#reed

FIX: bmet bser ext

#reactions
v_1:
 {1.0}met = {1.0}SAM
  0.4 * (0.23 + 0.8 * exp(-0.0026 * SAM)) * vmMATi * (met / kmMATimet) / (1 + met / kmMATimet) * (kiMATiGSSG + 66.71) / (kiMATiGSSG + cGSSG)
v_10:
 {1.0}ccys = {1.0}ext
  0.35/200*ccys**2
v_11:
 {1.0}ccys + {1.0}cglut = {1.0}cglc
  vmgcl * (cglut * ccys - cglc / keqgcl) / (kmgclccys * kmgclglut + kmgclccys * cglut + ccys * kmgclglut * (1 + cGSH / kmgclgsh + cglut / kmgclglut) + cglc / kmgclglc + cGSH / kmgclgsh) * (kagcl + H2O2) / (kagcl + H2O2ss)
v_12:
 {1.0}cglc + {1.0}cgly = {1.0}cGSH
  vmgs*(cgly*cglc - cGSH/keqgs)/(kmgscglc*kmgscgly + cglc*kmgscgly + cgly*kmgscglc*(1 + cglc/kmgscglc) + cGSH/kpcgsh)
v_13:
 {2.0}cGSH = {1.0}cGSSG
  vmGPX*((cGSH/(kmGPXgsh + cGSH))**2)* (H2O2/(9*kmGPXH2O2 + H2O2))
v_14:
 {1.0}cGSSG = {2.0}cGSH
  (vmgr*(cGSSG/kmgrGSSG) * (cNADPH/ kmgrNADPH))/(1 + cGSSG/kmgrGSSG + cNADPH/kmgrNADPH + (cGSSG/kmgrGSSG)*(cNADPH/kmgrNADPH))
v_15:
 {1.0}cGSSG = {1.0}bGSSG
  (vmGSSGl* cGSSG)/(kmGSSGl + cGSSG)*(kaGSSGl + H2O2)/(kaGSSGl + H2O2ss)
v_16:
 {1.0}cGSSG = {1.0}bGSSG
  (vmGSSGh* cGSSG)/(kmGSSGh + cGSSG)*(kaGSSGh + H2O2)/(kaGSSGh + H2O2ss)
v_17:
 {1.0}cGSH = {1.0}ext
  0.002*cGSH
v_18:
 {1.0}cGSH = {1.0}bGSH
  (vmgshoutl*cGSH*cGSH*cGSH)/((kmgshoutl)**3 + cGSH*cGSH*cGSH)
v_19:
 {1.0}cGSH = {1.0}bGSH
  (vmgshouth*cGSH)/(cGSH + kmgshouth)
v_2:
 {1.0}met = {1.0}SAM
  vmMATiii * met**1.21 / (kmMATiiimet + met**1.21) * (1 + 7.2 * SAM**2 / (kmMATiiiSAM + SAM**2)) * (kiMATiiiGSSG + 66.71) / (kiMATiiiGSSG + cGSSG)
v_20:
 {1.0}cGSSG = {1.0}ext
  0.1*cGSSG
v_21:
 {1.0}bglut = {1.0}cglut
  vmglutin*bglut/(kmbglut + bglut) - kglutin*cglut
v_22:
 {1.0}bcys = {1.0}ccys
  vmcysin*bcys/(kcysinbcys + bcys)
v_23:
 {1.0}bser = {1.0}cser
  vmserin*bser/(kbser + bser) - krserin*cser
v_24:
 {1.0}bgly = {1.0}cgly
  vmglyin*bgly/(kmbgly + bgly) - kcgly*cgly
v_25:
 {3.0}mgly = {1.0}cgly
  vmfgly*mgly/(3*(kgly+mgly)) - vmrgly*cgly/(kgly+cgly)
v_26:
 {3.0}mHCOOH = {1.0}cHCOOH
  khcooh*mHCOOH/3 - khcooh*cHCOOH
v_27:
 {3.0}mser = {1.0}cser
  Vmser*mser/(3*(Kmsermser + mser)) - Vmser*cser/(Kmsermser + cser)
v_28:
 {1.0}cser + {1.0}cTHF = {1.0}cCH2THF + {1.0}cgly
