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Copy pathICD_ExtendDy.cfg
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ICD_ExtendDy.cfg
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$nb_mutable = 0;
$rate_ATP_i = 0.0;
$rate_CALR_i = 0.0;
$rate_HMGB1_i = 0.0;
$rate_ANXA1_i = 0.0;
$rate_IFN1_i = 0.0;
$rate_CXCL10_i = 0.0;
$rate_CD80_i = 0.0;
$rate_MHC_II_i = 0.0;
$rate_IL1B_i = 0.0;
$rate_IL2_i = 0.0;
$rate_IL4_i = 0.0;
$rate_IL6_i = 0.0;
$rate_IL12_i = 0.0;
$rate_IL17_i = 0.0;
$rate_IFNg_i = 0.0;
$rate_TGFb_i = 0.0;
$rate_MHC_I_i = 0.0;
$rate_perforin = 0.0;
$pop_Tumor = 0.0;
$clonal_exp_rate = 0.05;
$growth_tumor = 0.00001;
$ChemoEffect = 0.00002;
$PerforinDeath = 1/240; // speed of death for CTL with perforin
$PerforinRecycled = 6; // decay factor of perforin according to tumor cells
$degChemo = 1/(24*3);
$effectChemo = 1;
$u_Tumor = 50;
$d_Tumor = 50;
$u_DC = 50;
$d_DC = 50;
$u_aDC = 50;
$d_aDC = 50;
$u_cd4 = 50;
$d_cd4 = 50;
$u_cd8 = 50;
$d_cd8 = 50;
$u_Th1 = 50;
$d_Th1 = 50; //not used
$u_Th2 = 50;
$d_Th2 = 50; //not used
$u_Th17 = 50;
$d_Th17 = 50; //not used
$u_Treg = 50;
$d_Treg = 50; //not used
$u_preCTL = 50;
$d_preCTL = 50;
$u_CTL = 5/12;
$d_CTL = 50;
$u_CD28 = $rate_CD80_i/6;
$d_CD28 = 50;
$u_CXCR3 = $rate_CXCL10_i/6;
$d_CXCR3 = 50; //Not used
$u_FPR1 = $rate_ANXA1_i/6;
$d_FPR1 = 50;
$u_IFN1_rec = $rate_IFN1_i/6;
// $d_IFN1_rec = 50;
$u_IFNg_rec = $rate_IFNg_i/6;
$d_IFNg_rec = 50; //Why ?
$u_IL12_rec = $rate_IL12_i/6;
$d_IL12_rec = 50; // Why ?
$u_IL17_rec = $rate_IL17_i/6;
$d_IL17_rec = 50; //Why ?
$u_IL1B_rec = $rate_IL1B_i/6;
// $d_IL1B_rec = 50;
$u_IL2_rec = $rate_IL2_i/6;
// $d_IL2_rec = 50;
$u_IL4_rec = $rate_IL4_i/6;
$d_IL4_rec = 50; // Why ?
$u_IL6_rec = $rate_IL6_i/6;
$d_IL6_rec = 50; //Why ?
$u_LRP1 = $rate_CALR_i/6;
$d_LRP1 = 50;
$u_P2X7R = $rate_ATP_i/6;
$d_P2X7R = 50;
$u_P2Y2R = $rate_ATP_i/6;
$d_P2Y2R = 50;
$u_TCR_I = $rate_MHC_I_i/6;
$d_TCR_I = 50;
$u_TCR_II = $rate_MHC_II_i/6;
$d_TCR_II = 50;
$u_TGFb_rec = $rate_TGFb_i/6;
$d_TGFb_rec = 50; //Why ?
$u_TLR4 = $rate_HMGB1_i/4;
$d_TLR4 = 50;
$u_ANXA1_o = 1/6 ; //why ? ANXA1 is not a receptor
$d_ANXA1_o = 50; //why ?
