpp $(ALL_OBJECTS) $(MaBoSS)
 	$(LINK_COMMAND) $(INC) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp $(LIB) -static-libgcc -static-libstdc++ $(STATIC_OPENMP)
@@ -134,16 +142,16 @@ PhysiCell_utilities.o: ./core/PhysiCell_utilities.cpp
 
 PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp 
-	
+
 PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
-	$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp 
-	
+	$(COMPILE_COMMAND) -c ./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 
-
+	
 # BioFVM core components (needed by PhysiCell)
 
 BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
@@ -189,19 +197,19 @@ PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp $(MaBoSS)
 
 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
 
 Compile_MaBoSS: ./addons/PhysiBoSS/MaBoSS/engine/src/BooleanNetwork.h
@@ -214,14 +222,24 @@ else
 	python3 addons/PhysiBoSS/setup_libmaboss.py
 endif
 
+maboss_intracellular.o: ./addons/PhysiBoSS/src/maboss_intracellular.cpp $(MaBoSS)
+	$(COMPILE_COMMAND) $(INC) -c ./addons/PhysiBoSS/src/maboss_intracellular.cpp
+
 maboss_network.o: ./addons/PhysiBoSS/src/maboss_network.cpp $(MaBoSS)
 	$(COMPILE_COMMAND) $(INC) -c ./addons/PhysiBoSS/src/maboss_network.cpp
 
-maboss_intracellular.o: ./addons/PhysiBoSS/src/maboss_intracellular.cpp $(MaBoSS)
-	$(COMPILE_COMMAND) $(INC) -c ./addons/PhysiBoSS/src/maboss_intracellular.cpp
+utils.o: ./addons/PhysiBoSS/src/utils.cpp #$(MaBoSS)
+	$(COMPILE_COMMAND) $(INC) -c ./addons/PhysiBoSS/src/utils.cpp
 
 custom.o: ./custom_modules/custom.cpp $(MaBoSS)
-	$(COMPILE_COMMAND) $(INC)  -c ./custom_modules/custom.cpp
+	$(COMPILE_COMMAND) $(INC) -c ./custom_modules/custom.cpp
+
+drug_sensitivity.o: ./custom_modules/drug_sensitivity.cpp
+	$(COMPILE_COMMAND) $(INC) -c ./custom_modules/drug_sensitivity.cpp
+
+boolean_model_interface.o: ./custom_modules/boolean_model_interface.cpp
+	$(COMPILE_COMMAND) $(INC) -c ./custom_modules/boolean_model_interface.cpp
+
 
 # cleanup
 
@@ -231,29 +249,31 @@ reset:
 	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 
-	rm -fr ./config/cells.csv ./config/cell_rules.csv
+	rm -rf ./config/boolean_network/
 	rm -rf ./scripts
 
 MaBoSS-clean:
 	rm -fr addons/PhysiBoSS/MaBoSS
 
-clean:
+clean: 
 	rm -f *.o
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
+	rm -f *.mat
+	rm -f *.xml
+	rm -f *.svg
 	rm -rf ./output
 	mkdir ./output
 	touch ./output/empty.txt
 
 # archival 
-	
+
 checkpoint: 
 	zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* 
-	
+
 zip:
 	zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* 
 	cp latest.zip $$(date +%b_%d_%Y_%H%M).zip
@@ -273,26 +293,10 @@ unzip:
 untar: 
 	cp ./archives/latest.tar .
 	tar -xzf latest.tar
-
-# easier animation 
-
-FRAMERATE := 24
-OUTPUT := output
-
-jpeg: 
-	@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt 
-	@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt 
-	@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt 
-	@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt 
-	@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt 
-	@magick mogrify -format jpg -resize $$(grep . __resize.txt) $(OUTPUT)/s*.svg
-	rm -f __H*.txt __W*.txt __resize.txt 
 
-gif: 
-	magick convert $(OUTPUT)/s*.svg $(OUTPUT)/out.gif 
-
 movie:
-	ffmpeg -r $(FRAMERATE) -f image2 -i $(OUTPUT)/snapshot%08d.jpg -vcodec libx264 -pix_fmt yuv420p -strict -2 -tune animation -crf 15 -acodec none $(OUTPUT)/out.mp4
+	ffmpeg -r 25 -i output/snapshot%08d.svg -pix_fmt yuv420p output.mp4
+	vlc output.mp4
 
 # upgrade rules 
 
@@ -322,7 +326,7 @@ upgrade: $(SOURCE)
 	mv -f PhysiCell/documentation/User_Guide.pdf documentation
 	rm -f -r PhysiCell
 	rm -f $(SOURCE) 
-
+	
 # use: make save PROJ=your_project_name
 PROJ := my_project
 
@@ -367,3 +371,4 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+

README.md

@@ -1,12 +1,21 @@
 # About
 
-This repository is a template for PhysiBoSS models, that can be used to submit a new model to the database.
+This repository is an update of the prostate model to version 2.2.3 of PhysiBoSS. The project does not rely on the cell rules to perform the inhibition, but on an ad-hoc cell sensitivity that depends on the cell line.
+
+A prior version of this model was used to simulate the drug response in prostate cell lines in Figures 6, 7 and 8 of [the PhysiBoSS 2.0 paper](https://www.nature.com/articles/s41540-023-00314-4).
 
 # Getting started
 
-- Fork this repository.
-- Make a new branch from main for your PhysiBoSS model. 
-- Update the new branch with your model
-- Update model.yml metadata file, as well as the readme for a quick description of the model
-- Open a pull request. Building of your model will be tested on Windows, Mac and Linux.
-- When your pull request is accepted by the editors a new repository will be created in the github PhysiBoSS-Models organization, and build/upload of your model will automatically be triggered. Once complete, the model is available on PhysiBoSS-Models.
+The XML in the `config` folder are: 
+- PhysiCell_settings_LNCaP.xml: LNCaP cell line simulation
+- PhysiCell_settings_LNCaP_Luminespib_2.xml: LNCaP cell line simulation adding Luminespib drug (anti_HSPs).
+- PhysiCell_settings_LNCaP_Pictilisib_2.xml: LNCaP cell line simulation adding Pictilisib drug (anti_PI3K).
+- PhysiCell_settings_LNCaP_Luminespib_Pictilisib_2.xml: LNCaP cell line simulation adding Luminespib and Pictilisib drugs.
+
+Files in the `scripts`  folder have post processing scripts.
+
+# Authors:
+
+Arnau Montagud, Annika Meert, Gerard Pradas and Miguel Ponce de Leon, BSC-CNS
+
+Contact: arnau.montagud at csic.es