/* * This code is generated by BioUML FrameWork * for BIOMD0000000051.xml diagram at 2008.03.20 15:04:30 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000051 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ private void __internalVarInitFunc_0(double time, double[] x) { catp = 4.27 - 4.163*(time/(0.657 + 1.43*time + 0.0364*Math.pow(time, 2))); cnadh = 0.0934 + 0.00111*Math.pow(2.371, (-0.123*time))*(0.844*time + 0.104*Math.pow(time, 3)); cnad = 1.314 + 1.314*Math.pow(2.73, (-0.0435*time - 0.342)) - (time + 7.871)*(Math.pow(2.73, (-0.0218*time - 0.171))/(8.481 + time)); cadp = 0.582 + 1.73*Math.pow(2.731, (-0.15*time))*(0.12*time + 2.14E-4*Math.pow(time, 3)); camp = 0.123 + 7.25*(time/(7.25 + 1.47*time + 0.17*Math.pow(time, 2))) + 1.073/(1.29 + 8.05*time); cnadph = 0.062 + 0.332*Math.pow(2.718, (-0.464*time))*(0.0166*Math.pow(time, 1.58) + 1.66E-4*Math.pow(time, 4.73) + 1.3120000000000002E-10*Math.pow(time, 7.89) + 1.362E-13*Math.pow(time, 11) + 1.2330000000000003E-16*Math.pow(time, 14.2)); cnadp = 0.159 - 0.00554*(time/(2.8 - 0.271*time + 0.01*Math.pow(time, 2))) + 0.182/(4.82 + 0.526*time); } /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_vALDO = _extracellular_cytosol_*vALDO_rmaxALDO*(x[4] - x[7]*x[1]/vALDO_kALDOeq)/(vALDO_kALDOfdp + x[4] + vALDO_kALDOgap*x[1]/(vALDO_kALDOeq*vALDO_VALDOblf) + vALDO_kALDOdhap*x[7]/(vALDO_kALDOeq*vALDO_VALDOblf) + x[4]*x[7]/vALDO_kALDOgapinh + x[7]*x[1]/(vALDO_VALDOblf*vALDO_kALDOeq)); rate_vDAHPS = _extracellular_cytosol_*vDAHPS_rmaxDAHPS*Math.pow(x[2], vDAHPS_nDAHPSe4p)*Math.pow(x[8], vDAHPS_nDAHPSpep)/((vDAHPS_KDAHPSe4p + Math.pow(x[2], vDAHPS_nDAHPSe4p))*(vDAHPS_KDAHPSpep + Math.pow(x[8], vDAHPS_nDAHPSpep))); rate_vDHAP = _extracellular_cytosol_*vDHAP_mu*x[1]; rate_vE4P = _extracellular_cytosol_*vE4P_mu*x[2]; rate_vENO = _extracellular_cytosol_*vENO_rmaxENO*(x[10] - x[8]/vENO_KENOeq)/(vENO_KENOpg2*(1 + x[8]/vENO_KENOpep) + x[10]); rate_vEXTER = extracellular*vEXTER_Dil*(vEXTER_cfeed - x[0]); rate_vG1PAT = _extracellular_cytosol_*vG1PAT_rmaxG1PAT*x[5]*catp*(1 + Math.pow((x[4]/vG1PAT_KG1PATfdp), vG1PAT_nG1PATfdp))/((vG1PAT_KG1PATatp + catp)*(vG1PAT_KG1PATg1p + x[5])); rate_vG3PDH = _extracellular_cytosol_*vG3PDH_rmaxG3PDH*x[1]/(vG3PDH_KG3PDHdhap + x[1]); rate_vG6P = _extracellular_cytosol_*vG6P_mu*x[6]; rate_vG6PDH = _extracellular_cytosol_*vG6PDH_rmaxG6PDH*x[6]*cnadp/((x[6] + vG6PDH_KG6PDHg6p)*(1 + cnadph/vG6PDH_KG6PDHnadphg6pinh)*(vG6PDH_KG6PDHnadp*(1 + cnadph/vG6PDH_KG6PDHnadphnadpinh) + cnadp)); rate_vGAP = _extracellular_cytosol_*vGAP_mu*x[7]; rate_vGAPDH = _extracellular_cytosol_*vGAPDH_rmaxGAPDH*(x[7]*cnad - x[12]*cnadh/vGAPDH_KGAPDHeq)/((vGAPDH_KGAPDHgap*(1 + x[12]/vGAPDH_KGAPDHpgp) + x[7])*(vGAPDH_KGAPDHnad*(1 + cnadh/vGAPDH_KGAPDHnadh) + cnad)); rate_vGLP = _extracellular_cytosol_*vGLP_mu*x[5]; rate_vMURSyNTH = _extracellular_cytosol_*vMURSyNTH_rmaxMurSynth; rate_vMethSynth = _extracellular_cytosol_*vMethSynth_rmaxMetSynth; rate_vPDH = _extracellular_cytosol_*vPDH_rmaxPDH*Math.pow(x[13], vPDH_nPDH)/(vPDH_KPDHpyr + Math.pow(x[13], vPDH_nPDH)); rate_vPEP = _extracellular_cytosol_*vPEP_mu*x[8]; rate_vPFK = _extracellular_cytosol_*vPFK_rmaxPFK*catp*x[3]/((catp + vPFK_KPFKatps*(1 + cadp/vPFK_KPFKadpc))*(x[3] + vPFK_KPFKf6ps*(1 + x[8]/vPFK_KPFKpep + cadp/vPFK_KPFKadpb + camp/vPFK_KPFKampb)/(1 + cadp/vPFK_KPFKadpa + camp/vPFK_KPFKampa))*(1 + vPFK_LPFK/Math.pow((1 + x[3]*(1 + cadp/vPFK_KPFKadpa + camp/vPFK_KPFKampa)/(vPFK_KPFKf6ps*(1 + x[8]/vPFK_KPFKpep + cadp/vPFK_KPFKadpb + camp/vPFK_KPFKampb))), vPFK_nPFK))); rate_vPG = _extracellular_cytosol_*vPG_mu*x[9]; rate_vPG3 = _extracellular_cytosol_*vPG3_mu*x[11]; rate_vPGDH = _extracellular_cytosol_*vPGDH_rmaxPGDH*x[9]*cnadp/((x[9] + vPGDH_KPGDHpg)*(cnadp + vPGDH_KPGDHnadp*(1 + cnadph/vPGDH_KPGDHnadphinh)*(1 + catp/vPGDH_KPGDHatpinh))); rate_vPGI = _extracellular_cytosol_*vPGI_rmaxPGI*(x[6] - x[3]/vPGI_KPGIeq)/(vPGI_KPGIg6p*(1 + x[3]/(vPGI_KPGIf6p*(1 + x[9]/vPGI_KPGIf6ppginh)) + x[9]/vPGI_KPGIg6ppginh) + x[6]); rate_vPGK = _extracellular_cytosol_*vPGK_rmaxPGK*(cadp*x[12] - catp*x[11]/vPGK_KPGKeq)/((vPGK_KPGKadp*(1 + catp/vPGK_KPGKatp) + cadp)*(vPGK_KPGKpgp*(1 + x[11]/vPGK_KPGKpg3) + x[12])); rate_vPGM = _extracellular_cytosol_*vPGM_rmaxPGM*(x[6] - x[5]/vPGM_KPGMeq)/(vPGM_KPGMg6p*(1 + x[5]/vPGM_KPGMg1p) + x[6]); rate_vPGP = _extracellular_cytosol_*vPGP_mu*x[12]; rate_vPK = _extracellular_cytosol_*vPK_rmaxPK*x[8]*Math.pow((x[8]/vPK_KPKpep + 1), (vPK_nPK - 1))*cadp/(vPK_KPKpep*(vPK_LPK*Math.pow(((1 + catp/vPK_KPKatp)/(x[4]/vPK_KPKfdp + camp/vPK_KPKamp + 1)), vPK_nPK) + Math.pow((x[8]/vPK_KPKpep + 1), vPK_nPK))*(cadp + vPK_KPKadp)); rate_vPPK = _extracellular_cytosol_*vPPK_rmaxRPPK*x[14]/(vPPK_KRPPKrib5p + x[14]); rate_vPTS = extracellular*vPTS_rmaxPTS*x[0]*(x[8]/x[13])/((vPTS_KPTSa1 + vPTS_KPTSa2*(x[8]/x[13]) + vPTS_KPTSa3*x[0] + x[0]*(x[8]/x[13]))*(1 + Math.pow(x[6], vPTS_nPTSg6p)/vPTS_KPTSg6p)); rate_vR5PI = _extracellular_cytosol_*vR5PI_rmaxR5PI*(x[15] - x[14]/vR5PI_KR5PIeq); rate_vRIB5P = _extracellular_cytosol_*vRIB5P_mu*x[14]; rate_vRibu5p = _extracellular_cytosol_*vRibu5p_mu*x[15]; rate_vRu5P = _extracellular_cytosol_*vRu5P_rmaxRu5P*(x[15] - x[17]/vRu5P_KRu5Peq); rate_vSED7P = _extracellular_cytosol_*vSED7P_mu*x[16]; rate_vSynth1 = _extracellular_cytosol_*vSynth1_rmaxSynth1*x[8]/(vSynth1_KSynth1pep + x[8]); rate_vSynth2 = _extracellular_cytosol_*vSynth2_rmaxSynth2*x[13]/(vSynth2_KSynth2pyr + x[13]); rate_vTA = _extracellular_cytosol_*vTA_rmaxTA*(x[7]*x[16] - x[2]*x[3]/vTA_KTAeq); rate_vTIS = _extracellular_cytosol_*vTIS_rmaxTIS*(x[1] - x[7]/vTIS_kTISeq)/(vTIS_kTISdhap*(1 + x[7]/vTIS_kTISgap) + x[1]); rate_vTKA = _extracellular_cytosol_*vTKA_rmaxTKa*(x[14]*x[17] - x[16]*x[7]/vTKA_KTKaeq); rate_vTKB = _extracellular_cytosol_*vTKB_rmaxTKb*(x[17]*x[2] - x[3]*x[7]/vTKB_KTKbeq); rate_vTRPSYNTH = _extracellular_cytosol_*vTRPSYNTH_rmaxTrpSynth; } public void __internalRateVarInitFunc_1(double time, double[] x) { rate_vXYL5P = _extracellular_cytosol_*vXYL5P_mu*x[17]; rate_vf6P = _extracellular_cytosol_*vf6P_mu*x[3]; rate_vfdP = _extracellular_cytosol_*vfdP_mu*x[4]; rate_vpepCxylase = _extracellular_cytosol_*vpepCxylase_rmaxpepCxylase*x[8]*(1 + Math.pow((x[4]/vpepCxylase_KpepCxylasefdp), vpepCxylase_npepCxylasefdp))/(vpepCxylase_KpepCxylasepep + x[8]); rate_vpg2 = _extracellular_cytosol_*vpg2_mu*x[10]; rate_vpyr = _extracellular_cytosol_*vpyr_mu*x[13]; rate_vrpGluMu = _extracellular_cytosol_*vrpGluMu_rmaxPGluMu*(x[11] - x[10]/vrpGluMu_KPGluMueq)/(vrpGluMu_KPGluMupg3*(1 + x[10]/vrpGluMu_KPGluMupg2) + x[11]); rate_vsersynth = _extracellular_cytosol_*vsersynth_rmaxSerSynth*x[11]/(vsersynth_KSerSynthpg3 + x[11]); } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _extracellular_cytosol_ = 1.0; // initial value of $"extracellular.cytosol" extracellular = 1.0; // initial value of $extracellular cadp = 0.595; // initial value of cadp camp = 0.955; // initial value of camp catp = 4.27; // initial value of catp cnad = 1.47; // initial value of cnad cnadh = 0.1; // initial value of cnadh cnadp = 0.195; // initial value of cnadp cnadph = 0.062; // initial value of cnadph vALDO_VALDOblf = 2.0; // initial value of vALDO_VALDOblf vALDO_kALDOdhap = 0.088; // initial value of vALDO_kALDOdhap vALDO_kALDOeq = 0.144; // initial value of vALDO_kALDOeq vALDO_kALDOfdp = 1.75; // initial value of vALDO_kALDOfdp vALDO_kALDOgap = 0.088; // initial value of vALDO_kALDOgap vALDO_kALDOgapinh = 0.6; // initial value of vALDO_kALDOgapinh vALDO_rmaxALDO = 17.41464425; // initial value of vALDO_rmaxALDO vDAHPS_KDAHPSe4p = 0.035; // initial value of vDAHPS_KDAHPSe4p vDAHPS_KDAHPSpep = 0.0053; // initial value of vDAHPS_KDAHPSpep vDAHPS_nDAHPSe4p = 2.6; // initial value of vDAHPS_nDAHPSe4p vDAHPS_nDAHPSpep = 2.2; // initial value of vDAHPS_nDAHPSpep vDAHPS_rmaxDAHPS = 0.1079531227; // initial value of vDAHPS_rmaxDAHPS vDHAP_mu = 2.78E-5; // initial value of vDHAP_mu vE4P_mu = 2.78E-5; // initial value of vE4P_mu vENO_KENOeq = 6.73; // initial value of vENO_KENOeq vENO_KENOpep = 0.135; // initial value of vENO_KENOpep vENO_KENOpg2 = 0.1; // initial value of vENO_KENOpg2 vENO_rmaxENO = 330.4476151; // initial value of vENO_rmaxENO vEXTER_Dil = 2.78E-5; // initial value of vEXTER_Dil vEXTER_cfeed = 110.96; // initial value of vEXTER_cfeed vG1PAT_KG1PATatp = 4.42; // initial value of vG1PAT_KG1PATatp vG1PAT_KG1PATfdp = 0.119; // initial value of vG1PAT_KG1PATfdp vG1PAT_KG1PATg1p = 3.2; // initial value of vG1PAT_KG1PATg1p vG1PAT_nG1PATfdp = 1.2; // initial value of vG1PAT_nG1PATfdp vG1PAT_rmaxG1PAT = 0.007525458026; // initial value of vG1PAT_rmaxG1PAT vG3PDH_KG3PDHdhap = 1.0; // initial value of vG3PDH_KG3PDHdhap vG3PDH_rmaxG3PDH = 0.01162042696; // initial value of vG3PDH_rmaxG3PDH vG6PDH_KG6PDHg6p = 14.4; // initial value of vG6PDH_KG6PDHg6p vG6PDH_KG6PDHnadp = 0.0246; // initial value of vG6PDH_KG6PDHnadp vG6PDH_KG6PDHnadphg6pinh = 6.43; // initial value of vG6PDH_KG6PDHnadphg6pinh vG6PDH_KG6PDHnadphnadpinh = 0.01; // initial value of vG6PDH_KG6PDHnadphnadpinh vG6PDH_rmaxG6PDH = 1.380196955; // initial value of vG6PDH_rmaxG6PDH vG6P_mu = 2.78E-5; // initial value of vG6P_mu vGAPDH_KGAPDHeq = 0.63; // initial value of vGAPDH_KGAPDHeq