# # This file is automatically generated with # the System Biology Format Converter (http://sbfc.sourceforge.net/) # from an SBML file. # # # Model name = Muller2008 - Simplified MAPK activation Dynamics (Model B) # # is http://identifiers.org/biomodels.db/MODEL8687732743 # isDescribedBy http://identifiers.org/pubmed/18171696 # isDescribedBy http://identifiers.org/pubmed/18171696 # is http://identifiers.org/biomodels.db/BIOMD0000000664 # # some function definitions that are allowed in SBML but not valid in xpp ceil(x)=flr(1+x) @delay=50 # FunctionDefinition id = function_1_1, name = function 1_1 function_(a1,b1,g1)=(a1*g1/(b1+g1)) # FunctionDefinition id = function_1_2, name = function 1_2 functio_1(a2,b2,g2)=(a2*g2/(b2+g2)) # FunctionDefinition id = function_2_1, name = function 2_1 functio_2(C_Raf,C_Raf_inactive,E,FGFR,f13)=(f13*(E-C_Raf-C_Raf_inactive)*FGFR) # FunctionDefinition id = function_3_1, name = function 3_1 functio_3(C_Raf,C_Raf_inactive,E,MAPK,f53)=(f53*(E-C_Raf-C_Raf_inactive)*MAPK) # FunctionDefinition id = function_4_1, name = function 4_1 functio_4(FGFR,f14)=(f14*FGFR) # FunctionDefinition id = function_4_2, name = function 4_2 functio_5(MSH,f24)=(f24*MSH) # FunctionDefinition id = function_4_3, name = function 4_3 functio_6(C_Raf,f35)=(f35*C_Raf) # FunctionDefinition id = function_4_4, name = function 4_4 functio_7(B_Raf,f45)=(f45*B_Raf) # FunctionDefinition id = function_5_1, name = function 5_1 functio_8(C_Raf,MSH,h36_y3)=(h36_y3*MSH*C_Raf) # Compartment: id = Compartment, name = Compartment, constant par Compartme=1.0 # Parameter: id = a1, name = a1, constant par a1=10.0 # Parameter: id = g1, name = g1, defined by a Rule # Parameter: id = b1, name = b1, constant par b1=10.0 # Parameter: id = d1, name = d1, constant par d1=0.2 # Parameter: id = a2, name = a2, constant par a2=10.0 # Parameter: id = g2, name = g2, defined by a Rule # Parameter: id = b2, name = b2, constant par b2=10.0 # Parameter: id = d2, name = d2, constant par d2=0.1 # Parameter: id = f53, name = f53, constant par f53=1.5 # Parameter: id = f13, name = f13, constant par f13=0.6 # Parameter: id = h36_y3, name = h36, constant par h36_y3=0.1 # Parameter: id = d3, name = d3, constant par d3=1.0 # Parameter: id = E, name = E, constant par E=10.0 # Parameter: id = f14, name = f14, constant par f14=0.1 # Parameter: id = f24, name = f24, constant par f24=0.8 # Parameter: id = d4, name = d4, constant par d4=1.1 # Parameter: id = f35, name = f35, constant par f35=0.3 # Parameter: id = f45, name = f45, constant par f45=0.1 # Parameter: id = d5, name = d5, constant par d5=1.0 # Parameter: id = d6, name = d6, constant par d6=0.001 # assignmentRule: variable = g1 g1= piecew2 aux g1=g1 # assignmentRule: variable = g1_0 g1_0=g1 aux g1_0=g1_0 # assignmentRule: variable = g2 g2= piecew3 aux g2=g2 # assignmentRule: variable = g2_0 g2_0=g2 aux g2_0=g2_0 # Reaction: id = FGFR_Activation, name = FGFR Stimulus FGFR_Acti=Compartme*function_(a1, b1, g1) # Reaction: id = FGFR_Degradation, name = FGFR Degradation FGFR_Degr=Compartme*d1*FGFR # Reaction: id = MSH_Activation, name = MSH Stimulus MSH_Activ=Compartme*functio_1(a2, b2, g2) # Reaction: id = MSH_Degradation, name = MSH Degradation MSH_Degra=Compartme*d2*MSH # Reaction: id = C_Raf_Activation_1, name = C-Raf Activation 1 C_Raf_Act=Compartme*functio_2(C_Raf, C_Raf_ina, E, FGFR, f13) # Reaction: id = C_Raf_Activation_2, name = C_Raf Activation 2 C_Raf_A_1=Compartme*functio_3(C_Raf, C_Raf_ina, E, MAPK, f53) # Reaction: id = C_Raf_Degradation, name = C-Raf Degradation C_Raf_Deg=Compartme*d3*C_Raf # Reaction: id = B_Raf_Activation_1, name = B-Raf Activation 1 B_Raf_Act=Compartme*functio_4(FGFR, f14) # Reaction: id = B_Raf_Activation_2, name = B-Raf Activation 2 B_Raf_A_1=Compartme*functio_5(MSH, f24) # Reaction: id = B_Raf_Degradation, name = B-Raf Degradation B_Raf_Deg=Compartme*d4*B_Raf # Reaction: id = MAPK_Activation_1, name = MAPK Activation 1 MAPK_Acti=Compartme*functio_6(C_Raf, f35) # Reaction: id = MAPK_Activation_2, name = MAPK Activation 2 MAPK_Ac_1=Compartme*functio_7(B_Raf, f45) # Reaction: id = MAPK_Degradation, name = MAPK Degradation MAPK_Degr=Compartme*d5*MAPK # Reaction: id = C_Raf_Inactivation, name = C-Raf Inactivation C_Raf_I_1=Compartme*functio_8(C_Raf, MSH, h36_y3) # Reaction: id = Inactive_C_Raf_degradation, name = Inactive C-Raf degradation Inactive_=Compartme*d6*C_Raf_ina # Species: id = FGFR, name = FGFR, affected by kineticLaw init FGFR=0.0 dFGFR/dt=(1/(Compartme))*(( 1.0 * FGFR_Acti) + (-1.0 * FGFR_Degr)) # Species: id = MSH, name = MSH, affected by kineticLaw init MSH=0.0 dMSH/dt=(1/(Compartme))*(( 1.0 * MSH_Activ) + (-1.0 * MSH_Degra)) # Species: id = B_Raf, name = B-Raf, affected by kineticLaw init B_Raf=0.0 dB_Raf/dt=(1/(Compartme))*(( 1.0 * B_Raf_Act) + ( 1.0 * B_Raf_A_1) + (-1.0 * B_Raf_Deg)) # Species: id = MAPK, name = MAPK, affected by kineticLaw init MAPK=0.0 dMAPK/dt=(1/(Compartme))*(( 1.0 * MAPK_Acti) + ( 1.0 * MAPK_Ac_1) + (-1.0 * MAPK_Degr)) # Species: id = C_Raf_inactive, name = C-Raf inactive, affected by kineticLaw par C_Raf_ina=0.0 aux C_Raf_ina=C_Raf_ina dC_Raf_ina/dt=(1/(Compartme))*(( 1.0 * C_Raf_I_1) + (-1.0 * Inactive_)) # Species: id = g2_0, name = g2, involved in a rule # Species: id = C_Raf, name = C-Raf, affected by kineticLaw init C_Raf=0.0 dC_Raf/dt=(1/(Compartme))*(( 1.0 * C_Raf_Act) + ( 1.0 * C_Raf_A_1) + (-1.0 * C_Raf_Deg) + (-1.0 * C_Raf_I_1)) # Species: id = g1_0, name = g1, involved in a rule # Piecewise functions : the mathML piecewise element is transformed into if/then/else expression piecew1=if ((t >= 5) && (t < 10)) then (1) else (0) piecew2=if ((t >= 0) && (t < 5)) then (0) else ( piecew1 ) piecew3=if ((t >= 0) && (t < 5)) then (1) else (0) @ meth=cvode, tol=1e-6, atol=1e-8 # @ maxstor=1e6 @ bound=40000, total=200 done