stuff

config/PhysiCell_settings.xml

@@ -14,7 +14,7 @@
     </domain>
 
     <overall>
-        <max_time units="min">720</max_time>
+        <max_time units="min">1440</max_time>
         <time_units>min</time_units>
         <space_units>micron</space_units>
         <dt_diffusion units="min">0.01</dt_diffusion>

config/cell_rules.csv

@@ -6,4 +6,5 @@ tumor cell,damage,increases,apoptosis,9e9,30,100,0
 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,0,100,10,0
+tumor cell,time,decreases,damage repair rate,0,15,10,0
+fast T cell,damage delivered,increases,transformation to exhausted T cell,...

config/cells.csv

@@ -17,4 +17,13 @@ x,y,z,type,apoptosis,necrosis,migration speed,phagocytose apoptotic cell,phagocy
 -100,115,0,fast T cell,skip,skip,0,0.00000,0.00,0.025,5,1,skip,skip
 -115,100,0,fast T cell,skip,skip,0,0.00000,0.00,0.025,5,1,skip,skip
 -85,100,0,fast T cell,skip,skip,0,0.00000,0.00,0.025,5,1,skip,skip
-0,-100,0,tumor cell,9e9,0,0,0,0,skip,skip,skip,1,0.05
+0,-100,0,tumor cell,9e9,0,0,0,0,skip,skip,skip,1,0.05
+-100,-100,0,slow T cell,skip,skip,0,0.00000,0.00,0.025,50,0.1,skip,skip
+-115,-100,0,tumor cell,0,0,0,0,0,skip,skip,skip,skip,skip
+-107.5,-113,0,tumor cell,0,0,0,0,0,skip,skip,skip,skip,skip
+-107.5,-87,0,tumor cell,0,0,0,0,0,skip,skip,skip,skip,skip
+-100,-115,0,tumor cell,0,0,0,0,0,skip,skip,skip,skip,skip
+-100,-85,0,tumor cell,0,0,0,0,0,skip,skip,skip,skip,skip
+-92.5,-113,0,tumor cell,0,0,0,0,0,skip,skip,skip,skip,skip
+-92.5,-87,0,tumor cell,0,0,0,0,0,skip,skip,skip,skip,skip
+-85,-100,0,tumor cell,0,0,0,0,0,skip,skip,skip,skip,skip

core/PhysiCell_standard_models.cpp

@@ -1220,7 +1220,7 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double
 			{
 				pCell->ingest_cell(pTarget); 
 				phagocytosed = true; // was missing : bugfix 
-				std::cout << "chomp apop " << PhysiCell_globals.current_time << " " << probability <<  std::endl;
+				// std::cout << "chomp apop " << PhysiCell_globals.current_time << " " << probability <<  std::endl;
 			} 
 
 			// necrotic phagocytosis 
@@ -1229,7 +1229,7 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double
 			{
 				pCell->ingest_cell(pTarget); 
 				phagocytosed = true; // was missing : bugfix 
-				std::cout << "chomp necro " << PhysiCell_globals.current_time << " " << probability <<  std::endl;
+				// std::cout << "chomp necro " << PhysiCell_globals.current_time << " " << probability <<  std::endl;
 			} 
 
 			// other dead phagocytosis 
@@ -1238,7 +1238,7 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double
 			{
 				pCell->ingest_cell(pTarget); 
 				phagocytosed = true; // was missing : bugfix 
-				std::cout << "chomp other " << PhysiCell_globals.current_time << " " << probability <<  std::endl;
+				// std::cout << "chomp other " << PhysiCell_globals.current_time << " " << probability <<  std::endl;
 			} 
 		}
 		else
@@ -1266,13 +1266,13 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double
 				if( UniformRandom() < probability ) 
 				{				
 					pCell->phenotype.cell_interactions.pAttackTarget = pTarget; 
-					std::cout << "*********   *********  ********  start atack **** " << PhysiCell_globals.current_time << std::endl; 
 					attacked = true; 
-
+					/*					
+					std::cout << "*********   *********  ********  start atack **** " << PhysiCell_globals.current_time << std::endl; 
 					std::cout 
 					<< "attack duration: " << pCell->phenotype.cell_interactions.attack_duration << " "  
 					<< "attack damage rate: " << pCell->phenotype.cell_interactions.attack_damage_rate <<  std::endl; 
-
+					*/
 					// spring-link these cells 
 					attach_cells_as_spring(pCell,pTarget); 
 				} 
@@ -1332,12 +1332,14 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double
 
 			if( UniformRandom() < probability || pTarget->phenotype.death.dead ) 
 			{
+				/*
 				std::cout << "*********   *********  ********  attack done **** " << PhysiCell_globals.current_time << " " 
 				<< probability << " "
 				<< "attack time: " << pTarget->state.total_attack_time << " " 		
 				<< "damage: " << pTarget->phenotype.cell_integrity.damage <<  " " 		
 				<< "dead? " << (int) pTarget->phenotype.death.dead << " " 
 				<< "damage delivered: " << pCell->phenotype.cell_interactions.total_damage_delivered << std::endl; 
+				*/
 
 				detach_cells_as_spring(pCell,pTarget); 
 

custom_modules/custom.cpp

@@ -216,28 +216,32 @@ std::vector<std::string> my_coloring_function( Cell* pCell )
 			out[0] = blah; 
 			out[2] = blah; 
 			out[3] = blah; 
-
-			if( damage > 30 )
-			{
-				std::cout << "\t" << damage << " " << get_single_behavior( pCell , "apoptosis" ) << std::endl; 
-			}
 		}
 		return out; 
 	}
 
 	if( pCell->type_name == "macrophage" ) 
-	{ out[0] = "maroon"; out[2] = "maroon" ; out[3] = "maroon"; return out; }
+	{ out[0] = "orange"; out[2] = "orange" ; out[3] = "orange"; return out; }
 
 
 	if( pCell->type_name == "fast T cell" ) 
 	{
-		std::string blah = "grey"; 
+		std::string blah = "rgb(255,164,164)";
 		if( get_single_signal(pCell, "attacking") > 0.5 )
-		{ blah = "red"; }
+		{ blah = "rgb(196,0,0)"; }
 		out[0] = blah; out[2] = blah; out[3] = blah; 
 		return out; 
 	}
 
+	if( pCell->type_name == "slow T cell" ) 
+	{
+		std::string blah = "rgb(164,255,164)";
+		if( get_single_signal(pCell, "attacking") > 0.5 )
+		{ blah = "rgb(0,128,0)"; }
+		out[0] = blah; out[2] = blah; out[3] = blah; 
+		return out; 
+	}	
+
 
 	return out; 
 }