vGAPDH_KGAPDHgap = 0.683; // initial value of vGAPDH_KGAPDHgap vGAPDH_KGAPDHnad = 0.252; // initial value of vGAPDH_KGAPDHnad vGAPDH_KGAPDHnadh = 1.09; // initial value of vGAPDH_KGAPDHnadh vGAPDH_KGAPDHpgp = 1.04E-5; // initial value of vGAPDH_KGAPDHpgp vGAPDH_rmaxGAPDH = 921.5942861; // initial value of vGAPDH_rmaxGAPDH vGAP_mu = 2.78E-5; // initial value of vGAP_mu vGLP_mu = 2.78E-5; // initial value of vGLP_mu vMURSyNTH_rmaxMurSynth = 4.3711E-4; // initial value of vMURSyNTH_rmaxMurSynth vMethSynth_rmaxMetSynth = 0.0022627; // initial value of vMethSynth_rmaxMetSynth vPDH_KPDHpyr = 1159.0; // initial value of vPDH_KPDHpyr vPDH_nPDH = 3.68; // initial value of vPDH_nPDH vPDH_rmaxPDH = 6.059531017; // initial value of vPDH_rmaxPDH vPEP_mu = 2.78E-5; // initial value of vPEP_mu vPFK_KPFKadpa = 128.0; // initial value of vPFK_KPFKadpa vPFK_KPFKadpb = 3.89; // initial value of vPFK_KPFKadpb vPFK_KPFKadpc = 4.14; // initial value of vPFK_KPFKadpc vPFK_KPFKampa = 19.1; // initial value of vPFK_KPFKampa vPFK_KPFKampb = 3.2; // initial value of vPFK_KPFKampb vPFK_KPFKatps = 0.123; // initial value of vPFK_KPFKatps vPFK_KPFKf6ps = 0.325; // initial value of vPFK_KPFKf6ps vPFK_KPFKpep = 3.26; // initial value of vPFK_KPFKpep vPFK_LPFK = 5629067.0; // initial value of vPFK_LPFK vPFK_nPFK = 11.1; // initial value of vPFK_nPFK vPFK_rmaxPFK = 1840.584747; // initial value of vPFK_rmaxPFK vPG3_mu = 2.78E-5; // initial value of vPG3_mu vPGDH_KPGDHatpinh = 208.0; // initial value of vPGDH_KPGDHatpinh vPGDH_KPGDHnadp = 0.0506; // initial value of vPGDH_KPGDHnadp vPGDH_KPGDHnadphinh = 0.0138; // initial value of vPGDH_KPGDHnadphinh vPGDH_KPGDHpg = 37.5; // initial value of vPGDH_KPGDHpg vPGDH_rmaxPGDH = 16.23235977; // initial value of vPGDH_rmaxPGDH vPGI_KPGIeq = 0.1725; // initial value of vPGI_KPGIeq vPGI_KPGIf6p = 0.266; // initial value of vPGI_KPGIf6p vPGI_KPGIf6ppginh = 0.2; // initial value of vPGI_KPGIf6ppginh vPGI_KPGIg6p = 2.9; // initial value of vPGI_KPGIg6p vPGI_KPGIg6ppginh = 0.2; // initial value of vPGI_KPGIg6ppginh vPGI_rmaxPGI = 650.9878687; // initial value of vPGI_rmaxPGI vPGK_KPGKadp = 0.185; // initial value of vPGK_KPGKadp vPGK_KPGKatp = 0.653; // initial value of vPGK_KPGKatp vPGK_KPGKeq = 1934.4; // initial value of vPGK_KPGKeq vPGK_KPGKpg3 = 0.473; // initial value of vPGK_KPGKpg3 vPGK_KPGKpgp = 0.0468; // initial value of vPGK_KPGKpgp vPGK_rmaxPGK = 3021.773771; // initial value of vPGK_rmaxPGK vPGM_KPGMeq = 0.196; // initial value of vPGM_KPGMeq vPGM_KPGMg1p = 0.0136; // initial value of vPGM_KPGMg1p vPGM_KPGMg6p = 1.038; // initial value of vPGM_KPGMg6p vPGM_rmaxPGM = 0.8398242773; // initial value of vPGM_rmaxPGM vPGP_mu = 2.78E-5; // initial value of vPGP_mu vPG_mu = 2.78E-5; // initial value of vPG_mu vPK_KPKadp = 0.26; // initial value of vPK_KPKadp vPK_KPKamp = 0.2; // initial value of vPK_KPKamp vPK_KPKatp = 22.5; // initial value of vPK_KPKatp vPK_KPKfdp = 0.19; // initial value of vPK_KPKfdp vPK_KPKpep = 0.31; // initial value of vPK_KPKpep vPK_LPK = 1000.0; // initial value of vPK_LPK