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ras_amp_pka.py
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from pysb import *
import numpy as np
from scipy.constants import N_A
Model()
Parameter('K0' , 1.0 )
Parameter('K1' , 1.0 )
Parameter('K2' , 1.5 )
Parameter('K3' , 1.0 )
Parameter('K4' , 1.0 )
Parameter('K5' , 1.0 )
Parameter('K6' , 1.0 )
Parameter('K7' , 1.0 )
Parameter('K8' , 0.01 )
Parameter('K9' , 0.25 )
Parameter('K10' , 0.001 )
Parameter('K11' , 2.1e-06 )
Parameter('K12' , 0.001 )
Parameter('K13' , 1e-05 )
Parameter('K14' , 1e-05 )
Parameter('K15' , 1e-05 )
Parameter('K16' , 1e-05 )
Parameter('K17' , 0.1 )
Parameter('K18' , 0.1 )
Parameter('K19' , 0.1 )
Parameter('K20' , 0.1 )
Parameter('K21' , 1.0 )
Parameter('K22' , 1.0 )
Parameter('K23' , 0.75 )
Parameter('K24' , 1.0 )
Parameter('K25' , 1e-06 )
Parameter('K26' , 0.1 )
Parameter('K27' , 0.1 )
Parameter('K28' , 7.5 )
Parameter('K29' , 0.0001 )
Parameter('K30' , 0.0001 )
Parameter('K31' , 1.0 )
Parameter('K32' , 1.7 )
Parameter('K33' , 1.0 )
Parameter('K34' , 0.01 )
Parameter('K35' , 0.001 )
Parameter('K36' , 1.25 )
Parameter('K37' , 2.5 )
Parameter('K38' , 10.0 )
Monomer('Ras2_GDP')
Monomer('Cdc25')
Monomer('Ras2_GDP_Cdc25')
Monomer('Ras2_Cdc25')
Monomer('GDP')
Monomer('GTP')
Monomer('Ras2_GTP_Cdc25')
Monomer('Ras2_GTP')
Monomer('Ira2')
Monomer('Ras2_GTP_Ira2')
Monomer('CYR1')
Monomer('Ras2_GTP_CYR1')
Monomer('ATP')
Monomer('cAMP')
Monomer('PKA')
Monomer('cAMP_PKA')
Monomer('IIcAMP_PKA')
Monomer('IIIcAMP_PKA')
Monomer('IVcAMP_PKA')
Monomer('C')
Monomer('R_2cAMP')
Monomer('R')
Monomer('R_C')
Monomer('Pde1')
Monomer('Pde1f')
Monomer('cAMP_Pde1f')
Monomer('AMP')
Monomer('PPA2')
Monomer('Pde2')
Monomer('cAMP_Pde2')
Monomer('Cdc25f')
Monomer('Ira2P')
Monomer('Ras2_GTP_Ira2P')
Initial(Ras2_GDP() ,Parameter("Ras2_GDP_0",20000.0) )
Initial(Cdc25() ,Parameter("Cdc25_0",300.0) )
Initial(GDP() ,Parameter("GDP_0",1500000.0) )
Initial(GTP() ,Parameter("GTP_0",5000000.0) )
Initial(Ira2() ,Parameter("Ira2_0",200.0) )
Initial(CYR1() ,Parameter("CYR1_0",200.0) )
Initial(ATP() ,Parameter("ATP_0",24000000.0) )
Initial(PKA() ,Parameter("PKA_0",2500.0) )
Initial(Pde1() ,Parameter("Pde1_0",1400.0) )
Initial(PPA2() ,Parameter("PPA2_0",4000.0) )
Initial(Pde2() ,Parameter("Pde2_0",6500.0) )
Observable("obs_Ras2_GDP" , Ras2_GDP() )
Observable("obs_Cdc25" , Cdc25() )
Observable("obs_Ras2_GDP_Cdc25" , Ras2_GDP_Cdc25() )
Observable("obs_Ras2_Cdc25" , Ras2_Cdc25() )
Observable("obs_GDP" , GDP() )
Observable("obs_GTP" , GTP() )
Observable("obs_Ras2_GTP_Cdc25" , Ras2_GTP_Cdc25() )
Observable("obs_Ras2_GTP" , Ras2_GTP() )
Observable("obs_Ira2" , Ira2() )
Observable("obs_Ras2_GTP_Ira2" , Ras2_GTP_Ira2() )
Observable("obs_CYR1" , CYR1() )
Observable("obs_Ras2_GTP_CYR1" , Ras2_GTP_CYR1() )
Observable("obs_ATP" , ATP() )
Observable("obs_cAMP" , cAMP() )
Observable("obs_PKA" , PKA() )
