/* * This code is generated by BioUML FrameWork * for BIOMD0000000070.xml diagram at 2008.03.20 15:04:57 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000070 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_vAK = compartment*(vAK_Vmaxv16/(vAK_KATPv16*vAK_KAMPv16)*(x[20]*x[1] - x[18]*x[0]/vAK_Keqv16)/((1 + x[20]/vAK_KATPv16)*(1 + x[1]/vAK_KAMPv16) + (x[18] + x[0])/vAK_KADPv16 + x[18]*x[0]/Math.pow(vAK_KADPv16, 2))); rate_vALD = compartment*(vALD_Vmaxv4/vALD_KFru16P2v4*(x[5] - x[12]*x[3]/vALD_Keqv4)/(1 + x[5]/vALD_KFru16P2v4 + x[12]/vALD_KiGraPv4 + x[3]*(x[12] + vALD_KGraPv4)/(vALD_KDHAPv4*vALD_KiGraPv4) + x[5]*x[12]/(vALD_KFru16P2v4*vALD_KiiGraPv4))); rate_vATPase = compartment*vATPase_kATPasev15*x[20]; rate_vBPGM = compartment*(vBPGM_kDPGMv8*(x[13] - (x[14] + x[21])/vBPGM_Keqv8)/(1 + (x[14] + x[21])/vBPGM_K23P2Gv8)); rate_vBPGP = compartment*(vBPGP_Vmaxv9*(x[14] + x[21] - x[16]/vBPGP_Keqv9)/(x[14] + x[21] + vBPGP_K23P2Gv9)); rate_vENO = compartment*(vENO_Vmaxv11*(x[15] - x[33]/vENO_Keqv11)/(x[15] + vENO_K2PGv11*(1 + x[33]/vENO_KPEPv11))); rate_vG6PDH = compartment*(vG6PDH_Vmaxv17/vG6PDH_KG6Pv17/vG6PDH_KNADPv17*(x[9]*x[26] - x[10]*x[25]/vG6PDH_Keqv17)/(1 + x[26]*(1 + x[9]/vG6PDH_KG6Pv17)/vG6PDH_KNADPv17 + (x[2] + x[20])/vG6PDH_KATPv17 + x[25]/vG6PDH_KNADPHv17 + (x[14] + x[21])/vG6PDH_KPGA23v17)); rate_vGAPDH = compartment*(vGAPDH_Vmaxv6/(vGAPDH_KNADv6*vGAPDH_KGraPv6*vGAPDH_KPv6)*(x[23]*x[12]*x[34] - x[13]*x[24]/vGAPDH_Keqv6)/((1 + x[23]/vGAPDH_KNADv6)*(1 + x[12]/vGAPDH_KGraPv6)*(1 + x[34]/vGAPDH_KPv6) + (1 + x[24]/vGAPDH_KNADHv6)*(1 + x[13]/vGAPDH_K13P2Gv6) - 1)); rate_vGLT = compartment*(vGLT_Vmaxv0/vGLT_KMoutv0*(_compartment_Glcout_ - x[11]/vGLT_Keqv0)/(1 + _compartment_Glcout_/vGLT_KMoutv0 + x[11]/vGLT_KMinv0 + vGLT_alfav0*_compartment_Glcout_*x[11]/vGLT_KMoutv0/vGLT_KMinv0)); rate_vGPI = compartment*(vGPI_Vmaxv2*(x[9] - x[6]/vGPI_Keqv2)/(x[9] + vGPI_KGlc6Pv2*(1 + x[6]/vGPI_KFru6Pv2))); rate_vGSHox = compartment*vGSHox_Kv20*x[7]; rate_vGSSGRD = compartment*(vGSSGRD_Vmaxv19*(x[8]*x[25]/(vGSSGRD_KGSSGv19*vGSSGRD_KNADPHv19) - Math.pow(x[7], 2)/Math.pow(vGSSGRD_KGSHv19, 2)*x[26]/(vGSSGRD_KNADPv19*vGSSGRD_Keqv19))/(1 + x[25]*(1 + x[8]/vGSSGRD_KGSSGv19)/vGSSGRD_KNADPHv19 + x[26]/vGSSGRD_KNADPv19*(1 + x[7]*(1 + x[7]/vGSSGRD_KGSHv19)/vGSSGRD_KGSHv19))); rate_vHEX = compartment*(vHEX_Inhibv1*x[11]/(x[11] + vHEX_KMGlcv1)*(vHEX_Vmax1v1/vHEX_KMgATPv1)*(x[20] + vHEX_Vmax2v1/vHEX_Vmax1v1*x[20]*x[22]/vHEX_KMgATPMgv1 - x[9]*x[18]/vHEX_Keqv1)/(1 + x[20]/vHEX_KMgATPv1*(1 + x[22]/vHEX_KMgATPMgv1) + x[22]/vHEX_KMgv1 + (1.55 + x[9]/vHEX_KGlc6Pv1)*(1 + x[22]/vHEX_KMgv1) + (x[14] + x[21])/vHEX_K23P2Gv1 + x[22]*(x[14] + x[21])/(vHEX_KMgv1*vHEX_KMg23P2Gv1))); rate_vLDHNADH = compartment*vLDHNADH_Vmaxv13*(x[35]*x[24] - x[17]*x[23]/vLDHNADH_Keqv13); rate_vLDHNADPH = compartment*vLDHNADPH_kLDHv14*(x[35]*x[25] - x[17]*x[26]/vLDHNADPH_Keqv14); rate_vLacexch = compartment*vLacexch_Vmaxv28*(_compartment_Lacex_ - x[17]/vLacexch_Keqv28); rate_vMgADP = compartment*vMgADP_EqMult*(x[18] - x[22]*x[0]/vMgADP_KdADP); rate_vMgAMP = compartment*vMgAMP_EqMult*(x[19] - x[22]*x[1]/vMgAMP_KdAMP); rate_vMgATP = compartment*vMgATP_EqMult*(x[20] - x[22]*x[2]/vMgATP_KdATP); rate_vMgGri23P2 = compartment*vMgGri23P2_EqMult*(x[21] - x[22]*x[14]/vMgGri23P2_Kd23P2G); rate_vP1NADP = compartment*vP1NADP_EqMult*(x[27] - x[29]*x[26]/vP1NADP_Kd1); rate_vP1NADPH = compartment*vP1NADPH_EqMult*(x[28] - x[29]*x[25]/vP1NADPH_Kd3); rate_vP2NADP = compartment*vP2NADP_EqMult*(x[30] - x[32]*x[26]/vP2NADP_Kd2); rate_vP2NADPH = compartment*vP2NADPH_EqMult*(x[31] - x[32]*x[25]/vP2NADPH_Kd4); rate_vPFK = compartment*(vPFK_Vmaxv3*(x[6]*x[20] - x[5]*x[18]/vPFK_Keqv3)/((x[6] + vPFK_KFru6Pv3)*(x[20] + vPFK_KMgATPv3)*(1 + vPFK_L0v3*Math.pow(((1 + x[2]/vPFK_KATPv3)*(1 + x[22]/vPFK_KMgv3)/((1 + (x[1] + x[19])/vPFK_KAMPv3)*(1 + x[6]/vPFK_KFru6Pv3))), 4)))); rate_vPGK = compartment*(vPGK_Vmaxv7/(vPGK_KMgADPv7*vPGK_K13P2Gv7)*(x[18]*x[13] - x[20]*x[16]/vPGK_Keqv7)/((1 + x[18]/vPGK_KMgADPv7)*(1 + x[13]/vPGK_K13P2Gv7) + (1 + x[20]/vPGK_KMgATPv7)*(1 + x[16]/vPGK_K3PGv7) - 1)); rate_vPGLDH = compartment*(vPGLDH_Vmaxv18/vPGLDH_K6PG1v18/vPGLDH_KNADPv18*(x[10]*x[26] - x[37]*x[25]/vPGLDH_Keqv18)/((1 + x[26]/vPGLDH_KNADPv18)*(1 + x[10]/vPGLDH_K6PG1v18 + (x[14] + x[21])/vPGLDH_KPGA23v18) + (x[2] + x[20])/vPGLDH_KATPv18 + x[25]*(1 + x[10]/vPGLDH_K6PG2v18)/vPGLDH_KNADPHv18)); rate_vPGM = compartment*(vPGM_Vmaxv10*(x[16] - x[15]/vPGM_Keqv10)/(x[16] + vPGM_K3PGv10*(1 + x[15]/vPGM_K2PGv10))); rate_vPK = compartment*(vPK_Vmaxv12*(x[33]*x[18] - x[35]*x[20]/vPK_Keqv12)/((x[33] + vPK_KPEPv12)*(x[18] + vPK_KMgADPv12)*(1 + vPK_L0v12*Math.pow((1 + (x[2] + x[20])/vPK_KATPv12), 4)/(Math.pow((1 + x[33]/vPK_KPEPv12), 