vPK_nPK = 4.0; // initial value of vPK_nPK vPK_rmaxPK = 0.06113150238; // initial value of vPK_rmaxPK vPPK_KRPPKrib5p = 0.1; // initial value of vPPK_KRPPKrib5p vPPK_rmaxRPPK = 0.01290045226; // initial value of vPPK_rmaxRPPK vPTS_KPTSa1 = 3082.3; // initial value of vPTS_KPTSa1 vPTS_KPTSa2 = 0.01; // initial value of vPTS_KPTSa2 vPTS_KPTSa3 = 245.3; // initial value of vPTS_KPTSa3 vPTS_KPTSg6p = 2.15; // initial value of vPTS_KPTSg6p vPTS_nPTSg6p = 3.66; // initial value of vPTS_nPTSg6p vPTS_rmaxPTS = 7829.78; // initial value of vPTS_rmaxPTS vR5PI_KR5PIeq = 4.0; // initial value of vR5PI_KR5PIeq vR5PI_rmaxR5PI = 4.83841193; // initial value of vR5PI_rmaxR5PI vRIB5P_mu = 2.78E-5; // initial value of vRIB5P_mu vRibu5p_mu = 2.78E-5; // initial value of vRibu5p_mu vRu5P_KRu5Peq = 1.4; // initial value of vRu5P_KRu5Peq vRu5P_rmaxRu5P = 6.739029475; // initial value of vRu5P_rmaxRu5P vSED7P_mu = 2.78E-5; // initial value of vSED7P_mu vSynth1_KSynth1pep = 1.0; // initial value of vSynth1_KSynth1pep vSynth1_rmaxSynth1 = 0.01953897003; // initial value of vSynth1_rmaxSynth1 vSynth2_KSynth2pyr = 1.0; // initial value of vSynth2_KSynth2pyr vSynth2_rmaxSynth2 = 0.07361855055; // initial value of vSynth2_rmaxSynth2 vTA_KTAeq = 1.05; // initial value of vTA_KTAeq vTA_rmaxTA = 10.87164108; // initial value of vTA_rmaxTA vTIS_kTISdhap = 2.8; // initial value of vTIS_kTISdhap vTIS_kTISeq = 1.39; // initial value of vTIS_kTISeq vTIS_kTISgap = 0.3; // initial value of vTIS_kTISgap vTIS_rmaxTIS = 68.67474392; // initial value of vTIS_rmaxTIS vTKA_KTKaeq = 1.2; // initial value of vTKA_KTKaeq vTKA_rmaxTKa = 9.473384783; // initial value of vTKA_rmaxTKa vTKB_KTKbeq = 10.0; // initial value of vTKB_KTKbeq vTKB_rmaxTKb = 86.55855855; // initial value of vTKB_rmaxTKb vTRPSYNTH_rmaxTrpSynth = 0.001037; // initial value of vTRPSYNTH_rmaxTrpSynth vXYL5P_mu = 2.78E-5; // initial value of vXYL5P_mu vf6P_mu = 2.78E-5; // initial value of vf6P_mu vfdP_mu = 2.78E-5; // initial value of vfdP_mu vpepCxylase_KpepCxylasefdp = 0.7; // initial value of vpepCxylase_KpepCxylasefdp vpepCxylase_KpepCxylasepep = 4.07; // initial value of vpepCxylase_KpepCxylasepep vpepCxylase_npepCxylasefdp = 4.21; // initial value of vpepCxylase_npepCxylasefdp vpepCxylase_rmaxpepCxylase = 0.1070205858; // initial value of vpepCxylase_rmaxpepCxylase vpg2_mu = 2.78E-5; // initial value of vpg2_mu vpyr_mu = 2.78E-5; // initial value of vpyr_mu vrpGluMu_KPGluMueq = 0.188; // initial value of vrpGluMu_KPGluMueq vrpGluMu_KPGluMupg2 = 0.369; // initial value of vrpGluMu_KPGluMupg2 vrpGluMu_KPGluMupg3 = 0.2; // initial value of vrpGluMu_KPGluMupg3 vrpGluMu_rmaxPGluMu = 89.04965407; // initial value of vrpGluMu_rmaxPGluMu vsersynth_KSerSynthpg3 = 1.0; // initial value of vsersynth_KSerSynthpg3 vsersynth_rmaxSerSynth = 0.025712107; // initial value of vsersynth_rmaxSerSynth } /* * Model variables initial values */ protected double _extracellular_cytosol_; protected double rate_vALDO; protected double rate_vDAHPS; protected double rate_vDHAP; protected double rate_vE4P; protected