Merge pull request #217 from sysbio-curie/update/physiboss

PhysiBoSS 2.2.3 update

CITATION.txt

@@ -23,13 +23,27 @@ with BioFVM [2] to solve the transport equations.
     llelized diffusive transport solver for 3-D biological simulations,     
     Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 
 
-If you use PhysiBoSS, please cite:
+If you use PhysiBoSS, please cite as below:
 
-    G. Letort, A. Montagud, G. Stoll, R. Heiland, E. Barillot, P. Macklin, 
+We implemented and solved the model using PhysiCell (Version 1.11.0) [1],    
+with PhysiBoSS[2,3] to simulate the intracellular mechanisms.                           
+
+[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] G. Letort, A. Montagud, G. Stoll, R. Heiland, E. Barillot, P. Macklin, 
     A. Zinovyev, and L. Calzone. PhysiBoSS: a multi-scale agent based 
     modelling framework integrating physical dimension and cell signalling. 
     Bioinformatics 35(7):1188-96, 2019. DOI: 10.1093/bioinformatics/bty766.
 
+[3] M. Ponce-de-Leon, A. Montagud, V. Noël, A. Meert, G. Pradas, E. Barillot,
+    L. Calzone, and A. Valencia. PhysiBoSS 2.0: a sustainable integration of
+    stochastic Boolean and agent-based modelling frameworks. NPJ Systems 
+    Biology and Applications 9(1):54, 2023.
+    DOI: 10.1038/s41540-023-00314-4 
+
 If you use libRoadrunner, please cite:
 
     Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias 

beta/setup_libmaboss.py → addons/PhysiBoSS/setup_libmaboss.py

@@ -9,9 +9,8 @@
 import os
 import sys
 import tarfile
-import zipfile
 
-if os.path.exists(os.path.join(os.path.dirname(os.path.dirname(__file__)), "addons", "PhysiBoSS", "MaBoSS-env-2.0")):
+if os.path.exists(os.path.join(os.path.dirname(__file__), "MaBoSS-env-2.0")):
     print('libMaBoSS already installed')
 
 else:
@@ -21,35 +20,26 @@
     # Assume Windows
     mb_file = ""
     url = ""
-    maboss_version = "v2.5.2"
+    maboss_version = "v2.5.4"
     if os_type.lower() == 'darwin':
         if "ARM64" in platform.uname().version:
             mb_file = "libMaBoSS-macos-arm64.tar.gz"
-            url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/boolean/libMaBoSS-macos-arm64.tar.gz"
         else:
             mb_file = "libMaBoSS-osx64.tar.gz"
-            url = "https://github.com/sysbio-curie/MaBoSS-env-2.0/releases/download/" + maboss_version + "/" + mb_file
     elif os_type.lower().startswith("win") or os_type.lower().startswith("msys_nt") or os_type.lower().startswith("mingw64_nt"):
         mb_file = "libMaBoSS-win64.tar.gz"
-        url = "https://github.com/sysbio-curie/MaBoSS-env-2.0/releases/download/" + maboss_version + "/" + mb_file
     elif os_type.lower().startswith("linux"):
         mb_file = "libMaBoSS-linux64.tar.gz"
-        url = "https://github.com/sysbio-curie/MaBoSS-env-2.0/releases/download/" + maboss_version + "/" + mb_file
     else:
         print("Your operating system seems to be unsupported. Please submit a ticket at https://sourceforge.net/p/physicell/tickets/ ")
         sys.exit(1)
 
-    # url = "https://github.com/sysbio-curie/MaBoSS-env-2.0/releases/download/v2.4.1/" + mb_file
+    url = "https://github.com/sysbio-curie/MaBoSS-env-2.0/releases/download/" + maboss_version + "/" + mb_file
 
-    fname = mb_file
-
-    home = os.path.expanduser("~")
     print('libMaBoSS will now be installed into the addon PhysiBoSS addon folder:')
-    dir_name = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'addons', 'PhysiBoSS')
+    dir_name = os.path.dirname(__file__)
     print(dir_name + '\n')
-    # print('   - Press ENTER to confirm the installation')
-    # print('   - Press CTL-C to abort the installation')
-
+
     if not os.path.exists(dir_name):
                 try:
                     os.makedirs(dir_name)
@@ -59,15 +49,9 @@
     print('Beginning download of libMaBoSS into ' + dir_name + ' ...')
     print(url)
 