4)*Math.pow((1 + x[5]/vPK_KFru16P2v12), 4))))); rate_vPPRPPS = compartment*(vPPRPPS_Vmaxv25*(x[36]*x[20] - _compartment_PRPP_*x[19]/vPPRPPS_Keqv25)/((vPPRPPS_KATPv25 + x[20])*(vPPRPPS_KR5Pv25 + x[36]))); rate_vPhiexch = compartment*vPhiexch_Vmaxv27*(_compartment_Phiex_ - x[34]/vPhiexch_Keqv27); rate_vPyrexch = compartment*vPyrexch_Vmaxv29*(_compartment_Pyrex_ - x[35]/vPyrexch_Keqv29); rate_vRibPepi = compartment*(vRibPepi_Vmaxv21*(x[37] - x[39]/vRibPepi_Keqv21)/(x[37] + vRibPepi_KRu5Pv21*(1 + x[39]/vRibPepi_KX5Pv21))); rate_vRibPiso = compartment*(vRibPiso_Vmaxv22*(x[37] - x[36]/vRibPiso_Keqv22)/(x[37] + vRibPiso_KRu5Pv22*(1 + x[36]/vRibPiso_KR5Pv22))); rate_vTPI = compartment*(vTPI_Vmaxv5*(x[3] - x[12]/vTPI_Keqv5)/(x[3] + vTPI_KDHAPv5*(1 + x[12]/vTPI_KGraPv5))); rate_vTrAld = compartment*(vTrAld_Vmaxv24*(x[38]*x[12] - x[4]*x[6]/vTrAld_Keqv24)/((vTrAld_K1v24 + x[12])*x[38] + (vTrAld_K2v24 + vTrAld_K6v24*x[6])*x[12] + (vTrAld_K3v24 + vTrAld_K5v24*x[6])*x[4] + vTrAld_K4v24*x[6] + vTrAld_K7v24*x[38]*x[4])); rate_vTrKet1 = compartment*(vTrKet1_Vmaxv23*(x[36]*x[39] - x[12]*x[38]/vTrKet1_Keqv23)/((vTrKet1_K1v23 + x[36])*x[39] + (vTrKet1_K2v23 + vTrKet1_K6v23*x[38])*x[36] + (vTrKet1_K3v23 + vTrKet1_K5v23*x[38])*x[12] + vTrKet1_K4v23*x[38] + vTrKet1_K7v23*x[39]*x[12])); rate_vTrKet2 = compartment*(vTrKet2_Vmaxv26*(x[4]*x[39] - x[12]*x[6]/vTrKet2_Keqv26)/((vTrKet2_K1v26 + x[4])*x[39] + (vTrKet2_K2v26 + vTrKet2_K6v26*x[6])*x[4] + (vTrKet2_K3v26 + vTrKet2_K5v26*x[6])*x[12] + vTrKet2_K4v26*x[6] + vTrKet2_K7v26*x[39]*x[12])); } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _compartment_Glcout_ = 5.0; // initial value of $"compartment.Glcout" _compartment_Lacex_ = 1.68; // initial value of $"compartment.Lacex" _compartment_PRPP_ = 1.0; // initial value of $"compartment.PRPP" _compartment_Phiex_ = 1.0; // initial value of $"compartment.Phiex" _compartment_Pyrex_ = 0.084; // initial value of $"compartment.Pyrex" compartment = 1.0; // initial value of $compartment vAK_KADPv16 = 0.11; // initial value of vAK_KADPv16 vAK_KAMPv16 = 0.08; // initial value of vAK_KAMPv16 vAK_KATPv16 = 0.09; // initial value of vAK_KATPv16 vAK_Keqv16 = 0.25; // initial value of vAK_Keqv16 vAK_Vmaxv16 = 1380.0; // initial value of vAK_Vmaxv16 vALD_KDHAPv4 = 0.0364; // initial value of vALD_KDHAPv4 vALD_KFru16P2v4 = 0.0071; // initial