double rate_vENO; protected double rate_vEXTER; protected double rate_vG1PAT; protected double rate_vG3PDH; protected double rate_vG6P; protected double rate_vG6PDH; protected double rate_vGAP; protected double rate_vGAPDH; protected double rate_vGLP; protected double rate_vMURSyNTH; protected double rate_vMethSynth; protected double rate_vPDH; protected double rate_vPEP; protected double rate_vPFK; protected double rate_vPG; protected double rate_vPG3; protected double rate_vPGDH; protected double rate_vPGI; protected double rate_vPGK; protected double rate_vPGM; protected double rate_vPGP; protected double rate_vPK; protected double rate_vPPK; protected double rate_vPTS; protected double rate_vR5PI; protected double rate_vRIB5P; protected double rate_vRibu5p; protected double rate_vRu5P; protected double rate_vSED7P; protected double rate_vSynth1; protected double rate_vSynth2; protected double rate_vTA; protected double rate_vTIS; protected double rate_vTKA; protected double rate_vTKB; protected double rate_vTRPSYNTH; protected double rate_vXYL5P; protected double rate_vf6P; protected double rate_vfdP; protected double rate_vpepCxylase; protected double rate_vpg2; protected double rate_vpyr; protected double rate_vrpGluMu; protected double rate_vsersynth; protected double extracellular; protected double cadp; protected double camp; protected double catp; protected double cnad; protected double cnadh; protected double cnadp; protected double cnadph; protected double time; protected double vALDO_VALDOblf; protected double vALDO_kALDOdhap; protected double vALDO_kALDOeq; protected double vALDO_kALDOfdp; protected double vALDO_kALDOgap; protected double vALDO_kALDOgapinh; protected double vALDO_rmaxALDO; protected double vDAHPS_KDAHPSe4p; protected double vDAHPS_KDAHPSpep; protected double vDAHPS_nDAHPSe4p; protected double vDAHPS_nDAHPSpep; protected double vDAHPS_rmaxDAHPS; protected double vDHAP_mu; protected double vE4P_mu; protected double vENO_KENOeq; protected double vENO_KENOpep; protected double vENO_KENOpg2; protected double vENO_rmaxENO; protected double vEXTER_Dil; protected double vEXTER_cfeed; protected double vG1PAT_KG1PATatp; protected double vG1PAT_KG1PATfdp; protected double vG1PAT_KG1PATg1p; protected double vG1PAT_nG1PATfdp; protected double vG1PAT_rmaxG1PAT; protected double vG3PDH_KG3PDHdhap; protected double vG3PDH_rmaxG3PDH; protected double vG6PDH_KG6PDHg6p; protected double vG6PDH_KG6PDHnadp; protected double vG6PDH_KG6PDHnadphg6pinh; protected double vG6PDH_KG6PDHnadphnadpinh; protected double vG6PDH_rmaxG6PDH; protected double vG6P_mu; protected double vGAPDH_KGAPDHeq; protected double vGAPDH_KGAPDHgap; protected double vGAPDH_KGAPDHnad; protected double vGAPDH_KGAPDHnadh; protected double vGAPDH_KGAPDHpgp; protected double vGAPDH_rmaxGAPDH; protected double vGAP_mu; protected double vGLP_mu; protected double vMURSyNTH_rmaxMurSynth; protected double vMethSynth_rmaxMetSynth; protected double vPDH_KPDHpyr; protected double vPDH_nPDH; protected double vPDH_rmaxPDH; protected