def extension_hypothesis__feedback1(self):
return HypothesisExtension(
name='Feedback1',
reaction='pA -> A',
rate_law='VmaxA * pA / (kmA + pA)',
mode='additive',
to_replace=None, # name of reaction we want to replace
)
def extension_hypothesis__feedback2(self):
return HypothesisExtension(
name='Feedback2',
reaction='pA -> A',
rate_law='k4 * pA', # mass action variant
mode='additive',
to_replace=None, # name of reaction we want to replace
)
def extension_hypothesis__additive2(self):
return HypothesisExtension(
name='AdditiveReaction2',
reaction='pC -> C',
rate_law='k3b * C',
mode='additive',
to_replace=None, # not needed for additive mode
)
def extension_hypothesis__replace_reaction(self):
return HypothesisExtension(
name='ReplaceReaction',
reaction='pB -> B',
rate_law='VmaxB * pB / (kmB + pB)',
mode='replace',
to_replace='R2f', # name of reaction we want to replace
)
def extension_hypothesis__additive1(self):
return HypothesisExtension(
name='AdditiveReaction1',
reaction='pB -> B',
rate_law='k2b * pB',
mode='additive',
to_replace=None, # not needed for additive mode
)
def extension_hypothesis__ErkActivateSmad2AktInhibit(self):
return HypothesisExtension(
name='CrossTalkR2',
reaction='Smad2 => pSmad2',
rate_law=
'NonCompetitiveInhibitionWithKcatAndExtraActivator(_kErkPhosSmad2_km, _kErkPhosSmad2_ki, _kErkPhosSmad2_kcat, TGFb, pErk, 1, pAkt, Smad2); //(km, ki, kcat, E, n, I, S)',
mode='replace',
to_replace='TGFbR1')
def extension_hypothesis__AktActivateSmad2ErkInhibit(self):
"""
This reaction must replace:
TGFbR1: Smad2 => pSmad2 ; _kSmad2PhosByTGFb*Smad2*TGFb;
Args:
type:
replacement_reaction:
Returns:
"""
return HypothesisExtension(
name='CrossTalkR1',
reaction='Smad2 => pSmad2',
rate_law=
'NonCompetitiveInhibitionWithKcatAndExtraActivator(_kAktPhosSmad2_km, _kAktPhosSmad2_ki, _kAktPhosSmad2_kcat, TGFb, pAkt, 1, pErk, Smad2)',
mode='replace',
to_replace='TGFbR1')
def extension_hypothesis__ErkActivatesS6K(self):
return HypothesisExtension(name='CrossTalkR6',
reaction='S6K => pS6K',
rate_law='_ErkActivateS6K*pErk*S6K',
mode='additive',
to_replace=None)
def extension_hypothesis__S6KActivateErk(self):
return HypothesisExtension(name='CrossTalkR5',
reaction='Erk => pErk',
rate_law='_kS6KActivateErk*Erk*pS6K',
mode='additive',
to_replace=None)