value of vALD_KFru16P2v4 vALD_KGraPv4 = 0.1906; // initial value of vALD_KGraPv4 vALD_Keqv4 = 0.114; // initial value of vALD_Keqv4 vALD_KiGraPv4 = 0.0572; // initial value of vALD_KiGraPv4 vALD_KiiGraPv4 = 0.176; // initial value of vALD_KiiGraPv4 vALD_Vmaxv4 = 98.91000366; // initial value of vALD_Vmaxv4 vATPase_kATPasev15 = 1.68; // initial value of vATPase_kATPasev15 vBPGM_K23P2Gv8 = 0.04; // initial value of vBPGM_K23P2Gv8 vBPGM_Keqv8 = 100000.0; // initial value of vBPGM_Keqv8 vBPGM_kDPGMv8 = 76000.0; // initial value of vBPGM_kDPGMv8 vBPGP_K23P2Gv9 = 0.2; // initial value of vBPGP_K23P2Gv9 vBPGP_Keqv9 = 100000.0; // initial value of vBPGP_Keqv9 vBPGP_Vmaxv9 = 0.53; // initial value of vBPGP_Vmaxv9 vENO_K2PGv11 = 1.0; // initial value of vENO_K2PGv11 vENO_KPEPv11 = 1.0; // initial value of vENO_KPEPv11 vENO_Keqv11 = 1.7; // initial value of vENO_Keqv11 vENO_Vmaxv11 = 1500.0; // initial value of vENO_Vmaxv11 vG6PDH_KATPv17 = 0.749; // initial value of vG6PDH_KATPv17 vG6PDH_KG6Pv17 = 0.0667; // initial value of vG6PDH_KG6Pv17 vG6PDH_KNADPHv17 = 0.00312; // initial value of vG6PDH_KNADPHv17 vG6PDH_KNADPv17 = 0.00367; // initial value of vG6PDH_KNADPv17 vG6PDH_KPGA23v17 = 2.289; // initial value of vG6PDH_KPGA23v17 vG6PDH_Keqv17 = 2000.0; // initial value of vG6PDH_Keqv17 vG6PDH_Vmaxv17 = 162.0; // initial value of vG6PDH_Vmaxv17 vGAPDH_K13P2Gv6 = 0.0035; // initial value of vGAPDH_K13P2Gv6 vGAPDH_KGraPv6 = 0.0050; // initial value of vGAPDH_KGraPv6 vGAPDH_KNADHv6 = 0.0083; // initial value of vGAPDH_KNADHv6 vGAPDH_KNADv6 = 0.05; // initial value of vGAPDH_KNADv6 vGAPDH_KPv6 = 3.9; // initial value of vGAPDH_KPv6 vGAPDH_Keqv6 = 1.92E-4; // initial value of vGAPDH_Keqv6 vGAPDH_Vmaxv6 = 4300.0; // initial value of vGAPDH_Vmaxv6 vGLT_KMinv0 = 6.9; // initial value of vGLT_KMinv0 vGLT_KMoutv0 = 1.7; // initial value of vGLT_KMoutv0 vGLT_Keqv0 = 1.0; // initial value of vGLT_Keqv0 vGLT_Vmaxv0 = 33.6; // initial value of vGLT_Vmaxv0 vGLT_alfav0 = 0.54; // initial value of vGLT_alfav0 vGPI_KFru6Pv2 = 0.071; // initial value of vGPI_KFru6Pv2 vGPI_KGlc6Pv2 = 0.182; // initial value of vGPI_KGlc6Pv2 vGPI_Keqv2 = 0.3925; // initial value of vGPI_Keqv2 vGPI_Vmaxv2 = 935.0; // initial value of vGPI_Vmaxv2 vGSHox_Kv20 = 0.03; // initial value of vGSHox_Kv20 vGSSGRD_KGSHv19 = 20.0; // initial value of vGSSGRD_KGSHv19 