Merge pull request #85 from sysbio-curie/update/physiboss

Updating PhysiBoSS to 2.1.0

.github/workflows/test-macosx.yml

@@ -5,9 +5,9 @@ on:
   pull_request:
 
 jobs:
-  build:
+  build_virus_macrophage:
 
-    runs-on: macos-latest
+    runs-on: macos-11
 
     steps:
     - uses: actions/checkout@v2
@@ -23,13 +23,23 @@ jobs:
     - name: Run Virus Macrophage cell lines project
       run: |
         ./virus-sample
-        
+
+
+  build_physiboss_cell_lines:
+
+    runs-on: macos-11
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run : brew install gcc@11
+
     - name: Build PhysiBoSS cell lines project
       run: |
-        make reset
         make physiboss-cell-lines-sample
         make clean
-        make PHYSICELL_CPP=g++-10
+        make PHYSICELL_CPP=g++-11
         
     - name: Run PhysiBoSS cell lines project
       run: |

addons/PhysiBoSS/src/maboss_intracellular.cpp

@@ -23,6 +23,7 @@ MaBoSSIntracellular::MaBoSSIntracellular(MaBoSSIntracellular* copy)
 	discrete_time = copy->discrete_time;
 	time_tick = copy->time_tick;
 	scaling = copy->scaling;
+	time_stochasticity = copy->time_stochasticity;
 	initial_values = copy->initial_values;
 	mutations = copy->mutations;
 	parameters = copy->parameters;
@@ -35,6 +36,7 @@ MaBoSSIntracellular::MaBoSSIntracellular(MaBoSSIntracellular* copy)
 		maboss.set_update_time_step(copy->time_step);
 		maboss.set_discrete_time(copy->discrete_time, copy->time_tick);
 		maboss.set_scaling(copy->scaling);
+		maboss.set_time_stochasticity(copy->time_stochasticity);
 		maboss.restart_node_values();
 		//maboss.set_state(copy->maboss.get_maboss_state());
 		//std::cout << get_state();
@@ -124,6 +126,13 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
 		scaling = PhysiCell::xml_get_my_double_value( node_scaling );
 		maboss.set_scaling(scaling);
 	}
+
+	pugi::xml_node node_time_stochasticity = node.child( "time_stochasticity" );
+	if( node_time_stochasticity )
+	{
+		time_stochasticity = PhysiCell::xml_get_my_double_value( node_time_stochasticity );
+		maboss.set_time_stochasticity(time_stochasticity);
+	}
 }
 
 MaBoSSIntracellular* getMaBoSSModel(PhysiCell::Phenotype& phenotype) {

addons/PhysiBoSS/src/maboss_intracellular.h

@@ -9,7 +9,7 @@
 #include "../../../modules/PhysiCell_pugixml.h"
 #include "maboss_network.h"
 
-static std::string PhysiBoSS_Version = "2.0.0"; 
+static std::string PhysiBoSS_Version = "2.1.0"; 
 
 class MaBoSSIntracellular : public PhysiCell::Intracellular {
  private:
@@ -24,7 +24,8 @@ class MaBoSSIntracellular : public PhysiCell::Intracellular {
 	bool discrete_time = false;
 	double time_tick = 0.5;
 	double scaling = 1.0;
-
+	double time_stochasticity = 0.0;
+
 	std::map<std::string, double> initial_values;
 	std::map<std::string, double> mutations;
 	std::map<std::string, double> parameters;

addons/PhysiBoSS/src/maboss_network.cpp

@@ -14,17 +14,23 @@ void MaBoSSNetwork::init_maboss( std::string networkFile, std::string configFile
 	if (this->engine != NULL) {
 		delete this->engine;
 	}
-	// Initialize MaBoSS Objects for a model
-	this->network = new Network();
-	this->network->parse(networkFile.c_str());
-
-	this->config = new RunConfig();
-	this->config->parse(this->network, configFile.c_str());
+
+	try{
+		// Initialize MaBoSS Objects for a model
+		this->network = new Network();
+		this->network->parse(networkFile.c_str());
 
-	IStateGroup::checkAndComplete(this->network);
+		this->config = new RunConfig();
+		this->config->parse(this->network, configFile.c_str());
 
-	engine = new StochasticSimulationEngine(this->network, this->config, PhysiCell::UniformInt());
+		IStateGroup::checkAndComplete(this->network);
 
+		engine = new StochasticSimulationEngine(this->network, this->config, PhysiCell::UniformInt());
+
+	} catch (BNException e) {
+		std::cerr << "MaBoSS ERROR : " << e.getMessage() << std::endl;
+		exit(1);
+	}
 	this->update_time_step = this->config->getMaxTime();
 
