# # This file is automatically generated with # the System Biology Format Converter (http://sbfc.sourceforge.net/) # from an SBML file. # # # Model name = Adlung2021 - Cell-to-cell variability in JAK2/STAT5 pathway # # unknownQualifier http://identifiers.org/mamo/MAMO_0000046 # isDescribedBy http://identifiers.org/pubmed:34380040 # is http://identifiers.org/biomodels.db/MODEL2103080001 # is http://identifiers.org/biomodels.db/BIOMD0000001077 # # some function definitions that are allowed in SBML but not valid in xpp ceil(x)=flr(1+x) @delay=50 # FunctionDefinition id = Function_for_v_5, name = Function for v_5 Function_(EpoRActJAK2,SOCS3,SOCS3Eqc,SOCS3Inh,p2EpoRpJAK2)=(EpoRActJAK2*p2EpoRpJAK2/(SOCS3*SOCS3Inh/SOCS3Eqc+1)) # FunctionDefinition id = Function_for_v_21, name = Function for v_21 Functio_1(CISEqc,CISRNA,CISTurn)=(CISRNA*CISEqc*CISTurn) # FunctionDefinition id = Function_for_v_0, name = Function for v_0 Functio_2(Epo,EpoRJAK2,JAK2ActEpo,SOCS3,SOCS3Eqc,SOCS3Inh)=(Epo*EpoRJAK2*JAK2ActEpo/(SOCS3*SOCS3Inh/SOCS3Eqc+1)) # FunctionDefinition id = Function_for_v_13, name = Function for v_13 Functio_3(EpoRpJAK2,SOCS3,SOCS3Eqc,SOCS3Inh,STAT5,STAT5ActJAK2,p12EpoRpJAK2,p1EpoRpJAK2,p2EpoRpJAK2)=(STAT5*STAT5ActJAK2*(EpoRpJAK2+p12EpoRpJAK2+p1EpoRpJAK2+p2EpoRpJAK2)/(SOCS3*SOCS3Inh/SOCS3Eqc+1)) # FunctionDefinition id = Function_for_v_25, name = Function for v_25 Functio_4(SOCS3Eqc,SOCS3EqcOE,SOCS3Turn,SOCS3oe)=(SOCS3oe*SOCS3Eqc*SOCS3Turn*SOCS3EqcOE) # FunctionDefinition id = Function_for_v_1, name = Function for v_1 Functio_5(DeaEpoRJAKActSHP1,EpoRpJAK2,SHP1Act,SHP1ActEpoR)=(DeaEpoRJAKActSHP1*EpoRpJAK2*SHP1Act/SHP1ActEpoR) # FunctionDefinition id = Function_for_v_6, name = Function for v_6 Functio_6(DeaEpoRJAKActSHP1,SHP1Act,SHP1ActEpoR,p1EpoRpJAK2)=(DeaEpoRJAKActSHP1*SHP1Act*p1EpoRpJAK2/SHP1ActEpoR) # FunctionDefinition id = Function_for_v_8, name = Function for v_8 Functio_7(DeaEpoRJAKActSHP1,SHP1Act,SHP1ActEpoR,p12EpoRpJAK2)=(DeaEpoRJAKActSHP1*SHP1Act*p12EpoRpJAK2/SHP1ActEpoR) # FunctionDefinition id = Function_for_v_7, name = Function for v_7 Functio_8(DeaEpoRJAKActSHP1,SHP1Act,SHP1ActEpoR,p2EpoRpJAK2)=(DeaEpoRJAKActSHP1*SHP1Act*p2EpoRpJAK2/SHP1ActEpoR) # FunctionDefinition id = Function_for_v_11, name = Function for v_11 Functio_9(EpoRpJAK2,SHP1,SHP1ActEpoR,p12EpoRpJAK2,p1EpoRpJAK2,p2EpoRpJAK2)=(SHP1*SHP1ActEpoR*(EpoRpJAK2+p12EpoRpJAK2+p1EpoRpJAK2+p2EpoRpJAK2)) # FunctionDefinition id = Function_for_v_16, name = Function for v_16 Functi_10(STAT5Exp,npSTAT5,nuc)=(nuc*STAT5Exp*npSTAT5) # FunctionDefinition id = Function_for_v_3, name = Function for v_3 Functi_11(EpoRActJAK2,EpoRpJAK2,SOCS3,SOCS3Eqc,SOCS3Inh)=(3*EpoRpJAK2*EpoRActJAK2/(SOCS3*SOCS3Inh/SOCS3Eqc+1)) # FunctionDefinition id = Function_for_v_2, name = Function for v_2 Functi_12(EpoRActJAK2,EpoRpJAK2,SOCS3,SOCS3Eqc,SOCS3Inh)=(EpoRpJAK2*EpoRActJAK2/(SOCS3*SOCS3Inh/SOCS3Eqc+1)) # FunctionDefinition id = Function_for_v_14, name = Function for v_14 Functi_13(CIS,CISEqc,CISInh,SOCS3,SOCS3Eqc,SOCS3Inh,STAT5,STAT5ActEpoR,p12EpoRpJAK2,p1EpoRpJAK2)=(STAT5*STAT5ActEpoR*(p12EpoRpJAK2+p1EpoRpJAK2)^2/((SOCS3*SOCS3Inh/SOCS3Eqc+1)*(CIS*CISInh/CISEqc+1))) # FunctionDefinition id = Function_for_v_19, name = Function for v_19 Functi_14(CISRNADelay,CISnRNA2,nuc)=(nuc*CISnRNA2*CISRNADelay) # FunctionDefinition id = Function_for_v_17, name = Function for v_17 Functi_15(ActD,CISRNAEqc,CISRNATurn,npSTAT5)=((-CISRNAEqc)*CISRNATurn*npSTAT5*(ActD-1)) # FunctionDefinition id = Function_for_v_15, name = Function for v_15 Functi_16(STAT5Imp,cyt,pSTAT5)=(cyt*STAT5Imp*pSTAT5) # FunctionDefinition id = Function_for_v_23, name = Function for v_23 Functi_17(ActD,SOCS3Eqc,SOCS3Turn,cyt,npSTAT5)=(cyt*(-SOCS3Eqc)*SOCS3Turn*npSTAT5*(ActD-1)) # FunctionDefinition id = Function_for_v_4, name = Function for v_4 Functi_18(EpoRActJAK2,SOCS3,SOCS3Eqc,SOCS3Inh,p1EpoRpJAK2)=(3*EpoRActJAK2*p1EpoRpJAK2/(SOCS3*SOCS3Inh/SOCS3Eqc+1)) # Compartment: id = cyt, name = cyt, constant par cyt=0.4 # Compartment: id = nuc, name = nuc, constant par nuc=0.275 # Parameter: id = ActD, name = ActD, constant par ActD=0.0 # Parameter: id = CISEqc, name = CISEqc, constant par CISEqc=0.767538787148837 # Parameter: id = CISInh, name = CISInh, constant par CISInh=4.3834039529483E8 # Parameter: id = CISRNADelay, name = CISRNADelay, constant par CISRNADel=0.119845304696486 # Parameter: id = CISRNAEqc, name = CISRNAEqc, constant par CISRNAEqc=1.0 # Parameter: id = CISRNATurn, name = CISRNATurn, constant par CISRNATur=0.119809412320528 # Parameter: id = CISTurn, name = CISTurn, constant par CISTurn=0.0178232876161209 # Parameter: id = DeaEpoRJAKActSHP1, name = DeaEpoRJAKActSHP1, constant par DeaEpoRJA=8.85910280224449E-4 # Parameter: id = EpoRActJAK2, name = EpoRActJAK2, constant par EpoRActJA=0.326237934674659 # Parameter: id = JAK2ActEpo, name = JAK2ActEpo, constant par JAK2ActEp=0.0520769792397573 # Parameter: id = SHP1ActEpoR, name = SHP1ActEpoR, constant par SHP1ActEp=1.0 # Parameter: id = SHP1Dea, name = SHP1Dea, constant par SHP1Dea=0.00557392820000894 # Parameter: id = SOCS3Eqc, name = SOCS3Eqc, constant par SOCS3Eqc=0.162493786913208 # Parameter: id = SOCS3EqcOE, name = SOCS3EqcOE, constant par SOCS3EqcO=828.06160444759 # Parameter: id = SOCS3Inh, name = SOCS3Inh, constant par SOCS3Inh=0.010341350346111 # Parameter: id = SOCS3Turn, name = SOCS3Turn, constant par SOCS3Turn=0.0806005449025786 # Parameter: id = SOCS3oe, name = SOCS3oe, constant par SOCS3oe=0.0 # Parameter: id = STAT5ActEpoR, name = STAT5ActEpoR, constant par STAT5ActE=0.299136651563824 # Parameter: id = STAT5ActJAK2, name = STAT5ActJAK2, constant par STAT5ActJ=0.0513253755320527 # Parameter: id = STAT5Exp, name = STAT5Exp, constant par STAT5Exp=0.0112157105187786 # Parameter: id = STAT5Imp, name = STAT5Imp, constant par STAT5Imp=0.0404763494591488 # Parameter: id = epo_level, name = epo_level, constant par epo_level=20.0 # Parameter: id = init_EpoRJAK2, name = init_EpoRJAK2, constant par init_EpoR=3.97504832099667 # Parameter: id = init_SHP1, name = init_SHP1, constant par init_SHP1=26.7236153222782 # Parameter: id = init_STAT5, name = init_STAT5, constant par init_STAT=79.7242077843376 # Parameter: id = Epo, name = Epo, defined by a Rule # Parameter: id = Total_STAT5, name = Total_STAT5, defined by a Rule # Parameter: id = measuralbe_pSTAT5, name = measuralbe_pSTAT5, defined by a Rule # Parameter: id = _pSTAT5_Total_STAT5, name = %pSTAT5/Total_STAT5, defined by a Rule # assignmentRule: variable = Epo Epo=epo_level aux Epo=Epo # assignmentRule: variable = Total_STAT5 Total_STA=STAT5+pSTAT5+0.275*npSTAT5 aux Total_STA=Total_STA # assignmentRule: variable = measuralbe_pSTAT5 measuralb=pSTAT5/Total_STA*100 aux measuralb=measuralb # assignmentRule: variable = _pSTAT5_Total_STAT5 _pSTAT5_T=pSTAT5/Total_STA*100 aux _pSTAT5_T=_pSTAT5_T # Reaction: id = v1_v_0, name = v_0 v1_v_0=cyt*Functio_2(Epo, EpoRJAK2, JAK2ActEp, SOCS3, SOCS3Eqc, SOCS3Inh) # Reaction: id = v2_v_1, name = v_1 v2_v_1=cyt*Functio_5(DeaEpoRJA, EpoRpJAK2, SHP1Act, SHP1ActEp) # Reaction: id = v3_v_2, name = v_2 v3_v_2=cyt*Functi_12(EpoRActJA, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh) # Reaction: id = v4_v_3, name = v_3 v4_v_3=cyt*Functi_11(EpoRActJA, EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh) # Reaction: id = v5_v_4, name = v_4 v5_v_4=cyt*Functi_18(EpoRActJA, SOCS3, SOCS3Eqc, SOCS3Inh, p1EpoRpJA) # Reaction: id = v6_v_5, name = v_5 v6_v_5=cyt*Function_(EpoRActJA, SOCS3, SOCS3Eqc, SOCS3Inh, p2EpoRpJA) # Reaction: id = v7_v_6, name = v_6 v7_v_6=cyt*Functio_6(DeaEpoRJA, SHP1Act, SHP1ActEp, p1EpoRpJA) # Reaction: id = v8_v_7, name = v_7 v8_v_7=cyt*Functio_8(DeaEpoRJA, SHP1Act, SHP1ActEp, p2EpoRpJA) # Reaction: id = v9_v_8, name = v_8 v9_v_8=cyt*Functio_7(DeaEpoRJA, SHP1Act, SHP1ActEp, p12EpoRpJ) # Reaction: id = v12_v_11, name = v_11 v12_v_11=cyt*Functio_9(EpoRpJAK2, SHP1, SHP1ActEp, p12EpoRpJ, p1EpoRpJA, p2EpoRpJA) # Reaction: id = v13_v_12, name = v_12 v13_v_12=cyt*SHP1Dea*SHP1Act # Reaction: id = v14_v_13, name = v_13 v14_v_13=cyt*Functio_3(EpoRpJAK2, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActJ, p12EpoRpJ, p1EpoRpJA, p2EpoRpJA) # Reaction: id = v15_v_14, name = v_14 v15_v_14=cyt*Functi_13(CIS, CISEqc, CISInh, SOCS3, SOCS3Eqc, SOCS3Inh, STAT5, STAT5ActE, p12EpoRpJ, p1EpoRpJA) # Reaction: id = v16_v_15, name = v_15 v16_v_15=Functi_16(STAT5Imp, cyt, pSTAT5) # Reaction: id = v17_v_16, name = v_16 v17_v_16=Functi_10(STAT5Exp, npSTAT5, nuc) # Reaction: id = v18_v_17, name = v_17 v18_v_17=nuc*Functi_15(ActD, CISRNAEqc, CISRNATur, npSTAT5) # Reaction: id = v19_v_18, name = v_18 v19_v_18=nuc*CISRNADel*CISnRNA1 # Reaction: id = v20_v_19, name = v_19 v20_v_19=Functi_14(CISRNADel, CISnRNA2, nuc) # Reaction: id = v21_v_20, name = v_20 v21_v_20=cyt*CISRNATur*CISRNA # Reaction: id = v22_v_21, name = v_21 v22_v_21=cyt*Functio_1(CISEqc, CISRNA, CISTurn) # Reaction: id = v23_v_22, name = v_22 v23_v_22=cyt*CISTurn*CIS # Reaction: id = v24_v_23, name = v_23 v24_v_23=Functi_17(ActD, SOCS3Eqc, SOCS3Turn, cyt, npSTAT5) # Reaction: id = v25_v_24, name = v_24 v25_v_24=cyt*SOCS3Turn*SOCS3 # Reaction: id = v26_v_25, name = v_25 v26_v_25=cyt*Functio_4(SOCS3Eqc, SOCS3EqcO, SOCS3Turn, SOCS3oe) # Species: id = EpoRJAK2, name = EpoRJAK2, affected by kineticLaw init EpoRJAK2=3.97504832099667 dEpoRJAK2/dt=(1/(cyt))*((-1.0 * v1_v_0) + ( 1.0 * v2_v_1) + ( 1.0 * v7_v_6) + ( 1.0 * v8_v_7) + ( 1.0 * v9_v_8)) # Species: id = EpoRpJAK2, name = EpoRpJAK2, affected by kineticLaw init EpoRpJAK2=0.0 dEpoRpJAK2/dt=(1/(cyt))*(( 1.0 * v1_v_0) + (-1.0 * v2_v_1) + (-1.0 * v3_v_2) + (-1.0 * v4_v_3)) # Species: id = p1EpoRpJAK2, name = p1EpoRpJAK2, affected by kineticLaw par p1EpoRpJA=0.0 aux p1EpoRpJA=p1EpoRpJA dp1EpoRpJA/dt=(1/(cyt))*(( 1.0 * v3_v_2) + (-1.0 * v5_v_4) + (-1.0 * v7_v_6)) # Species: id = p2EpoRpJAK2, name = p2EpoRpJAK2, affected by kineticLaw par p2EpoRpJA=0.0 aux p2EpoRpJA=p2EpoRpJA dp2EpoRpJA/dt=(1/(cyt))*(( 1.0 * v4_v_3) + (-1.0 * v6_v_5) + (-1.0 * v8_v_7)) # Species: id = p12EpoRpJAK2, name = p12EpoRpJAK2, affected by kineticLaw par p12EpoRpJ=0.0 aux p12EpoRpJ=p12EpoRpJ dp12EpoRpJ/dt=(1/(cyt))*(( 1.0 * v5_v_4) + ( 1.0 * v6_v_5) + (-1.0 * v9_v_8)) # Species: id = SHP1, name = SHP1 # Warning species is not changed by either rules or reactions par SHP1=26.7236153222782 aux SHP1=SHP1 # Species: id = SHP1Act, name = SHP1Act, affected by kineticLaw init SHP1Act=0.0 dSHP1Act/dt=(1/(cyt))*(( 1.0 * v12_v_11) + (-1.0 * v13_v_12)) # Species: id = STAT5, name = STAT5, affected by kineticLaw init STAT5=79.7242077843376 dSTAT5/dt=(1/(cyt))*((-1.0 * v14_v_13) + (-1.0 * v15_v_14) + ( 1.0 * v17_v_16)) # Species: id = pSTAT5, name = pSTAT5, affected by kineticLaw init pSTAT5=0.0 dpSTAT5/dt=(1/(cyt))*(( 1.0 * v14_v_13) + ( 1.0 * v15_v_14) + (-1.0 * v16_v_15)) # Species: id = npSTAT5, name = npSTAT5, affected by kineticLaw init npSTAT5=0.0 dnpSTAT5/dt=(1/(nuc))*(( 1.0 * v16_v_15) + (-1.0 * v17_v_16)) # Species: id = CISnRNA1, name = CISnRNA1, affected by kineticLaw init CISnRNA1=0.0 dCISnRNA1/dt=(1/(nuc))*(( 1.0 * v18_v_17) + (-1.0 * v19_v_18)) # Species: id = CISnRNA2, name = CISnRNA2, affected by kineticLaw init CISnRNA2=0.0 dCISnRNA2/dt=(1/(nuc))*(( 1.0 * v19_v_18) + (-1.0 * v20_v_19)) # Species: id = CISRNA, name = CISRNA, affected by kineticLaw init CISRNA=0.0 dCISRNA/dt=(1/(cyt))*(( 1.0 * v20_v_19) + (-1.0 * v21_v_20)) # Species: id = CIS, name = CIS, affected by kineticLaw init CIS=0.0 dCIS/dt=(1/(cyt))*(( 1.0 * v22_v_21) + (-1.0 * v23_v_22)) # Species: id = SOCS3, name = SOCS3, affected by kineticLaw init SOCS3=0.0 dSOCS3/dt=(1/(cyt))*(( 1.0 * v24_v_23) + (-1.0 * v25_v_24) + ( 1.0 * v26_v_25)) @ meth=cvode, tol=1e-6, atol=1e-8 # @ maxstor=1e6 @ bound=40000, total=200 done