-    my_file = os.path.join(dir_name, fname)
+    my_file = os.path.join(dir_name, mb_file)
     print('my_file = ',my_file)
 
-    # if os_type.lower().startswith("win"):
-    #     rrlib_dir = my_file[:-4]
-    # else:  # darwin or linux
-    #     rrlib_dir = my_file[:-7]
-    # print('rrlib_dir = ',rrlib_dir)
-
     def download_cb(blocknum, blocksize, totalsize):
         readsofar = blocknum * blocksize
         if totalsize > 0:

addons/PhysiBoSS/src/maboss_intracellular.cpp

@@ -69,32 +69,38 @@ void MaBoSSIntracellular::update_inputs(PhysiCell::Cell* cell, PhysiCell::Phenot
 	int i=0;
 	for (auto& input: listOfInputs) 
 	{
-		if (input.second.isNode()) {
-			maboss.set_node_value(
-				input.first,
-				input.second.updateNode(maboss.get_node_value(input.second.intracellular_name), signals[i])
-			);
-		} else if (input.second.isParameter()) {
-			maboss.set_parameter_value(
-				input.first,
-				input.second.updateParameter(signals[i])
-			);
+		if (cell->phenotype.death.dead == false || input.second.use_for_dead == true) {
+
+			if (input.second.isNode()) {
+				maboss.set_node_value(
+					input.first,
+					input.second.updateNode(maboss.get_node_value(input.second.intracellular_name), signals[i])
+				);
+			} else if (input.second.isParameter()) {
+				maboss.set_parameter_value(
+					input.first,
+					input.second.updateParameter(signals[i])
+				);
+			}
 		}
 		i++;
 	}
 }
 
 void MaBoSSIntracellular::update_outputs(PhysiCell::Cell* cell, PhysiCell::Phenotype& phenotype, double dt)
 {
-	std::vector<double> signals = std::vector<double>(listOfOutputs.size(), 0.0);
-
 	int i=0;
+
 	for (auto& output: listOfOutputs) 
 	{
-		signals[i] = output.second.update(maboss.get_node_value(output.second.intracellular_name));
+		if (cell->phenotype.death.dead == false || output.second.use_for_dead == true) {
+			PhysiCell::set_single_behavior(
+				cell, indicesOfOutputs[i], 
+				output.second.update(maboss.get_node_value(output.second.intracellular_name))
+			);
+		}
 		i++;
 	}
-	PhysiCell::set_selected_behaviors(cell, indicesOfOutputs, signals);
 }
 
 
@@ -366,7 +372,8 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
 					node_input.attribute( "physicell_name" ).value(),
 					intracellular_name,
 					(settings && settings.child( "scaling" ) ? PhysiCell::xml_get_my_double_value( settings.child( "scaling" )) : 1.0),
-					(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0)
+					(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0),
+					(settings && settings.child( "use_for_dead" ) ? PhysiCell::xml_get_my_bool_value( settings.child( "use_for_dead" )) : false)
 				);
 
 				// This construct is a trick to avoid making inputs and outputs constructible and assignable, or using c++17 insert_or_assign
@@ -382,7 +389,8 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
 					PhysiCell::xml_get_my_string_value(settings.child("action")),
 					PhysiCell::xml_get_my_double_value(settings.child("threshold")),
 					(settings && settings.child( "inact_threshold" ) ? PhysiCell::xml_get_my_double_value( settings.child( "inact_threshold" )) : PhysiCell::xml_get_my_double_value(settings.child("threshold"))),
-					(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0)
+					(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0),
+					(settings && settings.child( "use_for_dead" ) ? PhysiCell::xml_get_my_bool_value( settings.child( "use_for_dead" )) : false)
 				);
 
