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TestG2M.py
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TestG2M.py
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from pysb import *
from pysb.macros import catalyze, degrade, equilibrate, bind, bind_table, synthesize
# instantiate a model
Model()
#Declare Monomers
Monomer('Cb',['b', 'S'], {'S':['i', 'a']})
Monomer('Cdk1',['b', 'c', 'S'], {'S':['i', 'a']})
Monomer('p27_p21',['b', 'S'], {'S':['u', 'p']})
Monomer('Wee1',['b', 'S'], {'S':['a', 'i']})
Monomer('CDC25', ['b', 'S'], {'S':['a', 'i']})
Monomer('CDC20', ['b', 'S'], {'S':['a', 'i']})
Monomer('Cdh1', ['b', 'S'], {'S':['a', 'i']})
#Declare Parameters
#Parameter for Synthesis of Cyclin B
Parameter('kSCb', 8.0e-04) #FILL IN VALUE- THIS VALUE IS NOT IN IWAMOTO PAPER
#Parameter for Degradation of Cyclin B
Parameter('kDCb', 5.0e-04) #FILL IN VALUE- THIS VALUE IS NOT IN IWAMOTO PAPER
#Cyclin B/Cdk1 binding parameters:
Parameter('kcdk1f',1.0e-03)
Parameter('kcdk1r', 2.0e-04) #FILL IN VALUES- THESE VALUES ARE NOT IN IWAMOTO PAPER
#CyclinB/Cdk1 Complex Equilibrate Parameters:
Parameter('kfcbcdk', 1.9e-02) #FILL IN VALUE- THIS VALUE IS NOT IN IWAMOTO PAPER
Parameter('krcbcdk', 5.0e-04) #FILL IN VALUE- THIS VALUE IS NOT IN IWAMOTO PAPER
#Cyclin B/Cdk1/p27_p21 binding parameters:
Parameter('kfcp27_p21', 1.5e-03) #FILL IN VALUE- THIS VALUE IS NOT IN IWAMOTO PAPER
Parameter('krcp27_p21', 1.75e-04) #FILL IN VALUE- THIS VALUE IS NOT IN IWAMOTO PAPER
#Paramerers for CDC25 equilibration:
Parameter('kfCDC25', 5.0e-08) #THESE PARAMETERS ARE NOT CORRECT- ESTIMATED FOR NOW. CDC25 IS NOT IN IWAMOTO PAPER
Parameter('krCDC25', 2.5e-03) #THESE PARAMETERS ARE NOT CORRECT- ESTIMATED FOR NOW. CDC25 IS NOT IN IWAMOTO PAPER
#Parameters for CDC20 equilibration:
Parameter('kfCDC20', 5.0e-08) #THESE PARAMETERS ARE NOT CORRECT- ESTIMATED FOR NOW. CDC20 IS NOT IN IWAMOTO PAPER
Parameter('krCDC20', 2.5e-03) #THESE PARAMETERS ARE NOT CORRECT- ESTIMATED FOR NOW. CDC20 IS NOT IN IWAMOTO PAPER
#Parameters for Wee1 equilibration:
Parameter('kfWee1', 5.0e-08) #THESE PARAMETERS ARE NOT CORRECT- ESTIMATED FOR NOW. Check Iwamoto
Parameter('krWee1', 2.5e-03) #THESE PARAMETERS ARE NOT CORRECT- ESTIMATED FOR NOW. Check Iwamoto
#Observables
#Observable('obsCdh1i', Cdh1(b=None, S='i'))
#Observable('obsCdh1a', Cdh1(b=None, S='a'))
Observable('obsCbi', Cb(b=None, S='i'))
Observable('obsCba', Cb(b=None, S='a'))
Observable('obsCb_Cdk1i', Cb(b=1, S='a') % Cdk1(b=1, S ='i'))
