# # This file is automatically generated with # the System Biology Format Converter (http://sbfc.sourceforge.net/) # from an SBML file. # # # Model name = Bray1993_chemotaxis # # is urn:miriam:biomodels.db:BIOMD0000000404 # is urn:miriam:biomodels.db:MODEL6929313478 # isDescribedBy urn:miriam:pubmed:8334303 # # some function definitions that are allowed in SBML but not valid in xpp ceil(x)=flr(1+x) @delay=50 # FunctionDefinition id = function_4_motor_r1, name = function_4_motor_r1 function_(M,MYp,Yp,cell,ka,kappa)=(ka*(M*Yp-kappa/4*MYp)/cell) # FunctionDefinition id = function_4_motor_r2, name = function_4_motor_r2 functio_1(MYp,MYpYp,Yp,alpha,cell,ka,kappa)=(ka*(MYp*Yp-2*alpha*kappa/3*MYpYp)/cell) # FunctionDefinition id = function_4_motor_r3, name = function_4_motor_r3 functio_2(MYpYp,MYpYpYp,Yp,alpha,cell,ka,kappa)=(ka*(MYpYp*Yp-3*alpha*alpha*kappa/2*MYpYpYp)/cell) # FunctionDefinition id = function_4_motor_r4, name = function_4_motor_r4 functio_3(MYpYpYp,MYpYpYpYp,Yp,alpha,cell,ka,kappa)=(ka*(MYpYpYp*Yp-4*alpha*alpha*alpha*kappa*MYpYpYpYp)/cell) # FunctionDefinition id = Autophosphorylation, name = Autophosphorylation Autophosp(kcat,correction,E)=(kcat*correction*E) # FunctionDefinition id = ModAutophosphorylation, name = ModAutophosphorylation ModAutoph(M,S,kcat,correction)=(M*S*kcat*correction) # Compartment: id = cell, name = cell, constant par cell=1.41E-15 # Parameter: id = alpha, name = alpha, constant par alpha=0.14 # Parameter: id = kappa, name = kappa, constant par kappa=2.25E-7 # Parameter: id = ka, name = ka, constant par ka=0.1 # Parameter: id = Bias, name = Bias, defined by a Rule # Parameter: id = parameter_1, name = asp_pulse, constant par parameter=1.0E-7 # Parameter: id = parameter_2, name = autoPhospho, defined by a Rule # Parameter: id = parameter_3, name = KmATP, constant par paramet_2=3.0E-4 # assignmentRule: variable = Bias Bias=(M+MYp)/(M+MYp+MYpYp+MYpYpYp+MYpYpYpYp) aux Bias=Bias # assignmentRule: variable = parameter_2 paramet_1=species_1/(species_1+paramet_2) aux paramet_1=paramet_1 # Reaction: id = phosphorylation_r1, name = A->Ap # Local Parameter: id = kcat, name = kcat par kcat=0.0010 phosphory=cell*Autophosp(kcat, paramet_1, A) # Reaction: id = phosphorylation_r2, name = TWA+A->TWA+Ap # Local Parameter: id = kcat, name = kcat par kcat_1=75000.0 phospho_1=cell*ModAutoph(TWA, A, kcat_1, paramet_1) # Reaction: id = phosphorylation_r3, name = Tni_WA+A->Tni_WA+Ap # Local Parameter: id = kcat, name = kcat par kcat_1_2=200000.0 phospho_2=cell*ModAutoph(Tni_WA, A, kcat_1_2, paramet_1) # Reaction: id = phosphorylation_r4, name = Tasp_WA+Yp->Tasp_WA+Y # Local Parameter: id = k1, name = k1 par k1=1.0E8 phospho_3=cell*k1*Tasp_WA*Yp # Reaction: id = phosphorylation_r5, name = Ap+Y->A+Yp # Local Parameter: id = k1, name = k1 par k1_1=200000.0 phospho_4=cell*k1_1*Ap*Y # Reaction: id = phosphorylation_r6, name = Y ->Yp # Local Parameter: id = kcat, name = kcat par kcat_1__3=0.0 phospho_5=cell*Autophosp(kcat_1__3, paramet_1, Y) # Reaction: id = phosphorylation_r7, name = Yp->Y # Local Parameter: id = k1, name = k1 par k1_1_2=0.037 phospho_6=cell*k1_1_2*Yp # Reaction: id = phosphorylation_r8, name = Yp+Z->Y+Z # Local Parameter: id = k1, name = k1 par k1_1_2_3=500000.0 phospho_7=cell*k1_1_2_3*Yp*Z # Reaction: id = phosphorylation_r9, name = Ap+B->A+Bp # Local Parameter: id = k1, name = k1 par k1_1_2__4=1000000.0 phospho_8=cell*k1_1_2__4*Ap*B # Reaction: id = phosphorylation_r10, name = Bp->B # Local Parameter: id = k1, name = k1 par k1_1_2__5=1.0 phospho_9=cell*k1_1_2__5*Bp # Reaction: id = regulatory_r1, name = T+asp<->Tasp # Local Parameter: id = k1, name = k1 par k1_1_2__6=1000000.0 # Local Parameter: id = k2, name = k2 par k2=1.0 regulator=cell*(k1_1_2__6*T_renamed*asp-k2*Tasp) # Reaction: id = regulatory_r2, name = T+ni<->Tni # Local Parameter: id = k1, name = k1 par k1_1_2__7=1000.0 # Local Parameter: id = k2, name = k2 par k2_1=1.0 regulat_1=cell*(k1_1_2__7*T_renamed*ni-k2_1*Tni) # Reaction: id = regulatory_r3, name = T+W<->TW # Local Parameter: id = k1, name = k1 par k1_1_2__8=100000.0 # Local Parameter: id = k2, name = k2 par k2_1_2=1.0 regulat_2=cell*(k1_1_2__8*T_renamed*W-k2_1_2*TW) # Reaction: id = regulatory_r4, name = T+A<->TA # Local Parameter: id = k1, name = k1 par k1_1_2__9=10000.0 # Local Parameter: id = k2, name = k2 par k2_1_2_3=1.0 regulat_3=cell*(k1_1_2__9*T_renamed*A-k2_1_2_3*TA) # Reaction: id = regulatory_r5, name = W+A<->WA # Local Parameter: id = k1, name = k1 par k1_1_2_10=100000.0 # Local Parameter: id = k2, name = k2 par k2_1_2__4=1.0 regulat_4=cell*(k1_1_2_10*W*A-k2_1_2__4*WA) # Reaction: id = regulatory_r6, name = TW+A<->TWA # Local Parameter: id = k1, name = k1 par k1_1_2_11=400000.0 # Local Parameter: id = k2, name = k2 par k2_1_2__5=1.0 regulat_5=cell*(k1_1_2_11*TW*A-k2_1_2__5*TWA) # Reaction: id = regulatory_r7, name = TA+W<->TWA # Local Parameter: id = k1, name = k1 par k1_1_2_12=400000.0 # Local Parameter: id = k2, name = k2 par k2_1_2__6=1.0 regulat_6=cell*(k1_1_2_12*TA*W-k2_1_2__6*TWA) # Reaction: id = regulatory_r8, name = T+WA<->TWA # Local Parameter: id = k1, name = k1 par k1_1_2_13=400000.0 # Local Parameter: id = k2, name = k2 par k2_1_2__7=1.0 regulat_7=cell*(k1_1_2_13*T_renamed*WA-k2_1_2__7*TWA) # Reaction: id = regulatory_r9, name = Tasp+W<->Tasp_W # Local Parameter: id = k1, name = k1 par k1_1_2_14=100000.0 # Local Parameter: id = k2, name = k2 par k2_1_2__8=1.0 