 				auto const res = listOfInputs.insert(std::pair<std::string, MaBoSSInput>(intracellular_name, input));
@@ -403,7 +411,9 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
 				PhysiCell::xml_get_my_string_value(settings.child("action")),
 				PhysiCell::xml_get_my_double_value(settings.child("value")),
 				(settings && settings.child( "base_value" ) ? PhysiCell::xml_get_my_double_value( settings.child( "base_value" )) : PhysiCell::xml_get_my_double_value(settings.child("value"))),
-				(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0)
+				(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0),
+				(settings && settings.child( "steepness" ) ? PhysiCell::xml_get_my_int_value( settings.child( "steepness" )) : 10),
+				(settings && settings.child( "use_for_dead" ) ? PhysiCell::xml_get_my_bool_value( settings.child( "use_for_dead" )) : false)
 			);
 
 			auto const res = listOfOutputs.insert(std::pair<std::string, MaBoSSOutput>(physicell_name, output));
@@ -442,13 +452,16 @@ void MaBoSSIntracellular::display(std::ostream& os)
 	os	<< "\t\t " << listOfInputs.size() << " input mapping defined" << std::endl;
 	for (const auto& input : listOfInputs)
 		os 	<< "\t\t\t" << input.second.physicell_name << " = " << input.first
-			<< "(" << input.second.threshold << ", " << input.second.inact_threshold << ", " << input.second.smoothing << ")"
+			<< "(" << input.second.threshold << ", " << input.second.inact_threshold 
+			<< ", " << input.second.smoothing << ", " << input.second.use_for_dead << ")"
 			<< std::endl;
 
 	os	<< "\t\t " << listOfOutputs.size() << " output mapping defined" << std::endl;
 	for (const auto& output : listOfOutputs)
 		os 	<< "\t\t\t" << output.first << " = " << output.second.intracellular_name 
-			<< "(" << output.second.value << ", " << output.second.base_value << ", " << output.second.smoothing << ")"
+			<< "(" << output.second.value << ", " << output.second.base_value 
+			<< ", " << output.second.smoothing << ", " << output.second.steepness 
+			<< ", " << output.second.use_for_dead << ")"
 			<< std::endl;
 
 	os 	<< "\t\t global inheritance = " << inherit_state << std::endl;

addons/PhysiBoSS/src/maboss_intracellular.h

@@ -10,7 +10,9 @@
 #include "maboss_network.h"
 #include "utils.h"
 
-static std::string PhysiBoSS_Version = "2.2.2"; 
+static std::string PhysiBoSS_Version = "2.2.3"; 
+static std::string PhysiBoSS_DOI = "10.1038/s41540-023-00314-4"; 
+static std::string PhysiBoSS_URL = "https://github.com/PhysiBoSS/PhysiBoSS"; 
 
 class MaBoSSIntracellular : public PhysiCell::Intracellular {
  private:
@@ -68,12 +70,10 @@ class MaBoSSIntracellular : public PhysiCell::Intracellular {
 	}
 
 	void update(PhysiCell::Cell * cell, PhysiCell::Phenotype& phenotype, double dt) {
-		if (!cell->phenotype.death.dead) {
-			this->update_inputs(cell, phenotype, dt);
-			this->maboss.run_simulation();
-			this->update_outputs(cell, phenotype, dt);
-			this->next_physiboss_run += this->maboss.get_time_to_update();
-		}
+		this->update_inputs(cell, phenotype, dt);
+		this->maboss.run_simulation();
+		this->update_outputs(cell, phenotype, dt);
+		this->next_physiboss_run += this->maboss.get_time_to_update();
 	}
 
 	bool need_update() {

addons/PhysiBoSS/src/maboss_network.cpp

@@ -1,4 +1,5 @@
 #include "maboss_network.h"
+#include <fstream>
 
 /* Default constructor */
 void MaBoSSNetwork::init_maboss( std::string networkFile, std::string configFile)
@@ -19,6 +20,18 @@ void MaBoSSNetwork::init_maboss( std::string networkFile, std::string configFile
 
