- update generateLHS.py and configFile.xml

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"

config/PhysiCell_settings.xml

@@ -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>