  VmfcSHMT*(cser/KmcSHMTcser)*(cTHF/KmcSHMTcTHF)/(1 + (cser/KmcSHMTcser) + (cTHF/KmcSHMTcTHF) +  (cser/KmcSHMTcser)*(cTHF/KmcSHMTcTHF)) -  VmrcSHMT*(cgly/KmcSHMTcgly)*(cCH2THF/KmcSHMTcCH2THF)/(1 + (cgly/KmcSHMTcgly) + (cCH2THF/KmcSHMTcCH2THF) +  (cgly/KmcSHMTcgly)*(cCH2THF/KmcSHMTcCH2THF))
v_29:
 {1.0}cDHF = {1.0}cTHF
  VmcDHFR*(cDHF/KmcDHFRcDHF)*(cNADPH/KmcDHFRcNADPH)/(1 + (cDHF/KmcDHFRcDHF) + (cNADPH/KmcDHFRcNADPH) +  (cDHF/KmcDHFRcDHF)*(cNADPH/KmcDHFRcNADPH))
v_3:
 {1.0}SAM = {1.0}SAH
  Vmmeth*SAM/(KmmethSAM*(1 + SAH/KmmethSAH) + SAM)
v_30:
 {1.0}cTHF + {1.0}cHCOOH = {1.0}c10fTHF
  VmcFTS*(cTHF/KmcFTScTHF)*(cHCOOH/KmcFTScHCOOH)/(1 + (cTHF/KmcFTScTHF) + (cHCOOH/KmcFTScHCOOH) +  (cTHF/KmcFTScTHF)*(cHCOOH/KmcFTScHCOOH))
v_31:
 {1.0}c10fTHF = {1.0}cTHF
  VmcFTD*(c10fTHF/kmcFTDc10fTHF)/(1 + (c10fTHF/kmcFTDc10fTHF))
v_32:
 {1.0}c10fTHF = {1.0}aic + {1.0}cTHF
  VmcPGT*(c10fTHF/KmcPGTc10fTHF)*(GARP/KmcPGTGARP)/(1 + (c10fTHF/KmcPGTc10fTHF) + (GARP/KmcPGTGARP) +  (c10fTHF/KmcPGTc10fTHF)*(GARP/KmcPGTGARP))
v_33:
 {1.0}c10fTHF + {1.0}aic = {1.0}cTHF
  VmcART*(c10fTHF/KmcARTc10fTHF)*(aic/KmcARTaic)/(1 + (c10fTHF/KmcARTc10fTHF) + (aic/KmcARTaic) +  (c10fTHF/KmcARTc10fTHF)*(aic/KmcARTaic))
v_34:
 {1.0}cTHF = {1.0}cCH2THF
  kfcNE*cTHF*HCHO - krcNE*cCH2THF
v_35:
 {1.0}cCHTHF = {1.0}c10fTHF
  VmfcMTCH*(cCHTHF/KmcMTCHcCHTHF)/(1 + cCHTHF/KmcMTCHcCHTHF)  - VmrcMTCH*(c10fTHF/KmcMTCHc10fTHF)/(1 + c10fTHF/KmcMTCHc10fTHF)
v_36:
 {1.0}cCH2THF = {1.0}cDHF
  VmcTS*(DUMP/KmcTSDUMP)*(cCH2THF/KmcTScCH2THF)/(1 + (DUMP/KmcTSDUMP) + (cCH2THF/KmcTScCH2THF) +  (DUMP/KmcTSDUMP)*(cCH2THF/KmcTScCH2THF))
v_37:
 {1.0}cCH2THF = {1.0}cCHTHF
  VmfcMTD*(cCH2THF/KmcMTDcCH2THF)/(1 + cCH2THF/KmcMTDcCH2THF)  - VmrcMTD*(cCHTHF/KmcMTDcCHTHF)/(1 + cCHTHF/KmcMTDcCHTHF)
v_38:
 {1.0}cCH2THF = {1.0}c5mTHF
  VmcMTHFR * cCH2THF / KmcMTHFRcCH2THF * (cNADPH / KmcMTHFRcNADPH) / (1 + cCH2THF / KmcMTHFRcCH2THF + cNADPH / KmcMTHFRcNADPH + cCH2THF / KmcMTHFRcCH2THF * (cNADPH / KmcMTHFRcNADPH)) * 63.72 / (10 + piecewise(0, lt(SAM, SAH), SAM - SAH))
v_39:
 {1.0}mTHF + {1.0}mser = {1.0}mgly + {1.0}mCH2THF
  VmfmSHMT*(mser/KmmSHMTmser)*(mTHF/KmmSHMTmTHF)/(1 + (mser/KmmSHMTmser) + (mTHF/KmmSHMTmTHF) +  (mser/KmmSHMTmser)*(mTHF/KmmSHMTmTHF)) -  VmrmSHMT*(mgly/KmmSHMTmgly)*(mCH2THF/KmmSHMTmCH2THF)/(1 + (mgly/KmmSHMTmgly) + (mCH2THF/KmmSHMTmCH2THF) +  (mgly/KmmSHMTmgly)*(mCH2THF/KmmSHMTmCH2THF))
