Merge pull request #6 from heberlr/development

Development

Author: heberlr

beta/generate_LHS.py

@@ -40,8 +40,9 @@ def ResamplingWithConstrain(samples1, samples2, b1, h1, b2, h2):
     #Write file with samples
     for sample_id in range(Samples_number):
         for replica_id in range(Replicas_number):
+            path = '/N/slate/hlimadar/melanoma_v3/'
             folder = 'output_S'+str("%06d"%sample_id)+'_R'+str("%02d"%replica_id)
-            file.write("folder"+" "+folder+"\n")
+            file.write("folder"+" "+path+folder+"\n")
             # Set of parameters
             for id_par in range(0, len(parameters)):
                 file.write(parameters[id_par]+" "+str(samples[sample_id,id_par])+"\n")
@@ -112,7 +113,7 @@ def plot_samples(filename, label1, label2, default_value1, default_value2):
 
 if __name__ == '__main__':
     parameters = np.array(["macrophage_max_recruitment_rate","macrophage_recruitment_min_signal","macrophage_recruitment_saturation_signal","DC_max_recruitment_rate","DC_recruitment_min_signal","DC_recruitment_saturation_signal","DC_leave_prob","TC_death_rate","T_Cell_Recruitment","DM_decay"])
-    default_value = np.array([4e-9, 0.1, 0.3, 2e-9, 0.1, 0.3, 3.3e-9, 1.4e-6, 1.1e-4, 3.5e-4])
+    default_value = np.array([4e-9, 0.1, 0.3, 2e-9, 0.1, 0.3, 2e-3, 1.4e-6, 1.1e-4, 3.5e-4])
     variation = 1.0
     constrain = ([1,2],[4,5]) # parameters[1] < parameters[2] and parameters[4] < parameters[5]
     file = "ParameterSamples.txt"

beta/model_scheme.png

@@ -914,21 +914,21 @@
 		<DC_recruitment_min_signal type="double" units="substrate/micron^3" description="min concentration to attract DC">0.1</DC_recruitment_min_signal> <!--0.1 debug -->
 		<DC_recruitment_saturation_signal type="double" units="substrate/micron^3" description="saturating concentration to attract DC">0.3</DC_recruitment_saturation_signal> <!-- 0.3 debug -->
 
-		<TC_death_rate description="TC death rate" type="double" units="cells/min">0.0000014</TC_death_rate>
+		<TC_death_rate description="TC death rate" type="double" units="cells/min">1.4e-6</TC_death_rate>
 		<max_activation_TC description="max activation TC" type="double" units="cells/min">0.003</max_activation_TC>
 		<half_max_activation_TC description="half max activation TC" type="double" units="cells">2000</half_max_activation_TC>
 		<max_clearance_TC description="max clearance TC" type="double" units="cells/min">0.0007</max_clearance_TC>
 		<half_max_clearance_TC description="half max clearance TC" type="double" units="cells">200</half_max_clearance_TC>
 		<TC_population_threshold description="TC population threshold" type="double" units="cells">10</TC_population_threshold>
-		<DM_decay description="DM decay rate" type="double" units="cells/min">0.00035</DM_decay>
+		<DM_decay description="DM decay rate" type="double" units="cells/min">3.5e-4</DM_decay>
 		<Th1_max_activation type="double" units="cells/min" description="Th1 max activation speed">0.0007</Th1_max_activation>
 		<Th1_damping type="double" units="cells/min" description="Th1 damping factor">0.000015</Th1_damping>
 		<Th1_decay type="double" units="cells/min" description="Th1 active decay rate">7e-7</Th1_decay>
 		<Th_base_decay type="double" units="cells/min" description="Th base dacay rates">0.0000156</Th_base_decay>
 		<Th2_self_feeback type="double" units="cells/min" description="Th2 max self feeback speed">0.000028</Th2_self_feeback>
 		<Th2_max_conversion type="double" units="cells/min" description="Th2 max conversion speed">0.000002</Th2_max_conversion>
 		<Th1_Th2_conversion_weight type="double" units="cells/min" description="Th1 to Th2 conversion weight">1</Th1_Th2_conversion_weight>
-		<T_Cell_Recruitment description="T cell recruitment rate to tissue" type="double" units="cells/min">0.00011</T_Cell_Recruitment>
+		<T_Cell_Recruitment description="T cell recruitment rate to tissue" type="double" units="cells/min">1.1e-4</T_Cell_Recruitment>
 