regulat_8=cell*(k1_1_2_14*Tasp*W-k2_1_2__8*Tasp_W) # Reaction: id = regulatory_r10, name = Tasp+A<->Tasp_A # Local Parameter: id = k1, name = k1 par k1_1_2_15=10000.0 # Local Parameter: id = k2, name = k2 par k2_1_2__9=1.0 regulat_9=cell*(k1_1_2_15*Tasp*A-k2_1_2__9*Tasp_A) # Reaction: id = regulatory_r11, name = Tasp_W+A<->Tasp_WA # Local Parameter: id = k1, name = k1 par k1_1_2_16=400000.0 # Local Parameter: id = k2, name = k2 par k2_1_2_10=1.0 regula_10=cell*(k1_1_2_16*Tasp_W*A-k2_1_2_10*Tasp_WA) # Reaction: id = regulatory_r12, name = Tasp_A+W<->Tasp_WA # Local Parameter: id = k1, name = k1 par k1_1_2_17=400000.0 # Local Parameter: id = k2, name = k2 par k2_1_2_11=1.0 regula_11=cell*(k1_1_2_17*Tasp_A*W-k2_1_2_11*Tasp_WA) # Reaction: id = regulatory_r13, name = Tasp+WA<->Tasp_WA # Local Parameter: id = k1, name = k1 par k1_1_2_18=400000.0 # Local Parameter: id = k2, name = k2 par k2_1_2_12=1.0 regula_12=cell*(k1_1_2_18*Tasp*WA-k2_1_2_12*Tasp_WA) # Reaction: id = regulatory_r14, name = Tni+W<->Tni_W # Local Parameter: id = k1, name = k1 par k1_1_2_19=0.1 # Local Parameter: id = k2, name = k2 par k2_1_2_13=1.0 regula_13=cell*(k1_1_2_19*Tni*W-k2_1_2_13*Tni_W) # Reaction: id = regulatory_r15, name = Tni+A<->Tni_A # Local Parameter: id = k1, name = k1 par k1_1_2_20=0.01 # Local Parameter: id = k2, name = k2 par k2_1_2_14=1.0 regula_14=cell*(k1_1_2_20*Tni*A-k2_1_2_14*Tni_A) # Reaction: id = regulatory_r16, name = Tni_W+A<->Tni_WA # Local Parameter: id = k1, name = k1 par k1_1_2_21=0.4 # Local Parameter: id = k2, name = k2 par k2_1_2_15=1.0 regula_15=cell*(k1_1_2_21*Tni_W*A-k2_1_2_15*Tni_WA) # Reaction: id = regulatory_r17, name = Tni_A+W<->Tni_WA # Local Parameter: id = k1, name = k1 par k1_1_2_22=0.4 # Local Parameter: id = k2, name = k2 par k2_1_2_16=1.0 regula_16=cell*(k1_1_2_22*Tni_A*W-k2_1_2_16*Tni_WA) # Reaction: id = regulatory_r18, name = Tni+WA<->Tni_WA # Local Parameter: id = k1, name = k1 par k1_1_2_23=0.4 # Local Parameter: id = k2, name = k2 par k2_1_2_17=1.0 regula_17=cell*(k1_1_2_23*Tni*WA-k2_1_2_17*Tni_WA) # Reaction: id = motor_r1, name = M+Yp<->MYp motor_r1=cell*function_(M, MYp, Yp, cell, ka, kappa) # Reaction: id = motor_r2, name = MYp+Yp<->MYpYp motor_r2=cell*functio_1(MYp, MYpYp, Yp, alpha, cell, ka, kappa) # Reaction: id = motor_r3, name = MYpYp+Yp<->MYpYpYp motor_r3=cell*functio_2(MYpYp, MYpYpYp, Yp, alpha, cell, ka, kappa) # Reaction: id = motor_r4, name = MYpYpYp+Yp<->MYpYpYpYp motor_r4=cell*functio_3(MYpYpYp, MYpYpYpYp, Yp, alpha, cell, ka, kappa) # Reaction: id = reaction_1, name = TA + asp <-> Tasp_A # Local Parameter: id = k1, name = k1 par k1_1_2_24=1000000.0 # Local Parameter: id = k2, name = k2 par k2_1_2_18=1.0 reaction_=cell*(k1_1_2_24*TA*asp-k2_1_2_18*Tasp_A) # Reaction: id = reaction_2, name = TW+asp <-> Tasp_W # Local Parameter: id = k1, name = k1 par k1_1_2_25=1000000.0 # Local Parameter: id = k2, name = k2 par k2_1_2_19=1.0 reactio_1=cell*(k1_1_2_25*TW*asp-k2_1_2_19*Tasp_W) # Reaction: id = reaction_3, name = TWA+asp <-> Tasp_WA # Local Parameter: id = k1, name = k1 par k1_1_2_26=1000000.0 # Local Parameter: id = k2, name = k2 par k2_1_2_20=1.0 reactio_2=cell*(k1_1_2_26*TWA*asp-k2_1_2_20*Tasp_WA) # Species: id = asp, name = asp# Species is changed by 2 event(s) par asp=0.0 aux asp=asp # Species: id = ni, name = ni, constant par ni=0.0 # Species: id = T, name = T, affected by kineticLaw par T_renamed=3.12E-6 aux T_renamed=T_renamed dT_renamed/dt=(1/(cell))*((-1.0 * regulator) + (-1.0 * regulat_1) + (-1.0 * regulat_2) + (-1.0 * regulat_3) + (-1.0 * regulat_7)) # Species: id = Tasp, name = Tasp, affected by kineticLaw init Tasp=0.0 dTasp/dt=(1/(cell))*(( 1.0 * regulator) + (-1.0 * regulat_8) + (-1.0 * regulat_9) + (-1.0 * regula_12)) # Species: id = Tni, name = Tni, affected by kineticLaw init Tni=0.0 dTni/dt=(1/(cell))*(( 1.0 * regulat_1) + (-1.0 * regula_13) + (-1.0 * regula_14) + (-1.0 * regula_17)) # Species: id = W, name = W, affected by kineticLaw init W=2.89E-6 dW/dt=(1/(cell))*((-1.0 * regulat_2) + (-1.0 * regulat_4) + (-1.0 * regulat_6) + (-1.0 * regulat_8) + (-1.0 * regula_11) + (-1.0 * regula_13) + (-1.0 * regula_16)) # Species: id = TW, name = TW, affected by kineticLaw init TW=5.91E-7 dTW/dt=(1/(cell))*(( 1.0 * regulat_2) + (-1.0 * regulat_5) + (-1.0 * reactio_1)) # Species: id = Tasp_W, name = Tasp_W, affected by kineticLaw init Tasp_W=0.0 dTasp_W/dt=(1/(cell))*(( 1.0 * regulat_8) + (-1.0 * regula_10) + ( 1.0 * reactio_1)) # Species: id = Tni_W, name = Tni_W, affected by kineticLaw init Tni_W=0.0 dTni_W/dt=(1/(cell))*(( 1.0 * regula_13) + (-1.0 * regula_15)) # Species: id = TA, name = TA, affected by kineticLaw init TA=4.44E-7 dTA/dt=(1/(cell))*(( 1.0 * regulat_3) + (-1.0 * regulat_6) + (-1.0 * reaction_)) # Species: id = Tasp_A, name = Tasp_A, affected by kineticLaw init Tasp_A=0.0 dTasp_A/dt=(1/(cell))*(( 1.0 * regulat_9) + (-1.0 * regula_11) + ( 1.0 * reaction_)) # Species: id = Tni_A, name = Tni_A, affected by kineticLaw init Tni_A=0.0 dTni_A/dt=(1/(cell))*(( 1.0 * regula_14) + (-1.0 * regula_16)) # Species: id = WA, name = WA, affected by kineticLaw init WA=6.78E-7 dWA/dt=(1/(cell))*(( 1.0 * regulat_4) + (-1.0 * regulat_7) + (-1.0 * regula_12) + (-1.0 * regula_17)) # Species: id = TWA, name = TWA, affected by kineticLaw init TWA=8.47E-7 dTWA/dt=(1/(cell))*(( 1.0 * regulat_5) + ( 1.0 * regulat_6) + ( 1.0 * regulat_7) + (-1.0 * reactio_2)) # Species: id = Tasp_WA, name = Tasp_WA, affected