Difference between revisions of "Solver Script"

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(Script)
(Script)
 
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= Script =
 
= Script =
 
{| class="wikitable"
 
! % Model
 
  script
 
 
 
  function dydt = Model(t, y)
 
  %% Units
 
  of the model
 
 
 
  % time =
 
  min
 
  %
 
  quantity = mmol
 
  % volume
 
  = L
 
 
 
  %%
 
  Section 1: Parameters (Fixed)
 
 
 
  global LAT KfR1 c c2 AADT AAHL
 
  ABCdG TEMP R ATP ADP c3 c4 COX2DT COX2HL
 
 
 
  KfR1= 0.1;
 
  LAT=0;
 
  AAHL=420; %AA Half
 
  life
 
  AADT=420; %AA
 
  Doubling Time
 
  ABCdG=-50000; %Gibbs
 
  free energy of ABC transporter
 
  TEMP=310; %Kelvin
 
  R=8.314; 
 
  ATP=0.00274;
 
  ADP=0.00134;
 
  COX2DT =180; 
 
  COX2HL=1;
 
 
 
  %%
 
  Section 2: Metabolite number
 
 
 
  % BAA =
 
  y(1)
 
  % AA =
 
  y(2)
 
  % PGH2 =
 
  y(3)
 
  % PGF2A
 
  = y(4)
 
  % TXA2 =
 
  y(5)
 
  % PGI2 =
 
  y(6)
 
  % TXB2 =
 
  y(7)
 
  %
 
  6-Keto-PGF1A = y(8)
 
  % PGJ2 =
 
  y(9)
 
  % PGD2 =
 
  y(10)
 
  %
 
  15-DEOXY-PGJ2 = y(11)
 
  % PGE2 =
 
  y(12)
 
  %
 
  5-HPETE = y(13)
 
  % 5-HETE
 
  =y(14)
 
  % LTA4 =
 
  y(15)
 
  %
 
  5-OXO-ETE = y(16)
 
  % LTB4 =
 
  y(17)
 
  % LTC4 =
 
  y(18)
 
  %
 
  15-HPETE = y(19)
 
  %
 
  15-HETE = y(20)
 
  %
 
  12-HPETE = y(21)
 
  %
 
  12-HETE = y(22)
 
  %
 
  exPGF2A = y(23)
 
  % exTXB2
 
  = y(24)
 
  %
 
  ex6-KETO-PGF1A = y(25)
 
  % exPGE2
 
  = y(26)
 
  %
 
  ex15-DEOXY-PGJ2 = y(27)
 
  %
 
  ex5-OXO-ETE = y(28)
 
  %
 
  ex15-HETE =y(29)
 
  % exLTB4
 
  = y(30)
 
  % exLTC4
 
  = y(31)
 
  %
 
  exHETE12 = y(32)
 
  % exTXA2
 
  = y(33)
 
  % exPGI2
 
  = y(34)
 
  % exPGH2
 
  = y(35)
 
  % exPGD2
 
  = y(36)
 
  % exPGJ2
 
  = y(37)
 
  %
 
  ex12-HPETE = y(38)
 
  %
 
  ex15-HPETE = y(39)
 
  %
 
  ex5-HPETE = y(40)
 
  %
 
  ex5-HETE = y(41)
 
  % exLTA4
 
  = y(42)
 
  % exAA =
 
  y(43)
 
  %
 
  15-KETO-PGE2 = y(44)
 
  %
 
  ex15-KETO-PGE2 = y(45)
 
  %
 
  13,14-DIHYDRO-15-KETO-PGE2 = y(46)
 
  %
 
  ex13,14-DIHYDRO-15-KETO-PGE2 = y(47)
 
  % COX2 =
 
  y(48)
 
  %
 
  Mischellanous species = y(49)
 
 
 
  %%
 
  Section 3: Assignment of parameters as global values
 
 
 
  %INTRACELLULAR
 
  REACTION Parameters
 
  global KmsR1 KmpR1 PLA2Kcat
 
  KeqR1 %R1 Parameters
 
  global KmsR2 KmpR2 COX2Kcat
 
  KeqR2 %R2 Parameters
 
  global KmsR3 KmpR3 PGFSKcat
 
  KeqR3 %R3 Parameters
 
  global KmsR4 KmpR4 TXASKcat
 
  KeqR4 %R4 Parameters
 
  global KmsR5 KmpR5 PGISKcat
 
  KeqR5 %R5 Parameters
 
  global KfR6 KrR6 %R6
 
  Parameters
 
  global KfR7 KrR7 %R7
 
  Parameters
 
  global KfR8 KrR8 %R8
 
  Parameters
 
  global KfR9 KrR9 %R9
 
  Parameters
 
  global KmsR10 KmpR10 PGESKcat
 
  KeqR10 %R10 Parameters
 
  global KmsR11 KmpR11 LOX5Kcat
 
  KeqR11 %R11 Parameters
 
  global KmsR12 KmpR12
 
  PHGPxKcatR12 KeqR12 %R12 Parameters
 
  global KmsR13 KmpR13
 
  LOX5FLAPKcat KeqR13 %R13 Parameters
 
  global KmsR14 KmpR14 HEDH5Kcat
 
  KeqR14 %R14 Parameters
 
  global KmsR15 KmpR15 LTA4HKcat
 
  KeqR15 %R15 Parameters
 
  global KmsR16 KmpR16 LTC4SKcat
 
  KeqR16 %R16 Parameters
 
  global KmsR17 KmpR17 LOX15Kcat
 
  KeqR17 %R17 Parameters
 
  global KmsR19 KmpR19 LOX12Kcat
 
  KeqR19 %R19 Parameters
 
  global KmsR21 KmpR21 PGDSKcat
 
  KeqR21 %R21 Parameters
 
  global KmsR65 KmpR65 COX1Kcat
 
  KeqR65 %R65 Parameters
 
  global KmsR66 KmpR66 PGDH15Kcat
 
  KeqR66 %R66 Parameters
 
  global KmsR69 KmpR69 PTGR2Kcat
 
  KeqR69 %R69 Parameters
 
  global KmsR100 KmpR100 LATKcat
 
  KeqR100 %R100 Parameters
 
 
 