vGSSGRD_KGSSGv19 = 0.0652; // initial value of vGSSGRD_KGSSGv19 vGSSGRD_KNADPHv19 = 0.00852; // initial value of vGSSGRD_KNADPHv19 vGSSGRD_KNADPv19 = 0.07; // initial value of vGSSGRD_KNADPv19 vGSSGRD_Keqv19 = 1.04; // initial value of vGSSGRD_Keqv19 vGSSGRD_Vmaxv19 = 90.0; // initial value of vGSSGRD_Vmaxv19 vHEX_Inhibv1 = 1.0; // initial value of vHEX_Inhibv1 vHEX_K23P2Gv1 = 2.7; // initial value of vHEX_K23P2Gv1 vHEX_KGlc6Pv1 = 0.0045; // initial value of vHEX_KGlc6Pv1 vHEX_KMGlcv1 = 0.1; // initial value of vHEX_KMGlcv1 vHEX_KMg23P2Gv1 = 3.44; // initial value of vHEX_KMg23P2Gv1 vHEX_KMgATPMgv1 = 1.14; // initial value of vHEX_KMgATPMgv1 vHEX_KMgATPv1 = 1.44; // initial value of vHEX_KMgATPv1 vHEX_KMgv1 = 1.03; // initial value of vHEX_KMgv1 vHEX_Keqv1 = 3900.0; // initial value of vHEX_Keqv1 vHEX_Vmax1v1 = 15.8; // initial value of vHEX_Vmax1v1 vHEX_Vmax2v1 = 33.2; // initial value of vHEX_Vmax2v1 vLDHNADH_Keqv13 = 9090.0; // initial value of vLDHNADH_Keqv13 vLDHNADH_Vmaxv13 = 2800000.0; // initial value of vLDHNADH_Vmaxv13 vLDHNADPH_Keqv14 = 14181.8; // initial value of vLDHNADPH_Keqv14 vLDHNADPH_kLDHv14 = 243.4; // initial value of vLDHNADPH_kLDHv14 vLacexch_Keqv28 = 1.0; // initial value of vLacexch_Keqv28 vLacexch_Vmaxv28 = 10000.0; // initial value of vLacexch_Vmaxv28 vMgADP_EqMult = 1.0E7; // initial value of vMgADP_EqMult vMgADP_KdADP = 0.76; // initial value of vMgADP_KdADP vMgAMP_EqMult = 1.0E7; // initial value of vMgAMP_EqMult vMgAMP_KdAMP = 16.64; // initial value of vMgAMP_KdAMP vMgATP_EqMult = 1.0E7; // initial value of vMgATP_EqMult vMgATP_KdATP = 0.072; // initial value of vMgATP_KdATP vMgGri23P2_EqMult = 1.0E7; // initial value of vMgGri23P2_EqMult vMgGri23P2_Kd23P2G = 1.667; // initial value of vMgGri23P2_Kd23P2G vP1NADPH_EqMult = 1.0E7; // initial value of vP1NADPH_EqMult vP1NADPH_Kd3 = 1.0E-5; // initial value of vP1NADPH_Kd3 vP1NADP_EqMult = 1.0E7; // initial value of vP1NADP_EqMult vP1NADP_Kd1 = 2.0E-4; // initial value of vP1NADP_Kd1 vP2NADPH_EqMult = 1.0E7; // initial value of vP2NADPH_EqMult vP2NADPH_Kd4 = 2.0E-4; // initial value of vP2NADPH_Kd4 vP2NADP_EqMult = 1.0E7; // initial value of vP2NADP_EqMult vP2NADP_Kd2 = 1.0E-5; // initial value of vP2NADP_Kd2 vPFK_KAMPv3 = 0.033; // initial value of vPFK_KAMPv3 vPFK_KATPv3 = 0.01; // initial value of vPFK_KATPv3 vPFK_KFru6Pv3 = 0.1; // initial