by kineticLaw init Tasp_WA=0.0 dTasp_WA/dt=(1/(cell))*((-1.0 * phospho_3) + ( 1.0 * phospho_3) + ( 1.0 * regula_10) + ( 1.0 * regula_11) + ( 1.0 * regula_12) + ( 1.0 * reactio_2)) # Species: id = Tni_WA, name = Tni_WA, affected by kineticLaw init Tni_WA=0.0 dTni_WA/dt=(1/(cell))*(( 1.0 * regula_15) + ( 1.0 * regula_16) + ( 1.0 * regula_17)) # Species: id = A, name = A, affected by kineticLaw init A=3.0E-6 dA/dt=(1/(cell))*((-1.0 * phosphory) + (-1.0 * phospho_1) + (-1.0 * phospho_2) + ( 1.0 * phospho_4) + ( 1.0 * phospho_8) + (-1.0 * regulat_3) + (-1.0 * regulat_4) + (-1.0 * regulat_5) + (-1.0 * regulat_9) + (-1.0 * regula_10) + (-1.0 * regula_14) + (-1.0 * regula_15)) # Species: id = Ap, name = Ap, affected by kineticLaw init Ap=3.48E-8 dAp/dt=(1/(cell))*(( 1.0 * phosphory) + ( 1.0 * phospho_1) + ( 1.0 * phospho_2) + (-1.0 * phospho_4) + (-1.0 * phospho_8)) # Species: id = B, name = B, affected by kineticLaw init B=1.93E-6 dB/dt=(1/(cell))*((-1.0 * phospho_8) + ( 1.0 * phospho_9)) # Species: id = Bp, name = Bp, affected by kineticLaw init Bp=6.87E-8 dBp/dt=(1/(cell))*(( 1.0 * phospho_8) + (-1.0 * phospho_9)) # Species: id = Z, name = Z, affected by kineticLaw init Z=2.0E-5 dZ/dt=(1/(cell))*((-1.0 * phospho_7) + ( 1.0 * phospho_7)) # Species: id = Y, name = Y, affected by kineticLaw init Y=9.9E-6 dY/dt=(1/(cell))*(( 1.0 * phospho_3) + (-1.0 * phospho_4) + (-1.0 * phospho_5) + ( 1.0 * phospho_6) + ( 1.0 * phospho_7)) # Species: id = Yp, name = Yp, affected by kineticLaw init Yp=7.0E-9 dYp/dt=(1/(cell))*((-1.0 * phospho_3) + ( 1.0 * phospho_4) + ( 1.0 * phospho_5) + (-1.0 * phospho_6) + (-1.0 * phospho_7) + (-1.0 * motor_r1) + (-1.0 * motor_r2) + (-1.0 * motor_r3) + (-1.0 * motor_r4)) # Species: id = M, name = M, affected by kineticLaw init M=6.24E-9 dM/dt=(1/(cell))*((-1.0 * motor_r1)) # Species: id = MYp, name = MYp, affected by kineticLaw init MYp=7.77E-10 dMYp/dt=(1/(cell))*(( 1.0 * motor_r1) + (-1.0 * motor_r2)) # Species: id = MYpYp, name = MYpYp, affected by kineticLaw init MYpYp=2.99E-10 dMYpYp/dt=(1/(cell))*(( 1.0 * motor_r2) + (-1.0 * motor_r3)) # Species: id = MYpYpYp, name = MYpYpYp, affected by kineticLaw init MYpYpYp=3.78E-10 dMYpYpYp/dt=(1/(cell))*(( 1.0 * motor_r3) + (-1.0 * motor_r4)) # Species: id = MYpYpYpYp, name = MYpYpYpYp, affected by kineticLaw init MYpYpYpYp=2.31E-9 dMYpYpYpYp/dt=(1/(cell))*(( 1.0 * motor_r4)) # Species: id = species_1, name = ATP, constant par species_1=0.1 # event : event_1 event_1=if (t >= 5) then (1.5) else (0.2) global 1 {event_1 - 1.1} {asp=parameter} # event : event_2 event_2=if (t >= 10) then (1.5) else (0.2) global 1 {event_2 - 1.1} {asp=0} @ meth=cvode, tol=1e-6, atol=1e-8 # @ maxstor=1e6 @ bound=40000, total=200 done