  % Other
 
  reaction parameters
 
  global  ABCKcat   
 
  ABCKmR22    ABCKmR23    ABCKmR24    ABCKmR25    ABCKmR26    ABCKmR27    ABCKmR28    ABCKmR29    ABCKmR30    ABCKmR31    ABCKmR32    ABCKmR33    ABCKmR34    ABCKmR35    ABCKmR36    ABCKmR37    ABCKmR38    ABCKmR39    ABCKmR40    ABCKmR41    ABCKmR42    ABCKmR67    ABCKmR70    PGTKcat    PGTKmR101  PGTKmR102 
 
  PGTKmR103  PGTKmR104  PGTKmR105 
 
  PGTKmR106  PGTKmR107  PGTKmR108 
 
  PGTKmR109  PGTKmR110  PGTKmR111 
 
  KfR44 KfR45 KfR46 KfR47 KfR48 KfR49 KfR50 KfR51 KfR52 KfR53 KfR54
 
  KfR55 KfR56 KfR57 KfR58 KfR59 KfR60 KfR61 KfR62 KfR63 KfR64 KfR68 KfR71  ABCVmax ABCKeq  PGDH15 ABC COX1    HEDH5 
 
  LOX12  LOX15  LOX5 
 
  LTA4H  LTC4S  PGDS 
 
  PGES    PGFS    PGIS 
 
  PGT PHGPX  PLA2    PTGR2 
 
  TXAS
 
 
 
 
 
  %%
 
  Section 4: Reaction rate laws
 
 
 
  %R1(PLA2)
 
  - Turned off
 
  %BAA
 
  y(1) <-> AA y(2)
 
  %
 
  r1=(PLA2Kcat*PLA2*(y(1)-(y(2)/KeqR1)))/((KmsR1*(1+(y(2)/KmpR1)))+y(1));
 
  r1=(KfR1*y(1));
 
 
 
  %R2(COX2)y(48)
 
  %AA
 
  y(2)  <-> PGH2 y(3)
 
  r2=(COX2Kcat*y(48)*(y(2)-(y(3)/KeqR2)))/((KmsR2*(1+(y(3)/KmpR2)))+y(2));
 
 
 
  %R3(PGFS)
 
  % PGH2
 
  y(3) <-> PGF2A y(4)
 
  r3= (PGFSKcat*PGFS*(y(3)
 
  -(y(4)/KeqR3)))/((KmsR3*(1+(y(4)/KmpR3)))+y(3));
 
 
 
  %R4(TXAS)
 
  % PGH2
 
  y(3)<-> TXA2 y(5)
 
  r4= (TXASKcat*TXAS*(y(3)
 
  -(y(5)/KeqR4)))/((KmsR4*(1+(y(5)/KmpR4)))+y(3));
 
 
 
  %R5(PGIS)
 
  % PGH2
 
  y(3)<-> PGI2 y(6)
 
  r5= (PGISKcat*PGIS*(y(3) -(y(6)/KeqR5)))/((KmsR5*(1+(y(6)/KmpR5)))+y(3));
 
 
 
  % R6
 
  % TXA2
 
  y(5) <-> TXB2 y(7)
 
  r6=(KfR6*y(5))-(KrR6*y(7));
 
 
 
  % R7
 
  % PGI2
 
  y(6)<-> 6-Keto-PGF1A y(8)
 
  r7=
 
  (KfR7*y(6))-(KrR7*y(8));
 
 
 
  % R8
 
  % PGD2
 
  y(10) <-> PGJ2 y(9)
 
  r8=
 
  (KfR8*y(10))-(KrR8*y(9));
 
 
 
  % R9
 
  % PGJ2  y(9)<-> 15-DEOXY-PGJ2 y(11)
 
  r9=
 
  (KfR9*y(9))-(KrR9*y(11));
 
 
 
  %R10
 
  (PGES)
 
  % PGH2
 
  y(3)<-> PGE2 y(12)
 
  r10=
 
  (PGESKcat*PGES*(y(3)-(y(12)/KeqR10)))/((KmsR10*(1+(y(12)/KmpR10)))+y(3));
 
 
 
  % R11
 
  (LOX5)
 
  % AA
 
  y(2)<-> 5-HPETE y(13)
 
  r11= (LOX5Kcat*LOX5*(y(2)
 
  -(y(13)/KeqR11)))/((KmsR11*(1+(y(13)/KmpR11)))+y(2));
 
 
 
  % R12
 
  (PHGPX)
 
  %
 
  5-HPETE y(13)<-> 5-HETE y(14)
 
  r12=
 
  (PHGPxKcatR12*PHGPX*(y(13)
 
  -(y(14)/KeqR12)))/((KmsR12*(1+(y(14)/KmpR12)))+y(13));
 
 
 
  % R13
 
  (LOX5FLAP)
 