$u_ATP_o = 1/6;
$d_ATP_o = 50;
$u_CALR_o = (1/6);
$d_CALR_o = 50;
$u_HMGB1_o = 1/6;
$d_HMGB1_o = 50;
$u_IFN1_o = 1/6;
$d_IFN1_o = 50;
$u_CD80_o = 1/6;
$d_CD80_o = 50;
$u_CXCL10_o = 1/6;
$d_CXCL10_o = 50;
$u_MHC_I_o = 1/6;
$d_MHC_I_o = 50;
$u_MHC_II_o = 1/6;
$d_MHC_II_o = 50;
$u_IL1B_o = 1/6;
$d_IL1B_o = 50;
$u_IL2_o = 1/6;
$d_IL2_o = 50;
$u_IL4_o = 1/6;
$d_IL4_o = 50;
$u_IL6_o = 1/6;
$d_IL6_o = 50;
$u_IL12_o = 1/6;
$d_IL12_o = 50;
$u_IL17_o = 1/6;
$d_IL17_o = 50;
$u_IFNg_o = 1/6;
$d_IFNg_o = 50;
$u_TGFb_o = 1/6;
$d_TGFb_o = 50;
$u_Perforin_o = 1/6;
$u_cd4_Act = 50;
// $d_proliferation = 50;
$aggressivity = 1.0;
[aDC].istate = 1.0[0] , 0.0[1];
[cd4_Act].istate = 1.0[0] , 0.0[1];
[P2Y2R].istate = 1.0[0] , 0.0[1];
[P2X7R].istate = 1.0[0] , 0.0[1];
[FPR1].istate = 1.0[0] , 0.0[1];
[LRP1].istate = 1.0[0] , 0.0[1];
[TLR4].istate = 1.0[0] , 0.0[1];
[IFN1_rec].istate = 1.0[0] , 0.0[1];
[IL1B_rec].istate = 1.0[0] , 0.0[1];
[IL2_rec].istate = 1.0[0] , 0.0[1];
[IL4_rec].istate = 1.0[0] , 0.0[1];
[IL6_rec].istate = 1.0[0] , 0.0[1];
[IL12_rec].istate = 1.0[0] , 0.0[1];
[IFNg_rec].istate = 1.0[0] , 0.0[1];
[IL17_rec].istate = 1.0[0] , 0.0[1];
[TGFb_rec].istate = 1.0[0] , 0.0[1];
[CXCR3].istate = 1.0[0] , 0.0[1];
[CD28].istate = 1.0[0] , 0.0[1];
[TCR_I].istate = 1.0[0] , 0.0[1];
[TCR_II].istate = 1.0[0] , 0.0[1];
[Th1].istate = 1.0[0] , 0.0[1];
[Th2].istate = 1.0[0] , 0.0[1];
[Th17].istate = 1.0[0] , 0.0[1];
[Treg].istate = 1.0[0] , 0.0[1];
[CALR_o].istate = 1.0[0] , 0.0[1];
[ATP_o].istate = 1.0[0] , 0.0[1];
[ANXA1_o].istate = 1.0[0] , 0.0[1];
[HMGB1_o].istate = 1.0[0] , 0.0[1];
[CXCL10_o].istate = 1.0[0] , 0.0[1];
[CD80_o].istate = 1.0[0] , 0.0[1];
[MHC_I_o].istate = 1.0[0] , 0.0[1];
[MHC_II_o].istate = 1.0[0] , 0.0[1];
[IL1B_o].istate = 0.5[0] , 0.5[1];
[IL2_o].istate = 1.0[0] , 0.0[1];
[IL4_o].istate = 1.0[0] , 0.0[1];
[IL6_o].istate = 1.0[0] , 0.0[1];
[IL12_o].istate = 1.0[0] , 0.0[1];
[IL17_o].istate = 1.0[0] , 0.0[1];
[IFNg_o].istate = 1.0[0] , 0.0[1];
[TGFb_o].istate = 1.0[0] , 0.0[1];
[Perforin_o].istate = 1.0[0] , 0.0[1];
[preCTL].istate = 1.0[0] , 0.0[1];
[CTL].istate = 1.0[0] , 0.0[1];
[IFN1_o].istate = 1.0[0] , 0.0[1];
[Division].istate = 1.0[0] , 0.0[1];
[Death].istate = 1.0[0] , 0.0[1];
[DyingTumor].istate = 1.0[0] , 0.0[1];
$InitDC = 0.1;
$InitCD4 = 0.05;
$InitCD8 = 0.05;
[Tumor, ChemoT , DC, cd4, cd8].istate =(1-$InitDC-$InitCD4-$InitCD8)[1,1,0,0,0],$InitDC[0,0,1,0,0],$InitCD4[0,0,0,1,0],$InitCD8[0,0,0,0,1];
time_tick = 0.02;
max_time = 1.0;
sample_count = 130000;
discrete_time = 0.0;
use_physrandgen = 0.0;
seed_pseudorandom = 100.0;
display_traj = 0.0;
statdist_traj_count = 0.0;
statdist_cluster_threshold = 1.0;
thread_count = 4;
statdist_similarity_cache_max_size = 20000.0;
Tumor.is_internal = False;
DC.is_internal = False;
cd4.is_internal = False;
cd8.is_internal = False;
aDC.is_internal = False;
cd4_Act.is_internal = False;
P2Y2R.is_internal = False;
P2X7R.is_internal = False;
FPR1.is_internal = False;
LRP1.is_internal = False;
TLR4.is_internal = False;
IFN1_rec.is_internal = False;
IL1B_rec.is_internal = False;
IL2_rec.is_internal = False;
IL4_rec.is_internal = False;
IL6_rec.is_internal = False;
IL12_rec.is_internal = False;
IFNg_rec.is_internal = False;
IL17_rec.is_internal = False;
TGFb_rec.is_internal = False;
CXCR3.is_internal = False;
CD28.is_internal = False;
TCR_I.is_internal = False;
TCR_II.is_internal = False;
Th1.is_internal = False;
Th2.is_internal = False;
Th17.is_internal = False;
Treg.is_internal = False;
CALR_o.is_internal = False;
ATP_o.is_internal = False;
ANXA1_o.is_internal = False;
HMGB1_o.is_internal = False;
CXCL10_o.is_internal = False;
CD80_o.is_internal = False;
MHC_I_o.is_internal = False;
MHC_II_o.is_internal = False;
IL1B_o.is_internal = False;
IL2_o.is_internal = False;
IL4_o.is_internal = False;
IL6_o.is_internal = False;
IL12_o.is_internal = False;
IL17_o.is_internal = False;
IFNg_o.is_internal = False;
TGFb_o.is_internal = False;
Perforin_o.is_internal = False;
preCTL.is_internal = False;
CTL.is_internal = False;
IFN1_o.is_internal = False;
Division.is_internal = False;
Death.is_internal = False;