v_4:
 {1.0}SAM + {1.0}cgly = {1.0}SAH + {1.0}msarc
  260 * SAM / ((63 + SAM) * (1 + SAH / kmGNMTSAH)) * cgly / (kmGNMTcgly + cgly) * (4.8 / (0.35 + c5mTHF))
v_40:
 {1.0}mTHF + {1.0}mHCOOH = {1.0}m10fTHF
  VmfmFTS*(mTHF/KmmFTSmTHF)*(mHCOOH/KmmFTSmHCOOH)/(1 + (mTHF/KmmFTSmTHF) + (mHCOOH/KmmFTSmHCOOH) +  (mTHF/KmmFTSmTHF)*(mHCOOH/KmmFTSmHCOOH)) - VmrmFTS*(m10fTHF/KmmFTSm10fTHF)/(1+(m10fTHF/KmmFTSm10fTHF))
v_41:
 {1.0}m10fTHF = {1.0}mTHF
  VmmFTD*(m10fTHF/kmmFTDm10fTHF)/(1 + (m10fTHF/kmmFTDm10fTHF))
v_42:
 {1.0}mCHTHF = {1.0}m10fTHF
  VmfmMTCH*(mCHTHF/KmmMTCHmCHTHF)/(1 + mCHTHF/KmmMTCHmCHTHF)  - VmrmMTCH*(m10fTHF/KmmMTCHm10fTHF)/(1 + m10fTHF/KmmMTCHm10fTHF)
v_43:
 {1.0}mCH2THF = {1.0}mCHTHF
  VmfmMTD*(mCH2THF/KmmMTDmCH2THF)/(1 + mCH2THF/KmmMTDmCH2THF)  - VmrmMTD*(mCHTHF/KmmMTDmCHTHF)/(1 + mCHTHF/KmmMTDmCHTHF)
v_44:
 {1.0}mTHF + {1.0}mgly = {1.0}mCH2THF
  VmmGDC*(mgly/KmmGDCmgly)*(mTHF/KmmGDCmTHF)/(1 + (mgly/KmmGDCmgly) + (mTHF/KmmGDCmTHF) +  (mgly/KmmGDCmgly)*(mTHF/KmmGDCmTHF))
v_45:
 {1.0}mTHF + {1.0}msarc = {1.0}mgly + {1.0}mCH2THF
  VmmSDH*(msarc/KmmSDHsarc)*(mTHF/KmmSDHmTHF)/(1 + (msarc/KmmSDHsarc) + (mTHF/KmmSDHmTHF) +  (msarc/KmmSDHsarc)*(mTHF/KmmSDHmTHF))
v_46:
 {1.0}mTHF + {1.0}dmg = {1.0}msarc + {1.0}mCH2THF
  VmmDMGD*(dmg/KmmDMGDdmg)*(mTHF/KmmDMGDmTHF)/(1 + (dmg/KmmDMGDdmg) + (mTHF/KmmDMGDmTHF) +  (dmg/KmmDMGDdmg)*(mTHF/KmmDMGDmTHF))
v_47:
 {1.0}mTHF = {1.0}mCH2THF
  kfmNE*mTHF*HCHO - krmNE*mCH2THF
v_48:
 {1.0}bmet = {1.0}met
  vmmetin*bmet/(kmmetinoutmethionine + bmet) - kmetincmethionine*met
v_49:
 {1.0}ext = {1.0}bcys
  vocysb + k0 * bGSSG * bGSH
v_5:
 {1.0}SAH = {1.0}hcy
  Vmfah*(SAH/KmahSAH)/(1 + (SAH/KmahSAH)) -  (1)*6*Vmrah*(hcy/Kmahhcy)/(1 + (hcy/Kmahhcy))
v_50:
 {1.0}ext = {1.0}bglut
  voglub + k0 * bGSSG * bGSH
v_51:
 {1.0}ext = {1.0}bgly
  voglyb + k0 * bGSSG * bGSH
v_52:
 {1.0}cser = {1.0}ext
  1.2*cser
v_53:
 {1.0}cglut = {1.0}ext
  0.07*cglut
v_54:
 {1.0}bGSH = {1.0}bgly + {1.0}bcys + {1.0}bglut
  90*bGSH
v_55:
 {1.0}bGSSG = {2.0}bgly + {2.0}bcys + {2.0}bglut
  135/2*bGSSG
v_56:
 {1.0}bgly = {1.0}ext
  0.1*bgly
v_57:
 {1.0}bcys = {1.0}ext
  0.35*bcys
v_58:
 {1.0}bglut = {1.0}ext
  0.1*bglut
v_59:
 {1.0}bGSH = {1.0}ext
  0.7*bGSH
v_6:
 {1.0}hcy = {1.0}met + {1.0}dmg
