# # This file is automatically generated with # the System Biology Format Converter (http://sbfc.sourceforge.net/) # from an SBML file. # # # Model name = Markevich2004_MAPK_phosphoRandomElementary # # is http://identifiers.org/biomodels.db/MODEL6618552953 # is http://identifiers.org/biomodels.db/BIOMD0000000028 # isDescribedBy http://identifiers.org/pubmed/14744999 # # some function definitions that are allowed in SBML but not valid in xpp ceil(x)=flr(1+x) @delay=50 # Compartment: id = cell, name = cell, constant par cell=1.0 # Parameter: id = k1, name = k1, constant par k1=0.005 # Parameter: id = k_1, name = k_1, constant par k_1=1.0 # Parameter: id = k2, name = k2, constant par k2=1.08 # Parameter: id = k3, name = k3, constant par k3=0.025 # Parameter: id = k_3, name = k_3, constant par k_3=1.0 # Parameter: id = k4, name = k4, constant par k4=0.007 # Parameter: id = k5, name = k5, constant par k5=0.05 # Parameter: id = k_5, name = k_5, constant par k_5=1.0 # Parameter: id = k6, name = k6, constant par k6=0.008 # Parameter: id = k7, name = k7, constant par k7=0.005 # Parameter: id = k_7, name = k_7, constant par k_7=1.0 # Parameter: id = k8, name = k8, constant par k8=0.45 # Parameter: id = h1, name = h1, constant par h1=0.045 # Parameter: id = h_1, name = h_1, constant par h_1=1.0 # Parameter: id = h2, name = h2, constant par h2=0.092 # Parameter: id = h3, name = h3, constant par h3=1.0 # Parameter: id = h_3, name = h_3, constant par h_3=0.01 # Parameter: id = h4, name = h4, constant par h4=0.01 # Parameter: id = h_4, name = h_4, constant par h_4=1.0 # Parameter: id = h5, name = h5, constant par h5=0.5 # Parameter: id = h6, name = h6, constant par h6=0.086 # Parameter: id = h_6, name = h_6, constant par h_6=0.0011 # Parameter: id = h7, name = h7, constant par h7=0.01 # Parameter: id = h_7, name = h_7, constant par h_7=1.0 # Parameter: id = h8, name = h8, constant par h8=0.47 # Parameter: id = h9, name = h9, constant par h9=0.14 # Parameter: id = h_9, name = h_9, constant par h_9=0.0018 # Reaction: id = reaction_0000001, name = binding ERK and MEK reaction_=cell*(k1*M*MEK-k_1*M_MEK_Y) # Reaction: id = reaction_0000002, name = tyr phosphorylation of ERK reactio_1=cell*k2*M_MEK_Y # Reaction: id = reaction_0000003, name = binding ERK-PY and MEK reactio_2=cell*(k3*MpY*MEK-k_3*MpY_MEK) # Reaction: id = reaction_0000004, name = thr phosphorylation of ERK reactio_3=cell*k4*MpY_MEK # Reaction: id = reaction_0000005, name = binding ERK and MEK reactio_4=cell*(k5*M*MEK-k_5*M_MEK_T) # Reaction: id = reaction_0000006, name = thr phosphorylation of ERK reactio_5=cell*k6*M_MEK_T # Reaction: id = reaction_0000007, name = binding ERK-PT and MEK reactio_6=cell*(k7*MpT*MEK-k_7*MpT_MEK) # Reaction: id = reaction_0000008, name = tyr phosphorylation of ERK reactio_7=cell*k8*MpT_MEK # Reaction: id = reaction_0000009, name = binding ERK-PP and MKP3 reactio_8=cell*(h1*Mpp*MKP3-h_1*Mpp_MKP3) # Reaction: id = reaction_0000010, name = dephosphorylation of tyr on ERK-PP reactio_9=cell*h2*Mpp_MKP3 # Reaction: id = reaction_0000011, name = dissociation ERK-PT and MKP3 reacti_10=cell*(h3*MpT_MKP3_-h_3*MpT*MKP3) # Reaction: id = reaction_0000012, name = dephosphorylation of ERK-PT reacti_11=cell*h5*MpT_MKP_1 # Reaction: id = reaction_0000013, name = binding ERK-PT and MKP3 reacti_12=cell*(h4*MpT*MKP3-h_4*MpT_MKP_1) # Reaction: id = reaction_0000014, name = dephosphorylation of ERK-PY reacti_13=cell*h8*MpY_MKP3 # Reaction: id = reaction_0000015, name = dissociation ERK and MKP3 reacti_14=cell*(h6*M_MKP3_T-h_6*M*MKP3) # Reaction: id = reaction_0000017, name = binding ERK-PY and MKP3 reacti_15=cell*(h7*MpY*MKP3-h_7*MpY_MKP3) # Reaction: id = reaction_0000019, name = Dissociation ERK and MKP3 reacti_16=cell*(h9*M_MKP3_Y-h_9*M*MKP3) # Species: id = M, name = ERK, affected by kineticLaw init M=800.0 dM/dt=(1/(cell))*((-1.0 * reaction_) + (-1.0 * reactio_4) + ( 1.0 * reacti_14) + ( 1.0 * reacti_16)) # Species: id = MpY, name = ERK-PY, affected by kineticLaw init MpY=0.0 dMpY/dt=(1/(cell))*(( 1.0 * reactio_1) + (-1.0 * reactio_2) + (-1.0 * reacti_15)) # Species: id = MpT, name = ERK-PT, affected by kineticLaw init MpT=0.0 dMpT/dt=(1/(cell))*(( 1.0 * reactio_5) + (-1.0 * reactio_6) + ( 1.0 * reacti_10) + (-1.0 * reacti_12)) # Species: id = Mpp, name = ERK-PP, affected by kineticLaw init Mpp=0.0 dMpp/dt=(1/(cell))*(( 1.0 * reactio_3) + ( 1.0 * reactio_7) + (-1.0 * reactio_8)) # Species: id = MEK, name = MEK, affected by kineticLaw init MEK=180.0 dMEK/dt=(1/(cell))*((-1.0 * reaction_) + ( 1.0 * reactio_1) + (-1.0 * reactio_2) + ( 1.0 * reactio_3) + (-1.0 * reactio_4) + ( 1.0 * reactio_5) + (-1.0 * reactio_6) + ( 1.0 * reactio_7)) # Species: id = MKP3, name = MKP3, affected by kineticLaw init MKP3=100.0 dMKP3/dt=(1/(cell))*((-1.0 * reactio_8) + ( 1.0 * reacti_10) + (-1.0 * reacti_12) + ( 1.0 * reacti_14) + (-1.0 * reacti_15) + ( 1.0 * reacti_16)) # Species: id = MpY_MEK, name = ERK-PY_MEK, affected by kineticLaw init MpY_MEK=0.0 dMpY_MEK/dt=(1/(cell))*(( 1.0 * reactio_2) + (-1.0 * reactio_3)) # Species: id = MpT_MEK, name = ERK-PT_MEK, affected by kineticLaw init MpT_MEK=0.0 dMpT_MEK/dt=(1/(cell))*(( 1.0 * reactio_6) + (-1.0 * reactio_7)) # Species: id = M_MEK_Y, name = ERK_MEK_Y, affected by kineticLaw init M_MEK_Y=0.0 dM_MEK_Y/dt=(1/(cell))*(( 1.0 * reaction_) + (-1.0 * reactio_1)) # Species: id = M_MEK_T, name = ERK_MEK_T, affected by kineticLaw init M_MEK_T=0.0 dM_MEK_T/dt=(1/(cell))*(( 1.0 * reactio_4) + (-1.0 * reactio_5)) # Species: id = Mpp_MKP3, name = ERK-PP_MKP3, affected by kineticLaw init Mpp_MKP3=0.0 dMpp_MKP3/dt=(1/(cell))*(( 1.0 * reactio_8) + (-1.0 * reactio_9)) # Species: id = MpY_MKP3, name = ERK-PY_MKP3, affected by kineticLaw init MpY_MKP3=0.0 dMpY_MKP3/dt=(1/(cell))*((-1.0 * reacti_13) + ( 1.0 * reacti_15)) # Species: id = MpT_MKP3_Y, name = ERK-PT_MKP3_Y, affected by kineticLaw par MpT_MKP3_=0.0 aux MpT_MKP3_=MpT_MKP3_ dMpT_MKP3_/dt=(1/(cell))*(( 1.0 * reactio_9) + (-1.0 * reacti_10)) # Species: id = MpT_MKP3_T, name = ERK-PT_MKP3_T, affected by kineticLaw par MpT_MKP_1=0.0 aux MpT_MKP_1=MpT_MKP_1 dMpT_MKP_1/dt=(1/(cell))*((-1.0 * reacti_11) + ( 1.0 * reacti_12)) # Species: id = M_MKP3_T, name = ERK_MKP3_T, affected by kineticLaw init M_MKP3_T=0.0 dM_MKP3_T/dt=(1/(cell))*(( 1.0 * reacti_11) + (-1.0 * reacti_14)) # Species: id = M_MKP3_Y, name = ERK_MKP3_Y, affected by kineticLaw init M_MKP3_Y=0.0 dM_MKP3_Y/dt=(1/(cell))*(( 1.0 * reacti_13) + (-1.0 * reacti_16)) @ meth=cvode, tol=1e-6, atol=1e-8 # @ maxstor=1e6 @ bound=40000, total=200 done