 		#pragma omp critical
 		{
+			std::ifstream f_bnd(networkFile.c_str());
+			if (!f_bnd.good()) {
+				std::cerr << "PhysiBoSS ERROR : Could not open the BND file " << networkFile.c_str() << std::endl;
+				exit(1);
+			}
+
+			std::ifstream f_cfg(configFile.c_str());
+			if (!f_cfg.good()) {
+				std::cerr << "PhysiBoSS ERROR : Could not open the CFG file " << configFile.c_str() << std::endl;
+				exit(1);
+			}
+
 			// Initialize MaBoSS Objects for a model
 			this->network = new Network();
 			this->network->parse(networkFile.c_str());

addons/PhysiBoSS/src/utils.h

@@ -17,12 +17,14 @@ class MaBoSSInput
     double scaling;
     int smoothing;
     double smoothed_value;
-    MaBoSSInput(std::string physicell_name, std::string intracellular_name, std::string action, double threshold, double inact_threshold, int smoothing) : physicell_name(physicell_name), intracellular_name(intracellular_name), action(action), threshold(threshold), inact_threshold(inact_threshold), smoothing(smoothing) {
+    bool use_for_dead;
+
+    MaBoSSInput(std::string physicell_name, std::string intracellular_name, std::string action, double threshold, double inact_threshold, int smoothing, bool use_for_dead) : physicell_name(physicell_name), intracellular_name(intracellular_name), action(action), threshold(threshold), inact_threshold(inact_threshold), smoothing(smoothing), use_for_dead(use_for_dead){
         type = NODE;
         smoothed_value = 0;
     }
 
-    MaBoSSInput(std::string physicell_name, std::string intracellular_parameter, double scaling, int smoothing) : physicell_name(physicell_name), intracellular_parameter(intracellular_parameter), scaling(scaling), smoothing(smoothing) {
+    MaBoSSInput(std::string physicell_name, std::string intracellular_parameter, double scaling, int smoothing, bool use_for_dead) : physicell_name(physicell_name), intracellular_parameter(intracellular_parameter), scaling(scaling), smoothing(smoothing), use_for_dead(use_for_dead) {
         type = PARAMETER;
         smoothed_value = 0;
     }
@@ -83,13 +85,15 @@ class MaBoSSOutput
     int smoothing;
     double probability;
     bool initialized = false;
+    int steepness;
+    bool use_for_dead;
 
     MaBoSSOutput(std::string physicell_name, std::string intracellular_name,
                 std::string action, double value, double base_value,
-                int smoothing)
+                int smoothing, int steepness, bool use_for_dead)
         : physicell_name(physicell_name), intracellular_name(intracellular_name),
         action(action), value(value), base_value(base_value),
-        smoothing(smoothing) {
+        smoothing(smoothing), steepness(steepness), use_for_dead(use_for_dead) {
     probability = 0.5;
     }
 
@@ -115,10 +119,10 @@ class MaBoSSOutput
     }
 
     if (action == "activation") {
-        double hill = PhysiCell::Hill_response_function(hill_input * 2, 1, 10);
+        double hill = PhysiCell::Hill_response_function(hill_input * 2, 1, steepness);
         return (value - base_value) * hill + base_value;
     } else if (action == "inhibition") {
-        double hill = PhysiCell::Hill_response_function(hill_input * 2, 1, 10);
+        double hill = PhysiCell::Hill_response_function(hill_input * 2, 1, steepness);
         return ((value - base_value) * (1 - hill)) + base_value;
     }
 

licenses/MaBoSS.txt

@@ -0,0 +1,26 @@
+BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause)
+
+Copyright (c) 2011-2023 Institut Curie, 26 rue d'Ulm, Paris, France
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+    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.
+
+    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.

sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile

@@ -202,9 +202,9 @@ Compile_MaBoSS: ./addons/PhysiBoSS/MaBoSS-env-2.0/engine/src/BooleanNetwork.h
 
 $(MaBoSS): 
 ifeq ($(OS), Windows_NT)
-	python beta/setup_libmaboss.py
+	python addons/PhysiBoSS/setup_libmaboss.py
 else
-	python3 beta/setup_libmaboss.py
+	python3 addons/PhysiBoSS/setup_libmaboss.py
 endif
 
 maboss_network.o: ./addons/PhysiBoSS/src/maboss_network.cpp $(MaBoSS)