double vPEP_mu; protected double vPFK_KPFKadpa; protected double vPFK_KPFKadpb; protected double vPFK_KPFKadpc; protected double vPFK_KPFKampa; protected double vPFK_KPFKampb; protected double vPFK_KPFKatps; protected double vPFK_KPFKf6ps; protected double vPFK_KPFKpep; protected double vPFK_LPFK; protected double vPFK_nPFK; protected double vPFK_rmaxPFK; protected double vPG3_mu; protected double vPGDH_KPGDHatpinh; protected double vPGDH_KPGDHnadp; protected double vPGDH_KPGDHnadphinh; protected double vPGDH_KPGDHpg; protected double vPGDH_rmaxPGDH; protected double vPGI_KPGIeq; protected double vPGI_KPGIf6p; protected double vPGI_KPGIf6ppginh; protected double vPGI_KPGIg6p; protected double vPGI_KPGIg6ppginh; protected double vPGI_rmaxPGI; protected double vPGK_KPGKadp; protected double vPGK_KPGKatp; protected double vPGK_KPGKeq; protected double vPGK_KPGKpg3; protected double vPGK_KPGKpgp; protected double vPGK_rmaxPGK; protected double vPGM_KPGMeq; protected double vPGM_KPGMg1p; protected double vPGM_KPGMg6p; protected double vPGM_rmaxPGM; protected double vPGP_mu; protected double vPG_mu; protected double vPK_KPKadp; protected double vPK_KPKamp; protected double vPK_KPKatp; protected double vPK_KPKfdp; protected double vPK_KPKpep; protected double vPK_LPK; protected double vPK_nPK; protected double vPK_rmaxPK; protected double vPPK_KRPPKrib5p; protected double vPPK_rmaxRPPK; protected double vPTS_KPTSa1; protected double vPTS_KPTSa2; protected double vPTS_KPTSa3; protected double vPTS_KPTSg6p; protected double vPTS_nPTSg6p; protected double vPTS_rmaxPTS; protected double vR5PI_KR5PIeq; protected double vR5PI_rmaxR5PI; protected double vRIB5P_mu; protected double vRibu5p_mu; protected double vRu5P_KRu5Peq; protected double vRu5P_rmaxRu5P; protected double vSED7P_mu; protected double vSynth1_KSynth1pep; protected double vSynth1_rmaxSynth1; protected double vSynth2_KSynth2pyr; protected double vSynth2_rmaxSynth2; protected double vTA_KTAeq; protected double vTA_rmaxTA; protected double vTIS_kTISdhap; protected double vTIS_kTISeq; protected double vTIS_kTISgap; protected double vTIS_rmaxTIS; protected double vTKA_KTKaeq; protected double vTKA_rmaxTKa; protected double vTKB_KTKbeq; protected double vTKB_rmaxTKb; protected double vTRPSYNTH_rmaxTrpSynth; protected double vXYL5P_mu; protected double vf6P_mu; protected double vfdP_mu; protected double vpepCxylase_KpepCxylasefdp; protected double vpepCxylase_KpepCxylasepep; protected double vpepCxylase_npepCxylasefdp; protected double vpepCxylase_rmaxpepCxylase; protected double vpg2_mu; protected double vpyr_mu; protected double vrpGluMu_KPGluMueq; protected double vrpGluMu_KPGluMupg2; protected double vrpGluMu_KPGluMupg3; protected double vrpGluMu_rmaxPGluMu; protected double vsersynth_KSerSynthpg3; protected double vsersynth_rmaxSerSynth; public double[] extendResult(double time,double [] x) { this.time = time; __internalVarInitFunc_0(time, x); double[] y = new