  %
 
  5-HPETE y(13) <-> LTA4 y(15)
 
  r13=
 
  (LOX5FLAPKcat*LOX5*(y(13)-(y(15)/KeqR13)))/((KmsR13*(1+(y(15)/KmpR13)))+y(13));
 
 
 
  % R14
 
  (HEDH5)
 
  % 5-HETE
 
  y(14) <-> 5-OXO-ETE y(16)
 
  r14=
 
  (HEDH5Kcat*HEDH5*(y(14)-(y(16)/KeqR14)))/((KmsR14*(1+(y(16)/KmpR14)))+y(14));
 
 
 
  % R15
 
  (LTA4H)
 
  % LTA4
 
  y(15) <-> LTB4 y(17)
 
  r15=
 
  (LTA4HKcat*LTA4H*(y(15)
 
  -(y(17)/KeqR15)))/((KmsR15*(1+(y(17)/KmpR15)))+y(15));
 
 
 
  % R16
 
  (LTC4S)
 
  % LTA4
 
  y(15)<-> LTC4 y(18)
 
  r16=
 
  (LTC4SKcat*LTC4S*(y(15)
 
  -(y(18)/KeqR16)))/((KmsR16*(1+(y(18)/KmpR16)))+y(15));
 
 
 
  % R17
 
  (LOX15)
 
  % AA
 
  y(2)<-> 15-HPETE y(19)
 
  r17=
 
  (LOX15Kcat*LOX15*(y(2) -(y(19)/KeqR17)))/((KmsR17*(1+(y(19)/KmpR17)))+y(2));
 
 
 
  % R18
 
  (PHGPX)
 
  %
 
  15-HPETE y(19)<-> 15-HETE y(20)
 
  r18=
 
  (PHGPxKcatR12*PHGPX*(y(19)
 
  -(y(20)/KeqR12)))/((KmsR12*(1+(y(20)/KmpR12)))+y(19));
 
 
 
  % R19
 
  (LOX12)
 
  % AA y(2)<->
 
  12-HPETE y(21)
 
  r19=
 
  (LOX12Kcat*LOX12*(y(2) -(y(21)/KeqR19)))/((KmsR19*(1+(y(21)/KmpR19)))+y(2));
 
 
 
  % R20
 
  (PHGPX)
 
  %
 
  12-HPETE y(21)<-> 12-HETE y(22)
 
  r20=
 
  (PHGPxKcatR12*PHGPX*(y(21) -(y(22)/KeqR12)))/((KmsR12*(1+(y(22)/KmpR12)))+y(21));
 
 
 
  % R21
 
  (PGDS)
 
  % PGH2
 
  y(3)<-> PGD2 y(10)
 
  r21= (PGDSKcat*PGDS*(y(3)
 
  -(y(10)/KeqR21)))/((KmsR21*(1+(y(10)/KmpR21)))+y(3));
 
 
 
  % R22
 
  (ABC)
 
  % PGF2A
 
  y(4) <-> exPGF2A y(23)
 
  r22=
 
  ABC*ABCKcat*((y(4)/ABCKmR22)*(1-((y(23)/(y(4)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(4)/ABCKmR22)+(y(23)/ABCKmR22)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R23
 
  (ABC)
 
  %
 
  TXB2  y(7)<-> exTXB2 y(24)
 
  r23=
 
  ABC*ABCKcat*((y(7)/ABCKmR23)*(1-((y(24)/(y(7)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(7)/ABCKmR23)+(y(24)/ABCKmR23)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R24
 
  (ABC)
 
  %
 
  6-KETO-PGF1A y(8)<-> ex6-KETO-PGF1A y(25)
 
  r24= ABC*ABCKcat*((y(8)/ABCKmR24)*(1-((y(25)/(y(8)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(8)/ABCKmR24)+(y(25)/ABCKmR24)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R25
 
  (ABC)
 
  % PGE2
 
  y(12)<-> exPGE2 y(26)
 
  r25=
 
  ABC*ABCKcat*((y(12)/ABCKmR25)*(1-((y(26)/(y(12)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(12)/ABCKmR25)+(y(26)/ABCKmR25)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
  %
 
  r25=(ABCVmax*(y(12)
 
  -(y(26)/ABCKeq)))/((ABCKmR25*(1+(y(26)/ABCKmR25)))+y(12));
 
 
 
  % R26
 
  (ABC)
 
  %
 
  15-DEOXY-PGJ2 y(11)<-> ex15-DEOXY-PGJ2 y(27)
 
  r26=
 
  ABC*ABCKcat*((y(11)/ABCKmR26)*(1-((y(27)/(y(11)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(11)/ABCKmR26)+(y(27)/ABCKmR26)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(46)/ABCKmR70)));
 
 
 
  % R27
 
  (ABC)
 
  %
 
  5-Oxo-ETE y(16)<-> ex5-OXO-ETE y(28)
 
  r27= ABC*ABCKcat*((y(16)/ABCKmR27)*(1-((y(28)/(y(16)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(16)/ABCKmR27)+(y(28)/ABCKmR27)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R28
 
  (ABC)
 
  %
 
  15-HETE y(20)<-> ex15-HETE y(29)
 
  r28=
 
  ABC*ABCKcat*((y(20)/ABCKmR28)*(1-((y(29)/(y(20)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(20)/ABCKmR28)+(y(29)/ABCKmR28)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R29
 
  (ABC)
 
  % LTB4
 
  y(17)<-> exLTB4 y(30)
 
  r29=
 
  ABC*ABCKcat*((y(17)/ABCKmR29)*(1-((y(30)/(y(17)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(17)/ABCKmR29)+(y(30)/ABCKmR29)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R30
 
  (ABC)
 