Observable('obsCb_Cdk1a', Cb(b=1, S='a') % Cdk1(b=1, S ='a'))
Observable('obsCb_Cdk1a_p27', Cb(b=1, S='i') % Cdk1(b=1, c=2, S ='i') % p27_p21(b=2, S='u'))
Observable('obsp27_p21u', p27_p21(b=None, S='u'))
Observable('obsp27_p21p', p27_p21(b=None, S='p'))
Observable('obsWee1i', Wee1(b=None, S='i'))
Observable('obsWee1a', Wee1(b=None, S='a'))
Observable('obsCDC25i', CDC25(b=None, S='i'))
Observable('obsCDC25a', CDC25(b=None, S='a'))
Observable('obsCDC20i', CDC25(b=None, S='i'))
Observable('obsCDC20a', CDC25(b=None, S='a'))
Observable('obsCdk1i', Cdk1(b=None, c= None, S='i'))
Observable('obsCdk1a', Cdk1(b=None, c= None, S='a'))
#Initial Conditions
Parameter('Cb_0', 4.0e-05) #VALUE NOT CORRECT
Initial(Cb(b=None, S='a'), Cb_0)
Parameter('Cdk1_0', 1.35e01) #VALUE NOT CORRECT
Initial(Cdk1(b=None, c=None, S='i'),Cdk1_0)
Parameter('Cb_Cdk1i_0', 4.0e-04) #VALUE NOT CORRECT
Initial(Cb(b=1, S='a') % Cdk1(b=1, c=None, S='i'), Cb_Cdk1i_0)
Parameter('Cb_Cdk1a_0', 1.0e-04) ##VALUE NOT CORRECT
Initial(Cb(b=1, S='a') % Cdk1(b=1, c=None, S='a'), Cb_Cdk1a_0)
Parameter('p27_21_0', 1.0e01) #Y10 in Iwamoto
Initial(p27_p21(b=None, S='u'),p27_21_0)
Parameter('Cb_Cdk1_p27_p21_0', 1.0e-04) #VALUE NOT CORRECT
Initial(Cb(b=1, S='a') % Cdk1(b=1, c=2, S='a') % p27_p21(b=2, S='u'), Cb_Cdk1_p27_p21_0)
Parameter('CDC25_0', 1.0e01) #THIS PARAMETER IS NOT CORRECT- ESTIMATED FOR NOW- NOT IN IWAMOTO PAPER
Initial(CDC25(b=None, S='i'), CDC25_0)
#Declare Rules
#Cyclin B Synthesis and Degradation
synthesize(Cb(b=None, S = 'a'), kSCb)
degrade(Cb(b=None, S='a'),kDCb)
#Cyclin B binds to Cdk1
Rule('Cb_Cdk1_bind',Cb(b=None, S='a') + Cdk1(b=None, c=None, S='i') <> Cb(b=1, S='a') % Cdk1(b=1, c=None, S ='i'), *[kcdk1f, kcdk1r])
#The Cb/Cdk1 complex equilibrates from inactive to active
equilibrate(Cb(b=1, S='a') % Cdk1(b=1, c=None, S='i'),Cb(b=1, S='a') % Cdk1(b=1, c=None, S='a'),[kfcbcdk,krcbcdk])
#The Cb/Cdk1 complex binds to p27_p21 - this complex is inactive
Rule ('Cb_Cdk1_p27_p21_bind',p27_p21(b=None, S='u') + Cb(b=1, S='a') % Cdk1(b=1, c=None, S='a') <> Cb(b=1, S='i') % Cdk1(b=1, c=2, S ='i') % p27_p21(b=2, S='u') , *[kfcp27_p21, krcp27_p21])
#Equilibrate CDC25
equilibrate(CDC25(b=None,S='i'),CDC25(b=None, S='a'),[kfCDC25, krCDC25])
#Equilibrate CDC20
equilibrate(CDC20(b=None,S='i'),CDC20(b=None, S='a'),[kfCDC20, krCDC20])
#Equilibrate Wee1
equilibrate(Wee1(b=None,S='i'),Wee1(b=None, S='a'),[kfWee1, krWee1])
##JUST NEED TO SHOW THE EFFECTS OF MONOMERS AND COMPLEXES ON OTHER MONOMERS AND COMPLEXES NOW