double[25]; y[0] = x[0]; y[1] = x[1]; y[2] = x[2]; y[3] = x[3]; y[4] = x[4]; y[5] = x[5]; y[6] = x[6]; y[7] = x[7]; y[8] = x[8]; y[9] = x[9]; y[10] = x[10]; y[11] = x[11]; y[12] = x[12]; y[13] = x[13]; y[14] = x[14]; y[15] = x[15]; y[16] = x[16]; y[17] = x[17]; y[18] = cadp; y[19] = camp; y[20] = catp; y[21] = cnad; y[22] = cnadh; y[23] = cnadp; y[24] = cnadph; return y; } public double[] getInitialValues() { double [] x = new double[18]; this.time = 0.0; x[0] = 2.0; // - $"extracellular.cglcex" x[1] = 0.167; // - $"extracellular.cytosol.cdhap" x[2] = 0.098; // - $"extracellular.cytosol.ce4p" x[3] = 0.6; // - $"extracellular.cytosol.cf6p" x[4] = 0.272; // - $"extracellular.cytosol.cfdp" x[5] = 0.653; // - $"extracellular.cytosol.cg1p" x[6] = 3.48; // - $"extracellular.cytosol.cg6p" x[7] = 0.218; // - $"extracellular.cytosol.cgap" x[8] = 2.67; // - $"extracellular.cytosol.cpep" x[9] = 0.808; // - $"extracellular.cytosol.cpg" x[10] = 0.399; // - $"extracellular.cytosol.cpg2" x[11] = 2.13; // - $"extracellular.cytosol.cpg3" x[12] = 0.0080; // - $"extracellular.cytosol.cpgp" x[13] = 2.67; // - $"extracellular.cytosol.cpyr" x[14] = 0.398; // - $"extracellular.cytosol.crib5p" x[15] = 0.111; // - $"extracellular.cytosol.cribu5p" x[16] = 0.276; // - $"extracellular.cytosol.csed7p" x[17] = 0.138; // - $"extracellular.cytosol.cxyl5p" __internalVarInitFunc_0(time, x); __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); return x; } /* * code for algebraic rules calculations */ /* * end of code for algebraic rules calculations */ protected void calculateRates(double time, double[] x) { __internalVarInitFunc_0(time, x); __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); } /* * calculate dy/dt for 'BIOMD0000000051.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = +rate_vEXTER-rate_vPTS; result[1] = +rate_vALDO-rate_vDHAP-rate_vG3PDH-rate_vTIS; result[2] = -rate_vDAHPS-rate_vE4P+rate_vTA-rate_vTKB; result[3] = -rate_vMURSyNTH*2-rate_vPFK+rate_vPGI+rate_vTA+rate_vTKB-rate_vf6P; result[4] = -rate_vALDO+rate_vPFK-rate_vfdP; result[5] = -rate_vG1PAT-rate_vGLP+rate_vPGM; result[6] = -rate_vG6P-rate_vG6PDH-rate_vPGI-rate_vPGM+rate_vPTS*65; result[7] = +rate_vALDO-rate_vGAP-rate_vGAPDH-rate_vTA+rate_vTIS+rate_vTKA+rate_vTKB+rate_vTRPSYNTH; result[8] = -rate_vDAHPS+rate_vENO-rate_vPEP-rate_vPK-rate_vPTS*65-rate_vSynth1-rate_vpepCxylase; result[9] = +rate_vG6PDH-rate_vPG-rate_vPGDH; result[10] = -rate_vENO-rate_vpg2+rate_vrpGluMu; result[11] = -rate_vPG3+rate_vPGK-rate_vrpGluMu-rate_vsersynth; result[12] = +rate_vGAPDH-rate_vPGK-rate_vPGP; result[13] = +rate_vMethSynth-rate_vPDH+rate_vPK+rate_vPTS*65-rate_vSynth2+rate_vTRPSYNTH-rate_vpyr; result[14] = -rate_vPPK+rate_vR5PI-rate_vRIB5P-rate_vTKA; result[15] = +rate_vPGDH-rate_vR5PI-rate_vRibu5p-rate_vRu5P; result[16] = -rate_vSED7P-rate_vTA+rate_vTKA; result[17] = +rate_vRu5P-rate_vTKA-rate_vTKB-rate_vXYL5P; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[18]; __internalDyDt_0(time, x, result); return result; } public double[] dy_dt(double time, double[] x) { this.time = time; calculateRates( time,x ); return calculateResult( time,x ); } } // class ...