Observable("obs_cAMP_PKA" , cAMP_PKA() )
Observable("obs_IIcAMP_PKA" , IIcAMP_PKA() )
Observable("obs_IIIcAMP_PKA" , IIIcAMP_PKA() )
Observable("obs_IVcAMP_PKA" , IVcAMP_PKA() )
Observable("obs_C" , C() )
Observable("obs_R_2cAMP" , R_2cAMP() )
Observable("obs_R" , R() )
Observable("obs_R_C" , R_C() )
Observable("obs_Pde1" , Pde1() )
Observable("obs_Pde1f" , Pde1f() )
Observable("obs_cAMP_Pde1f" , cAMP_Pde1f() )
Observable("obs_AMP" , AMP() )
Observable("obs_PPA2" , PPA2() )
Observable("obs_Pde2" , Pde2() )
Observable("obs_cAMP_Pde2" , cAMP_Pde2() )
Observable("obs_Cdc25f" , Cdc25f() )
Observable("obs_Ira2P" , Ira2P() )
Observable("obs_Ras2_GTP_Ira2P" , Ras2_GTP_Ira2P() )
Rule("R0" , Ras2_GDP() + Cdc25() >> Ras2_GDP_Cdc25() , K0)
Rule("R1" , Ras2_GDP_Cdc25() >> Ras2_GDP() + Cdc25() , K1)
Rule("R2" , Ras2_GDP_Cdc25() >> Ras2_Cdc25() + GDP() , K2)
Rule("R3" , Ras2_Cdc25() + GDP() >> Ras2_GDP_Cdc25() , K3)
Rule("R4" , Ras2_Cdc25() + GTP() >> Ras2_GTP_Cdc25() , K4)
Rule("R5" , Ras2_GTP_Cdc25() >> Ras2_Cdc25() + GTP() , K5)
Rule("R6" , Ras2_GTP_Cdc25() >> Cdc25() + Ras2_GTP() , K6)
Rule("R7" , Cdc25() + Ras2_GTP() >> Ras2_GTP_Cdc25() , K7)
Rule("R8" , Ras2_GTP() + Ira2() >> Ras2_GTP_Ira2() , K8)
Rule("R9" , Ras2_GTP_Ira2() >> Ras2_GDP() + Ira2() , K9)
Rule("R10" , Ras2_GTP() + CYR1() >> Ras2_GTP_CYR1() , K10)
Rule("R11" , Ras2_GTP_CYR1() + ATP() >> Ras2_GTP_CYR1() + cAMP() , K11)
Rule("R12" , Ira2() + Ras2_GTP_CYR1() >> Ras2_GDP() + Ira2() + CYR1() , K12)
Rule("R13" , cAMP() + PKA() >> cAMP_PKA() , K13)
Rule("R14" , cAMP() + cAMP_PKA() >> IIcAMP_PKA() , K14)
Rule("R15" , cAMP() + IIcAMP_PKA() >> IIIcAMP_PKA() , K15)
Rule("R16" , cAMP() + IIIcAMP_PKA() >> IVcAMP_PKA() , K16)
Rule("R17" , IVcAMP_PKA() >> cAMP() + IIIcAMP_PKA() , K17)
Rule("R18" , IIIcAMP_PKA() >> cAMP() + IIcAMP_PKA() , K18)
Rule("R19" , IIcAMP_PKA() >> cAMP() + cAMP_PKA() , K19)
Rule("R20" , cAMP_PKA() >> cAMP() + PKA() , K20)
Rule("R21" , IVcAMP_PKA() >> C() + C() + R_2cAMP() + R_2cAMP() , K21)
Rule("R22" , R_2cAMP() >> cAMP() + cAMP() + R() , K22)
Rule("R23" , C() + R() >> R_C() , K23)
Rule("R24" , R_C() + R_C() >> PKA() , K24)
Rule("R25" , C() + Pde1() >> C() + Pde1f() , K25)
Rule("R26" , cAMP() + Pde1f() >> cAMP_Pde1f() , K26)
Rule("R27" , cAMP_Pde1f() >> cAMP() + Pde1f() , K27)
Rule("R28" , cAMP_Pde1f() >> Pde1f() + AMP() , K28)
Rule("R29" , Pde1f() + PPA2() >> Pde1() + PPA2() , K29)
Rule("R30" , cAMP() + Pde2() >> cAMP_Pde2() , K30)
Rule("R31" , cAMP_Pde2() >> cAMP() + Pde2() , K31)
Rule("R32" , cAMP_Pde2() >> AMP() + Pde2() , K32)
Rule("R33" , Cdc25() + C() >> C() + Cdc25f() , K33)
Rule("R34" , PPA2() + Cdc25f() >> Cdc25() + PPA2() , K34)
Rule("R35" , Ira2() + C() >> C() + Ira2P() , K35)
Rule("R36" , Ras2_GTP() + Ira2P() >> Ras2_GTP_Ira2P() , K36)
Rule("R37" , Ras2_GTP_Ira2P() >> Ras2_GDP() + Ira2P() , K37)
Rule("R38" , Ira2P() >> Ira2() , K38)