  % LTC4
 
  y(18)<-> exLTC4 y(31)
 
  r30= ABC*ABCKcat*((y(18)/ABCKmR30)*(1-((y(31)/(y(18)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(18)/ABCKmR30)+(y(31)/ABCKmR30)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R31
 
  (ABC)
 
  %
 
  12-HETE y(22)<-> ex12-HETE y(32)
 
  r31=
 
  ABC*ABCKcat*((y(22)/ABCKmR31)*(1-((y(32)/(y(22)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(22)/ABCKmR31)+(y(32)/ABCKmR31)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R32
 
  (ABC)
 
  % TXA2
 
  y(5)<-> exTXA2 y(33)
 
  r32=
 
  ABC*ABCKcat*((y(5)/ABCKmR32)*(1-((y(33)/(y(5)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(5)/ABCKmR32)+(y(33)/ABCKmR32)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R33
 
  (ABC)
 
  % PGI2
 
  y(6)<-> exPGI2 y(34)
 
  r33=
 
  ABC*ABCKcat*((y(6)/ABCKmR33)*(1-((y(34)/(y(6)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(6)/ABCKmR33)+(y(34)/ABCKmR33)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R34
 
  (ABC)
 
  % PGH2
 
  y(3)<-> exPGH2 y(35)
 
  r34=
 
  ABC*ABCKcat*((y(3)/ABCKmR34)*(1-((y(35)/(y(3)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(3)/ABCKmR34)+(y(35)/ABCKmR34)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R35
 
  (ABC)
 
  % PGD2
 
  y(10)<-> exPGD2 y(36)
 
  r35= ABC*ABCKcat*((y(10)/ABCKmR35)*(1-((y(36)/(y(10)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(10)/ABCKmR35)+(y(36)/ABCKmR35)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R36
 
  (ABC)
 
  % PGJ2
 
  y(9)<-> exPGJ2 y(37)
 
  r36= ABC*ABCKcat*((y(9)/ABCKmR36)*(1-((y(37)/(y(9)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(9)/ABCKmR36)+(y(37)/ABCKmR36)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R37
 
  (ABC)
 
  %
 
  12-HPETE y(21) <-> ex12-HPETE y(38)
 
  r37=
 
  ABC*ABCKcat*((y(21)/ABCKmR37)*(1-((y(38)/(y(21)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(21)/ABCKmR37)+(y(38)/ABCKmR37)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R38
 
  (ABC)
 
  %
 
  15-HPETE y(19) <-> ex15-HPETE
 
  y(39)
 
  r38=
 
  ABC*ABCKcat*((y(19)/ABCKmR38)*(1-((y(39)/(y(19)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(19)/ABCKmR38)+(y(39)/ABCKmR38)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R39
 
  (ABC)
 
  %
 
  5-HPETE y(13)<-> ex5-HPETE y(40)
 
  r39=
 
  ABC*ABCKcat*((y(13)/ABCKmR39)*(1-((y(40)/(y(13)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(13)/ABCKmR39)+(y(40)/ABCKmR39)+(y(2)/ABCKmR42)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R40
 
  (ABC)
 
  % 5-HETE
 
  y(14)<-> ex5-HETE y(41)
 
  r40= ABC*ABCKcat*((y(14)/ABCKmR40)*(1-((y(41)/(y(14)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(14)/ABCKmR40)+(y(41)/ABCKmR40)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R41
 
  (ABC)
 
  % LTA4
 
  y(15) <-> exLTA4 y(42)
 
  r41=
 
  ABC*ABCKcat*((y(15)/ABCKmR41)*(1-((y(42)/(y(15)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(15)/ABCKmR41)+(y(42)/ABCKmR41)+(y(2)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % R42
 
  (ABC)
 
  % AA
 
  y(2)<-> exAA y(43)
 
  r42 =
 
  ABC*ABCKcat*((y(2)/ABCKmR42)*(1-((y(43)/(y(2)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(2)/ABCKmR42)+(y(43)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
  % NO R43
 
 
 
  % R44
 
  %
 
  exPGF2A y(23)-> Mischellanous species
 
  r44 = KfR44*y(23);
 
 
 
  % R45
 
  % exTXB2
 
  y(24)-> Mischellanous species
 
  r45= KfR45*y(24);
 
 
 
  % R46
 
  % exTXA2
 
  y(33)-> Mischellanous species
 
  r46= KfR46*y(33);
 
 
 
  % R47
 
  %
 
  ex6-KETO-PGF1A y(25)-> Mischellanous species
 
  r47= KfR47*y(25);
 
 
 
  % R48
 
  % exPGI2
 
  y(34)-> Mischellanous species
 
  r48= KfR48*y(34);
 
 
 
  % R49
 
  % exPGE2
 
  y(26)-> Mischellanous species
 
  r49= KfR49*y(26);
 
 
 
  % R50
 
  %
 
  ex15-DEOXY-PGJ2 y(27)-> Mischellanous species
 
  r50= KfR50*y(27);
 
 
 
  % R51
 
  % exPGJ2
 
  y(37)-> Mischellanous species
 
  r51= KfR51* y(37);
 
 
 
  % R52
 
  % exPGD2
 
  y(36)-> Mischellanous species
 
  r52= KfR52*y(36);
 
 
 
  % R53
 
  % exPGH2
 
  y(35)-> Mischellanous species
 
  r53= KfR53*y(35);
 
 
 
  % R54
 
  %
 
  ex-5-OXO-ETE y(28)-> Mischellanous species
 
  r54= KfR54*y(28);
 
 
 