  Vmbhmt * (hcy / Kmbhmthcy) / (1 + hcy / Kmbhmthcy) * BET / (Kmbhmtbet + BET) * exp(-0.0021 * (SAH + SAM)) * exp(0.0021 * 102.59) * (H2O2ss + KibhmtH2O2) / (H2O2 + KibhmtH2O2)
v_60:
 {1.0}bGSSG = {1.0}ext
  7.5*bGSSG
v_7:
 {1.0}hcy + {1.0}c5mTHF = {1.0}met + {1.0}cTHF
  vmMS*(hcy/kmMShcy)/(1 + (hcy/kmMShcy))*(c5mTHF/kmMSmTH4)/(1 + (c5mTHF/kmMSmTH4))*(kiMSH2O2 + H2O2ss)/(kiMSH2O2 + H2O2)
v_8:
 {1.0}hcy + {1.0}cser = {1.0}cyt
  Vmcbs * cser / (Kmcbsserine + cser) * hcy / Kmcbshcy / (1 + hcy / Kmcbshcy) * 1.2 / ((30 / (SAM + SAH))**2 + 1) * (1.2 / ((30 / 102.59)**2 + 1))**-1 * (kaH2O2 + H2O2) / (kaH2O2 + H2O2ss)
v_9:
 {1.0}cyt = {1.0}ccys
  vmctgl*(cyt/kmctglcyt)/(1 + (cyt/kmctglcyt))


#parameters
BET = 50.0
DUMP = 20.0
GARP = 10.0
H2O2 = 0.01
H2O2ss = 0.01
HCHO = 500.0
KibhmtH2O2 = 0.01
KmahSAH = 6.5
Kmahhcy = 150.0
Kmbhmtbet = 100.0
Kmbhmthcy = 12.0
KmcARTaic = 100.0
KmcARTc10fTHF = 5.9
KmcDHFRcDHF = 0.5
KmcDHFRcNADPH = 4.0
KmcFTScHCOOH = 43.0
KmcFTScTHF = 3.0
KmcMTCHc10fTHF = 100.0
KmcMTCHcCHTHF = 250.0
KmcMTDcCH2THF = 2.0
KmcMTDcCHTHF = 10.0
KmcMTHFRcCH2THF = 50.0
KmcMTHFRcNADPH = 16.0
KmcPGTGARP = 520.0
KmcPGTc10fTHF = 4.9
KmcSHMTcCH2THF = 3200.0
KmcSHMTcTHF = 50.0
KmcSHMTcgly = 10000.0
KmcSHMTcser = 600.0
KmcTSDUMP = 6.3
KmcTScCH2THF = 14.0
Kmcbshcy = 1000.0
Kmcbsserine = 2000.0
Kmcdoccys = 3100.0
KmmDMGDdmg = 50.0
KmmDMGDmTHF = 50.0
KmmFTSm10fTHF = 22.0
KmmFTSmHCOOH = 43.0
KmmFTSmTHF = 3.0
KmmGDCmTHF = 50.0
KmmGDCmgly = 3400.0
KmmMTCHm10fTHF = 100.0
KmmMTCHmCHTHF = 250.0
KmmMTDmCH2THF = 2.0
KmmMTDmCHTHF = 10.0
KmmSDHmTHF = 50.0
KmmSDHsarc = 320.0
KmmSHMTmCH2THF = 3200.0
KmmSHMTmTHF = 50.0
KmmSHMTmgly = 10000.0
KmmSHMTmser = 600.0
KmmethSAH = 1.4
KmmethSAM = 1.4
Kmsermser = 5700.0
Vmbhmt = 2160.0
VmcART = 55000.0
VmcDHFR = 2000.0
VmcFTD = 500.0
VmcFTS = 3900.0
VmcMTHFR = 6000.0
VmcPGT = 24300.0
VmcTS = 5000.0
Vmcbs = 420000.0
Vmcdo = 1327.15
Vmfah = 320.0
VmfcMTCH = 500000.0
VmfcMTD = 80000.0
VmfcSHMT = 5200.0
VmfmFTS = 2000.0
VmfmMTCH = 790000.0
VmfmMTD = 180000.0
VmfmSHMT = 11440.0
VmmDMGD = 15000.0
VmmFTD = 1050.0
VmmGDC = 15000.0
VmmSDH = 15000.0
Vmmeth = 180.0
Vmrah = 755.0
VmrcMTCH = 20000.0
VmrcMTD = 600000.0
VmrcSHMT = 15000000.0
VmrmFTS = 6300.0
VmrmMTCH = 20000.0
VmrmMTD = 594000.0
VmrmSHMT = 30000000.0
Vmser = 10000.0
cNADPH = 50.0
k0 = 0.0