 		<div_initialization description="---Initialization Options--" type="divider" />
 		<cell_confluence_lung_cells description="cell confluence of normal cell in tissue" type="double" units="none">0.7</cell_confluence_lung_cells>
@@ -947,7 +947,7 @@
 		<DC_induced_CD8_proliferation description="DC induced CD8 proliferation rate" type="double" units="cells/min/micron^3">0.00208</DC_induced_CD8_proliferation>
 		<DC_induced_CD8_attachment description="DC induced CD8 attachement rate" type="double" units="cells/min/micron^3">0.6</DC_induced_CD8_attachment>
 
-		<DC_leave_prob description="probability of DC leaving to lymph node" type="double" units="cells/min">3.3e-6</DC_leave_prob>
+		<DC_leave_prob description="probability of DC leaving to lymph node" type="double" units="cells/min">2e-3</DC_leave_prob>
 
 		<epsilon_distance descriptions="Multiple of interaction distance for immune cells" type="double" units="dimensionless">1.75</epsilon_distance>
 

config/PhysiCell_settings.xml

@@ -11,16 +11,16 @@ extern LymphNode lympNode;
 
 void DC_history_model_setup( void )
 {
-		// set version
+	// set version
 	DC_history_info.name = "DC history";
 	DC_history_info.version = DC_history_version;
-		// set functions
+	// set functions
 	DC_history_info.main_function = DC_history_main_model;
 	DC_history_info.phenotype_function = NULL; // pushed into the "main" model
 	DC_history_info.mechanics_function = NULL;
-		// what microenvironment variables do you need
+	// what microenvironment variables do you need
 
-		// what cell variables and parameters do you need?
+	// what cell variables and parameters do you need?
 
 	// submodel_registry.register_model( receptor_dynamics_info );
 	DC_history_info.register_model();
@@ -31,12 +31,11 @@ void DC_history_model_setup( void )
 void DC_history_model( Cell* pCell, Phenotype& phenotype, double dt )
 {
 	static int DC_type = get_cell_definition( "DC" ).type;
-
 	// bookkeeping -- find microenvironment variables we need
 
 	// bookkeeping -- find custom data we need
 	static double DCprob = parameters.doubles( "DC_leave_prob" );
-	// extern double DCAMOUNT; //declare existance of counter
+
 	// do nothing if dead
 	if( phenotype.death.dead == true )
 	{ return; }
@@ -62,7 +61,6 @@ void DC_history_model( Cell* pCell, Phenotype& phenotype, double dt )
 
 void DC_history_main_model( double dt )
 {
-	// extern double DCAMOUNT;
 	extern std::vector<int>history;
 	lympNode.DCAMOUNT=0;
 
@@ -76,8 +74,5 @@ void DC_history_main_model( double dt )
 	std::rotate(history.rbegin(),history.rbegin()+1,history.rend());
 	history.front() = lympNode.DCAMOUNT;
 
-	/* std::copy(history.begin(), history.end(), std::ostream_iterator<int>(std::cout, " "));
-	std::cout << std::endl;
-	 */
 	return;
 }

custom_modules/DC_history.cpp

@@ -13,10 +13,8 @@ using namespace PhysiCell;
 extern Submodel_Information DC_history_info;
 
 void DC_history_model_setup( void );
-
 // don't put into individual cell models
 void DC_history_model( Cell* pCell, Phenotype& phenotype, double dt );
-
 // this needs to be done on faster time scale;
 void DC_history_main_model( double dt );