  % R55
 
  %
 
  ex5-HETE y(41)-> Mischellanous species
 
  r55= KfR55*y(41);
 
 
 
  % R56
 
  % exLTB4
 
  y(30)-> Mischellanous species
 
  r56= KfR56*y(30);
 
 
 
  % R57
 
  % exLTC4
 
  y(31)-> Mischellanous species
 
  r57= KfR57*y(31);
 
 
 
  % R58
 
  % exLTA4
 
  y(42)-> Mischellanous species
 
  r58= KfR58*y(42);
 
 
 
  % R59
 
  %
 
  ex5-HPETE y(40)-> Mischellanous species
 
  r59 = KfR59*y(40);
 
 
 
  % R60
 
  %
 
  ex15-HETE y(29)-> Mischellanous species
 
  r60= KfR60*y(29);
 
 
 
  % R61
 
  %
 
  ex15-HPETE y(39)-> Mischellanous species
 
  r61= KfR61*y(39);
 
 
 
  % R62
 
  %
 
  ex12-HETE y(32)-> Mischellanous species
 
  r62= KfR62*y(32);
 
 
 
  % R63
 
  %
 
  ex12-HPETE y(38)-> Mischellanous species
 
  r63= KfR63*y(38);
 
 
 
  % R64
 
  % exAA
 
  y(43)-> Mischellanous species
 
  r64= KfR64*y(43);
 
 
 
  % R65
 
  % AA
 
  y(2)<-> PGH2 y(3) (COX1)
 
  r65=(COX1Kcat*COX1*(y(2)-(y(3)/KeqR65)))/((KmsR65*(1+(y(3)/KmpR65)))+y(2));
 
 
 
  % R66
 
  (PGDH15)
 
  % PGE2
 
  y(12)<-> 15-KETO-PGE2 y(44)
 
  r66=
 
  (PGDH15Kcat*PGDH15*(y(12) -(y(44)/KeqR66)))/((KmsR66*(1+(y(44)/KmpR66)))+y(12));
 
 
 
 
 
  % R67
 
  (ABC)
 
  %
 
  15-KETO-PGE2 y(44) <-> ex15-KETO-PGE2 y(45)
 
  r67=
 
  ABC*ABCKcat*((y(44)/ABCKmR67)*(1-((y(45)/(y(44)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(44)/ABCKmR67)+(y(45)/ABCKmR67)+(y(21)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)+(y(46)/ABCKmR70)));
 
 
 
 
 
  % R68
 
  %
 
  ex15-KETO-PGE2 y(45)-> Mischellanous species
 
  r68= KfR68*y(45);
 
 
 
  % R69
 
  (PTGR2)
 
  %
 
  15-KETO-PGE2 y(44) <-> 13,14-DIHYDRO-15-KETO-PGE2 y(46)
 
  r69=
 
  (PTGR2Kcat*PTGR2*(y(44)-(y(46)/KeqR69)))/((KmsR69*(1+(y(46)/KmpR69)))+y(44));
 
 
 
  % R70
 
  (ABC)
 
  %
 
  13,14-DIHYDRO-15-KETO-PGE2  y(46)
 
  <-> ex13,14-DIHYDRO-15-KETO-PGE2 y(47)
 
  r70=
 
  ABC*ABCKcat*((y(46)/ABCKmR70)*(1-((y(47)/(y(46)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(46)/ABCKmR70)+(y(47)/ABCKmR70)+(y(21)/ABCKmR42)+(y(13)/ABCKmR39)+(y(21)/ABCKmR37)+(y(19)/ABCKmR38)+(y(3)/ABCKmR34)+(y(15)/ABCKmR41)+(y(14)/ABCKmR40)+(y(22)/ABCKmR31)+(y(20)/ABCKmR28)+(y(12)/ABCKmR25)+(y(10)/ABCKmR35)+(y(6)/ABCKmR33)+(y(5)/ABCKmR32)+(y(4)/ABCKmR22)+(y(18)/ABCKmR30)+(y(17)/ABCKmR29)+(y(16)/ABCKmR27)+(y(9)/ABCKmR36)+(y(44)/ABCKmR67)+(y(8)/ABCKmR24)+(y(7)/ABCKmR23)+(y(11)/ABCKmR26)));
 
 
 
  % R71
 
  %
 
  ex13,14-DIHYDRO-15-KETO-PGE2 y(47)-> Mischellanous species
 
  r71= KfR71*y(47);
 
 
 
  %
 
  INTRACELLULAR DECAY REACTIONS
 
 
 
  % R72
 
  % PGF2A
 
  y(4-> Mischellanous species
 
  r72 = KfR44*y(4);
 
 
 
  % R73
 
  % TXB2
 
  y(7-> Mischellanous species
 
  r73= KfR45*y(7);
 
 
 
  % R74
 
  % TXA2
 
  y(5)-> Mischellanous species
 
  r74= KfR46*y(5);
 
 
 
  % R75
 
  %
 
  6-KETO-PGF1A y(8)-> Mischellanous species
 
  r75= KfR47*y(8);
 
 
 
  % R76
 
  % PGI2
 
  y(6)-> Mischellanous species
 
  r76= KfR48*y(6);
 
 
 
  % R77
 
  % PGE2
 
  y(12)-> Mischellanous species
 
  r77= KfR49*y(12);
 
 
 
  % R78
 
  %
 
  15-DEOXY-PGJ2 y(11)-> Mischellanous species
 
  r78= KfR50*y(11);
 
 
 
  % R79
 
  % PGJ2
 
  y(9)-> Mischellanous species
 
  r79= KfR51* y(9);
 