 	// Building map of nodes for fast later access 
@@ -47,7 +53,12 @@ void MaBoSSNetwork::init_maboss( std::string networkFile, std::string configFile
 void MaBoSSNetwork::mutate(std::map<std::string, double> mutations) 
 {
 	for (auto mutation : mutations) {
-		nodesByName[mutation.first]->mutate(mutation.second);
+		if (nodesByName.find(mutation.first) != nodesByName.end())
+			nodesByName[mutation.first]->mutate(mutation.second);
+		else{
+			std::cerr << "Mutation set for unknown node : can't find node " << mutation.first << std::endl;
+			exit(1);
+		}
 	}
 }
 
@@ -77,9 +88,13 @@ void MaBoSSNetwork::restart_node_values()
 	this->network->initStates(state, engine->random_generator);
 
 	for (auto initial_value : initial_values) {
-		state.setNodeState(nodesByName[initial_value.first], PhysiCell::UniformRandom() < initial_value.second);
+		if (nodesByName.find(initial_value.first) != nodesByName.end()) {
+			state.setNodeState(nodesByName[initial_value.first], PhysiCell::UniformRandom() < initial_value.second);	
+		} else {
+			std::cerr << "Initial value set for unknown node : can't find node " << initial_value.first << std::endl;
+			exit(1);
+		}
 	}
-
 	this->set_time_to_update();
 }
 

addons/PhysiBoSS/src/maboss_network.h

@@ -35,8 +35,12 @@ class MaBoSSNetwork
 		/** \brief Real time to update, after applying noise */
 		double time_to_update;
 
+		/** \brief Scaling coefficient for time */
 		double scaling = 1.0;
 
+		/** \brief Noise coefficient for time to update */
+		double time_stochasticity = 0;
+
 		/** \brief Initial value probabilities, by node */
 		std::map< std::string, double > initial_values;
 
@@ -46,7 +50,7 @@ class MaBoSSNetwork
 		std::map< std::string, Node*> nodesByName;
 		std::map< std::string, const Symbol*> parametersByName;
 
-		inline void set_time_to_update(){this->time_to_update = this->get_update_time_step();}
+		inline void set_time_to_update(){this->time_to_update = ( 1 + (PhysiCell::UniformRandom()*2-1)*time_stochasticity ) * this->get_update_time_step();}
 
 
 	public:
@@ -130,6 +134,8 @@ class MaBoSSNetwork
 
 		inline void set_scaling(double scaling) { this->scaling = scaling; }
 
+		inline void set_time_stochasticity(double t_stochasticity) { this->time_stochasticity = t_stochasticity; }
+
 		/** 
 		 * \brief Print current state of all the nodes of the network 
 		 * \param node_values Boolean vector mapping a boolean network

beta/setup_libmaboss.py

@@ -25,15 +25,15 @@
 
     if os_type.lower() == 'darwin':
         mb_file = "libMaBoSS-osx64.tar.gz"
-    elif os_type.lower().startswith("win"):
+    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"
     elif os_type.lower().startswith("linux"):
         mb_file = "libMaBoSS-linux64.tar.gz"
     else:
         print("Your operating system seems to be unsupported. Please submit a ticket at https://sourceforge.net/p/physicell/tickets/ ")
         sys.exit(1)
 
-    url = "http://maboss.curie.fr/pub/" + mb_file
+    url = "https://github.com/sysbio-curie/MaBoSS-env-2.0/releases/download/v2.4.1/" + mb_file
 
     fname = mb_file
 
@@ -83,6 +83,7 @@ def download_cb(blocknum, blocksize, totalsize):
         tar = tarfile.open(mb_file)
         tar.extractall()
         tar.close()
+        os.remove(mb_file)
     except:
         print('error untarring the file')
         exit(1)

sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile

@@ -176,6 +176,9 @@ PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
 
 # user-defined PhysiCell modules
 
+Compile_MaBoSS: MaBoSS
+	cd ./addons/PhysiBoSS/MaBoSS-env-2.0/engine/src;make install_alib;make clean; cd ../../../../..
+
 MaBoSS: 
 ifeq ($(OS), Windows_NT)
 	python beta/setup_libmaboss.py
@@ -209,7 +212,7 @@ reset:
 MaBoSS-clean:
 	rm -fr addons/PhysiBoSS/MaBoSS-env-2.0
 
-clean: MaBoSS-clean
+clean:
 	rm -f *.o
 	rm -f $(PROGRAM_NAME)*
 

sample_projects_intracellular/boolean/physiboss_cell_lines/config/PhysiCell_settings.xml

@@ -147,9 +147,9 @@
 			<phenotype>
 				<cycle code="2" name="live">  
 					<!-- using higher than normal significant digits to match divisions in default code -->
-					<transition_rates units="1/min"> 
+					<phase_transition_rates units="1/min"> 
 						<rate start_index="0" end_index="0" fixed_duration="true">0.0</rate>
-					</transition_rates>
+					</phase_transition_rates>
 				</cycle>
 
 				<death>