kaGSSGh = 0.01
kaGSSGl = 0.01
kaH2O2 = 0.035
kagcl = 0.01
kbser = 150.0
kcgly = 1.0
kcysin = 70.0
kcysinbcys = 2100.0
keqgcl = 5597.0
keqgs = 5600.0
kfcNE = 0.03
kfmNE = 0.03
kglutin = 1.0
kgly = 5700.0
kglyin = 630.0
khcooh = 100.0
kiMATiGSSG = 2140.0
kiMATiiiGSSG = 4030.0
kiMSH2O2 = 0.01
kmGNMTSAH = 18.0
kmGNMTcgly = 130.0
kmGPXH2O2 = 0.01
kmGPXgsh = 1330.0
kmGSSGh = 1250.0
kmGSSGl = 7110.0
kmMATiSAM = 50.0
kmMATiiiSAM = 129600.0
kmMATiiimet = 300.0
kmMATimet = 41.0
kmMShcy = 1.0
kmMSmTH4 = 25.0
kmbglut = 300.0
kmbgly = 150.0
kmcFTDc10fTHF = 20.0
kmctglcyt = 500.0
kmetin = 30.0
kmetincmethionine = 1.0
kmgclccys = 100.0
kmgclglc = 300.0
kmgclglut = 1900.0
kmgclgsh = 8200.0
kmgrGSSG = 107.0
kmgrNADPH = 10.4
kmgscglc = 22.0
kmgscgly = 300.0
kmgshe = 3300.0
kmgshout = 240.0
kmgshouth = 150.0
kmgshoutl = 3000.0
kmmFTDm10fTHF = 20.0
kmmetinoutmethionine = 150.0
kpcgsh = 30.0
krcNE = 22.0
krmNE = 20.0
krserin = 1.0
kserin = 150.0
vmGPX = 4500.0
vmGSSGh = 40.0
vmGSSGl = 4025.0
vmMATi = 650.0
vmMATiii = 220.0
vmMS = 500.0
vmctgl = 1500.0
vmcysin = 14950.0
vmfgly = 10000.0
vmgcl = 3600.0
vmglutin = 28000.0
vmglyin = 4600.0
vmgr = 892.5
vmgs = 5400.0
vmgshe = 304.0
vmgshout = 1000.0
vmgshouth = 150.0
vmgshoutl = 1100.0
vmmetin = 913.4
vmrgly = 10000.0
vmserin = 2700.0
vocysb = 70.0
voglub = 273.0
voglyb = 630.0
bmet = 30.0
bser = 150.0
ext = 1.0
default_compartment = 1.0


#initial values
SAH = 19.1432773636787
SAM = 81.1684566962769
aic = 0.942750394171554
bGSH = 12.6996048211362
bGSSG = 0.484328542816829
bcys = 185.50378543937
bglut = 60.4330872702655
bgly = 221.101111778807
c10fTHF = 3.40907070478307
c5mTHF = 4.4965335653401
cCH2THF = 0.506278119133034
cCHTHF = 0.278602708139276
cDHF = 0.0385952337473159
cGSH = 6590.56824161192
cGSSG = 61.3019611792609
cHCOOH = 13.0888186429922
cTHF = 4.61991966766058
ccys = 194.96740946034
cglc = 9.80842470037426
cglut = 3219.39793573653
cgly = 924.429820216685
cser = 562.834377270222
cyt = 36.8825861752429
dmg = 0.707382712261505
hcy = 1.12248362561721
m10fTHF = 15.9087989350187
mCH2THF = 1.66610924423152
mCHTHF = 1.54929073348709
mHCOOH = 55.820116666595
mTHF = 20.995801088388
met = 49.1868215837869
mgly = 2040.43402532595
msarc = 9.16245914628594
mser = 2114.87119909779


#assignment rules