 
 
  % R80
 
  % PGD2
 
  y(10)-> Mischellanous species
 
  r80= KfR52*y(10);
 
 
 
  % R81
 
  % PGH2
 
  y(3)-> Mischellanous species
 
  r81= KfR53*y(3);
 
 
 
  % R82
 
  %
 
  5-OXO-ETE y(16)-> Mischellanous species
 
  r82= KfR54*y(16);
 
 
 
  % R83
 
  % 5-HETE
 
  y(14)-> Mischellanous species
 
  r83= KfR55*y(14);
 
 
 
  % R84
 
  % LTB4
 
  y(17)-> Mischellanous species
 
  r84= KfR56*y(17);
 
 
 
  % R85
 
  % LTC4
 
  y(18)-> Mischellanous species
 
  r85= KfR57*y(18);
 
 
 
  % R86
 
  % LTA4
 
  y(15)-> Mischellanous species
 
  r86= KfR58*y(15);
 
 
 
  % R87
 
  %
 
  5-HPETE y(13)-> Mischellanous species
 
  r87 = KfR59*y(13);
 
 
 
  % R88
 
  %
 
  15-HETE y(20)-> Mischellanous species
 
  r88= KfR60*y(20);
 
 
 
  % R89
 
  %
 
  15-HPETE y(19)-> Mischellanous species
 
  r89= KfR61*y(19);
 
 
 
  % R90
 
  %
 
  12-HETE  y(22)-> Mischellanous
 
  species
 
  r90= KfR62*y(22);
 
 
 
  % R91
 
  %
 
  12-HPETE y(21)-> Mischellanous species
 
  r91= KfR63*y(21);
 
 
 
  % R92
 
  % AA
 
  y(2)-> Mischellanous species
 
  r92= KfR64*y(2);
 
 
 
  % R93
 
  %
 
  13,14-DIHYDRO-15-KETO-PGE2 y(46)-> Mischellanous species
 
  r93= KfR71*y(46);
 
 
 
  % R94
 
  %
 
  15-KETO-PGE2 y(44)-> Mischellanous species
 
  r94= KfR68*y(44);
 
 
 
  % AA
 
  ACTIVATION
 
  % ->
 
  AA
 
  r95=
 
  (c/AADT)-((c2*log(2)*y(2))/AAHL);
 
 
 
  % R96
 
  % exTXA2
 
  y(33) <-> exTXB2 y(24)
 
  r96=(KfR6*y(33))-(KrR6*y(24));
 
 
 
  % R97
 
  % exPGI2
 
  y(34)<-> ex6-Keto-PGF1A y(25)
 
  r97=
 
  (KfR7*y(34))-(KrR7*y(25));
 
 
 
  % R98
 
  % exPGD2
 
  y(36) <-> exPGJ2 y(37)
 
  r98=
 
  (KfR8*y(36))-(KrR8*y(37));
 
 
 
  % R99
 
  %
 
  exPGJ2  y(37)<-> ex15-DEOXY-PGJ2
 
  y(27)
 
  r99= (KfR9*y(37))-(KrR9*y(27));
 
 
 
  %R100 -
 
  Turned off
 
  %AA y(2)
 
  <-> BAA y(1)
 
  r100=(LATKcat*LAT*(y(2)-(y(1)/KeqR100)))/((KmsR100*(1+(y(1)/KmpR100)))+y(2));
 
 
 
  % PGT
 
  Transporter
 
 
 
  % R101
 
  (PGT)
 
  % PGF2A
 
  y(4) <-> exPGF2A y(23)
 
  r101=PGT*PGTKcat*((y(4)/PGTKmR101)*(1-((y(23)/(y(4)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(4)/PGTKmR101)+(y(23)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  % R102
 
  (PGT)
 
  % PGE2
 
  y(12)<-> exPGE2 y(26)
 
  r102=
 
  PGT*PGTKcat*((y(12)/PGTKmR102)*(1-((y(26)/(y(12)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(4)/PGTKmR102)+(y(23)/PGTKmR102)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  % R103
 
  (PGT)
 
  % PGI2
 
  y(6)<-> exPGI2 y(34)
 
  r103= PGT*PGTKcat*((y(6)/PGTKmR103)*(1-((y(34)/(y(6)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(6)/PGTKmR103)+(y(34)/PGTKmR103)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  % R104
 
  (PGT)
 
  % PGD2
 
  y(10)<-> exPGD2 y(36)
 
  r104=
 
  PGT*PGTKcat*((y(10)/PGTKmR104)*(1-((y(36)/(y(10)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(10)/PGTKmR104)+(y(36)/PGTKmR104)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  %
 
  R105(PGT)
 
  % PGJ2
 
  y(9)<-> exPGJ2 y(37)
 
  r105=
 
  PGT*PGTKcat*((y(9)/PGTKmR105)*(1-((y(37)/(y(9)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(9)/PGTKmR105)+(y(37)/PGTKmR105)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  % R106
 
  (PGT)
 
  %
 
  TXB2  y(7)<-> exTXB2 y(24)
 
  r106=
 
  PGT*PGTKcat*((y(7)/PGTKmR106)*(1-((y(24)/(y(7)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(7)/PGTKmR106)+(y(24)/PGTKmR106)+(y(4)/PGTKmR101)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  % R107
 
  (PGT)
 
  %
 
  13,14-DIHYDRO-15-KETO-PGE2  y(46)
 
  <-> ex13,14-DIHYDRO-15-KETO-PGE2 y(47)
 
  r107= PGT*PGTKcat*((y(46)/PGTKmR107)*(1-((y(47)/(y(46)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(46)/PGTKmR107)+(y(47)/PGTKmR107)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)));
 
 
 
  % R108
 
  (PGT)
 
  %
 
  15-KETO-PGE2 y(44) <-> ex15-KETO-PGE2 y(45)
 
  r108=
 
  PGT*PGTKcat*((y(44)/PGTKmR108)*(1-((y(45)/(y(44)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(44)/PGTKmR108)+(y(45)/PGTKmR108)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(46)/PGTKmR107)));
 
 
 
  % R109
 
  (PGT)
 
  %
 
  6-KETO-PGF1A y(8)<-> ex6-KETO-PGF1A y(25)
 
  r109=
 
  PGT*PGTKcat*((y(8)/PGTKmR109)*(1-((y(25)/(y(8)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(8)/PGTKmR109)+(y(25)/PGTKmR109)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  % R110
 
  (PGT)
 
  % TXA2
 
  y(5)<-> exTXA2 y(33)
 
  r110= PGT*PGTKcat*((y(5)/PGTKmR110)*(1-((y(33)/(y(5)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(5)/PGTKmR110)+(y(33)/PGTKmR110)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(11)/PGTKmR111)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  % R111
 
  (PGT)
 
  %
 
  15-DEOXY-PGJ2 y(11)<-> ex15-DEOXY-PGJ2 y(27)
 
  r111=
 
  PGT*PGTKcat*((y(11)/PGTKmR111)*(1-((y(27)/(y(11)*exp((((-0.5*(ABCdG+(R*TEMP*log(ATP/ADP))))))/(R*TEMP))))))/(1+(y(11)/PGTKmR111)+(y(27)/PGTKmR111)+(y(4)/PGTKmR101)+(y(7)/PGTKmR106)+(y(8)/PGTKmR109)+(y(12)/PGTKmR102)+(y(5)/PGTKmR110)+(y(6)/PGTKmR103)+(y(10)/PGTKmR104)+(y(9)/PGTKmR105)+(y(44)/PGTKmR108)+(y(46)/PGTKmR107)));
 
 
 
  % COX2
 
  Induction event
 
  % ->
 
  COX2 (y(48)
 
  r112= (c3/COX2DT)-((c4*log(2)*y(48))/COX2HL);
 
 
 
  %%
 
  Section 5: ODE
 
 
 
  %BAA
 
  y(1)
 
  %dydt(1)=r100-r1;
 
 
 
  %AA y(2)
 
  %dydt(2)=r95+r1-r2-r11-r17-r19-r42-r65-r92-r100;
 
 
 
  %PGH2
 
  y(3)
 
  %dydt(3)=r2+r65-r3-r4-r5-r10-r21-r81-r34;
 
 
 
  %PGF2A
 
  y(4)
 
  %dydt(4)=r3-r22-r72-r101;
 
 
 
  %TXA2
 
  y(5)
 
  %dydt(5)=r4-r6-r32-r74-r110;
 
 
 
  %PGI2
 
  y(6)
 
  %dydt(6)=r5-r7-r33-r76-r103;
 
 
 
  %TXB2
 
  y(7)
 
  %dydt(7)=r6-r106-r73-r23;
 
 
 
 
 
  %6-KETO-PGF1A
 
  y(8)
 
  %dydt(8)=r7-r24-r75-r109;
 
 
 
 
 
  %PGJ2
 
  y(9)
 
  %dydt(9)=r8-r9-r36-r79-r105;
 
 
 
  %PGD2 =
 
  y(10)
 
  %dydt(10)=r21-r8-r35-r80-r104;
 
 
 
 
 
  %15-DEOXY-PGJ2
 
  = y(11)
 
  %dydt(11)=r9-r26-r78-r111;
 
 
 
 
 
  %PGE2 =
 
  y(12)
 
  %dydt(12)=r10-r25-r66-r77-r102;
 
 
 
  %5-HPETE
 
  %dydt(13)=r11-r12-r13-r39-r87;
 
 
 
  %5-HETE
 
  =y(14)
 
  %dydt(14)=r12-r14-r40-r83;
 
 
 
  %LTA4 =
 
  y(15)
 
  %dydt(15)=r13-r15-r16-r41-r86;
 
 
 
  %5-OXO-ETE  = y(16)
 
  %dydt(16)=r14-r27-r82;
 
 
 
  %LTB4 =
 
  y(17)
 
  %dydt(17)=r15-r29-r84;
 
 
 
  %LTC4  = y(18)
 
  %dydt(18)=r16-r30-r85;
 
 
 
  %15-HPETE  = y(19)
 
  %dydt(19)=r17-r18-r38-r89;
 
 
 
  %15-HETE
 
  = y(20)
 
  %dydt(20)=r18-r28-r88;
 
 
 
 
 
  %12-HPETE
 
  = y(21)
 
  %dydt(21)=r19-r20-r37-r91;
 
 
 
  %12-HETE
 
  = y(22)
 
  %dydt(22)=r20-r31-r90;
 
 
 
  %exPGF2A  = y(23)
 
  %dydt(23)=r22+r101-r44;
 
 
 
  %exTXB2
 
  = y(24)
 
  %dydt(24)=r23+r106-r45+r96;
 
 
 
  %ex6-KETO-PGF1A
 
  = y(25)
 
  %dydt(25)=r24+r109-r47+r97;
 
 
 
  %exPGE2
 
  = y(26)
 
  %dydt(26)=r25+r102-r49;
 
 
 
  %ex15-DEOXY-PGJ2
 
  = y(27)
 
  %dydt(27)=r26+r111-r50+r99;
 
 
 
 
 
  %ex5-OXO-ETE
 
  = y(28)
 
  %dydt(28)=r27-r54;
 
 
 
  %ex15-HETE
 
  =y(29)
 
  %dydt(29)=r28-r60;
 
 
 
  %exLTB4
 
  = y(30)
 
  %dydt(30)=r29-r56;
 
 
 
  %exLTC4
 
  = y(31)
 
  %dydt(31)=r30-r57;
 
 
 
  %exHETE12
 
  = y(32)
 
  %dydt(32)=r31-r62;
 
 
 
  %exTXA2
 
  = y(33)
 
  %dydt(33)=r32+r110-r46-r96;
 
 
 
  %exPGI2
 
  = y(34)
 
  %dydt(34)=r33+r103-r48-r97;
 
 
 
  %exPGH2
 
  = y(35)
 
  %dydt(35)=-r53;
 
 
 
  %exPGD2
 
  = y(36)
 
  %dydt(36)=r35+r104-r52-r98;
 
 
 
  %exPGJ2
 
  = y(37)
 
  %dydt(37)=r36+r105-r51+r98-r99;
 
 
 
  %ex12-HPETE
 
  = y(38)
 
  %dydt(38)=r37-r63;
 
 
 
  %ex15-HPETE
 
  = y(39)
 
  %dydt(39)=r38-r61;
 
 
 
  %ex5-HPETE
 
  = y(40)
 
  %dydt(40)=r39-r59;
 
 
 
  %ex5-HETE
 
  = y(41)
 
  %dydt(41)=r40-r55;
 
 
 
  %exLTA4
 
  = y(42)
 
  %dydt(42)=r41-r58;
 
 
 
  %exAA =
 
  y(43)
 
  %dydt(43)=-r64;
 
 
 
  %15-KETO-PGE2
 
  = y(44)
 
  %dydt(44)=r66-r67-r69-r94-r108;
 
 
 
  %ex15-KETO-PGE2
 
  = y(45)
 
  %dydt(45)=r67+r108-r68;
 
 
 
  %13,14-DIHYDRO-15-KETO-PGE2
 
  = y(46)
 
  %dydt(46)=r69-r70-r93-r107;
 
 
 
  %ex13,14-DIHYDRO-15-KETO-PGE2  = y(47)
 
  %dydt(47)=r70+r107-r71;
 
 
 
  % COX2 =
 
  y(48)
 
  %dydt(48)=r112-r2;
 
 
 
  %
 
  Mischellanous species = y(49)
 
  %dydt(49)=r44+r45+r46+r47+r48+r49+r50+r51+r52+r53+r54+r55+r56+r57+r58+r59+r60+r61+r62+r63+r64+r68+r71+r72+r73+r74+r75+r76+r77+r78+r79+r80+r81+r82+r83+r84+r85+r86+r87+r88+r89+r90+r91+r92
 
 
 
  dydt=[r100-r1;r95+r1-r2-r11-r17-r19-r42-r65-r92-r100;r2+r65-r3-r4-r5-r10-r21-r81-r34;r3-r22-r72-r101;r4-r6-r32-r74-r110;r5-r7-r33-r76-r103;r6-r23-r73-r106;r7-r24-r75-r109;r8-r9-r36-r79-r105;r21-r8-r35-r80-r104;r9-r26-r78-r111;r10-r25-r66-r77;r11-r12-r13-r39-r87;r12-r14-r40-r83;r13-r15-r16-r41-r86;r14-r27-r82;r15-r29-r84;r16-r30-r85;r17-r18-r38-r89;r18-r28-r88;r19-r20-r37-r91;r20-r31-r90;r22+r101-r44;r23+r106-r45+r96;r24+r109-r47+r97;r25+r102-r49;r26+r111-r50+r99;r27-r54;r28-r60;r29-r56;r30-r57;r31-r62;r32+r110-r46-r96;r33+r103-r48-r97;r34-r53;r35+r104-r52-r98;r36+r105-r51+r98-r99;r37-r63;r38-r61;r39-r59;r40-r55;r41-r58;r42-r64;r66-r67-r69-r94-r108;r67+r108-r68;r69-r70-r93-r107;r70+r107-r71;
 
  r112-r2; r44+r45+r46+r47+r48+r49+r50+r51+r52+r53+r54+r55+r56+r57+r58+r59+r60+r61+r62+r63+r64+r68+r71+r72+r73+r74+r75+r76+r77+r78+r79+r80+r81+r82+r83+r84+r85+r86+r87+r88+r89+r90+r91+r92];
 
  end
 
|}
 

Latest revision as of 10:31, 20 May 2019

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The “Solver script” described the log-normal distributions of uncertain parameters and solves the ODEs. To begin the script, the number of model variants were defined (section 1). For each uncertain parameter, a parameter distribution was generated based upon the µ and σ defined in section * (section 3). For parameters which were thermodynamically connected, multivariate distributions were created (section 4). From these distributions, parameter values were randomly selected to generate unique parameter sets for every model variant (section 5). In the latter half of the “Solver script”, the event parameters are assigned a value and a time at which it changes, and the initial concentration of every metabolite is set (section 6). The ODEs are then solved using MATLABs inbuilt stiff ordinary differential equation solver, ode15 (section 5). The result of these models was then defined as failed if the numerical values cannot be calculated by the solver, as abnormal if the concentration of certain metabolites went below zero, and normal if not (section 6). The choice of metabolite is user defined and for the purposes of this model was arbitrarily set as PGE2. The models which were classified as normal were then analysed.

Script