value of vPFK_KFru6Pv3 vPFK_KMgATPv3 = 0.068; // initial value of vPFK_KMgATPv3 vPFK_KMgv3 = 0.44; // initial value of vPFK_KMgv3 vPFK_Keqv3 = 100000.0; // initial value of vPFK_Keqv3 vPFK_L0v3 = 0.001072; // initial value of vPFK_L0v3 vPFK_Vmaxv3 = 239.0; // initial value of vPFK_Vmaxv3 vPGK_K13P2Gv7 = 0.0020; // initial value of vPGK_K13P2Gv7 vPGK_K3PGv7 = 1.2; // initial value of vPGK_K3PGv7 vPGK_KMgADPv7 = 0.35; // initial value of vPGK_KMgADPv7 vPGK_KMgATPv7 = 0.48; // initial value of vPGK_KMgATPv7 vPGK_Keqv7 = 1455.0; // initial value of vPGK_Keqv7 vPGK_Vmaxv7 = 5000.0; // initial value of vPGK_Vmaxv7 vPGLDH_K6PG1v18 = 0.01; // initial value of vPGLDH_K6PG1v18 vPGLDH_K6PG2v18 = 0.058; // initial value of vPGLDH_K6PG2v18 vPGLDH_KATPv18 = 0.154; // initial value of vPGLDH_KATPv18 vPGLDH_KNADPHv18 = 0.0045; // initial value of vPGLDH_KNADPHv18 vPGLDH_KNADPv18 = 0.018; // initial value of vPGLDH_KNADPv18 vPGLDH_KPGA23v18 = 0.12; // initial value of vPGLDH_KPGA23v18 vPGLDH_Keqv18 = 141.7; // initial value of vPGLDH_Keqv18 vPGLDH_Vmaxv18 = 1575.0; // initial value of vPGLDH_Vmaxv18 vPGM_K2PGv10 = 1.0; // initial value of vPGM_K2PGv10 vPGM_K3PGv10 = 5.0; // initial value of vPGM_K3PGv10 vPGM_Keqv10 = 0.145; // initial value of vPGM_Keqv10 vPGM_Vmaxv10 = 2000.0; // initial value of vPGM_Vmaxv10 vPK_KATPv12 = 3.39; // initial value of vPK_KATPv12 vPK_KFru16P2v12 = 0.0050; // initial value of vPK_KFru16P2v12 vPK_KMgADPv12 = 0.474; // initial value of vPK_KMgADPv12 vPK_KPEPv12 = 0.225; // initial value of vPK_KPEPv12 vPK_Keqv12 = 13790.0; // initial value of vPK_Keqv12 vPK_L0v12 = 19.0; // initial value of vPK_L0v12 vPK_Vmaxv12 = 570.0; // initial value of vPK_Vmaxv12 vPPRPPS_KATPv25 = 0.03; // initial value of vPPRPPS_KATPv25 vPPRPPS_KR5Pv25 = 0.57; // initial value of vPPRPPS_KR5Pv25 vPPRPPS_Keqv25 = 100000.0; // initial value of vPPRPPS_Keqv25 vPPRPPS_Vmaxv25 = 1.1; // initial value of vPPRPPS_Vmaxv25 vPhiexch_Keqv27 = 1.0; // initial value of vPhiexch_Keqv27 vPhiexch_Vmaxv27 = 100.0; // initial value of vPhiexch_Vmaxv27 vPyrexch_Keqv29 = 1.0; // initial value of vPyrexch_Keqv29 vPyrexch_Vmaxv29 = 10000.0; // initial value of vPyrexch_Vmaxv29 vRibPepi_KRu5Pv21 = 0.19; // initial value of vRibPepi_KRu5Pv21 vRibPepi_KX5Pv21 = 0.5; // initial value of vRibPepi_KX5Pv21 vRibPepi_Keqv21 = 2.7; // initial value of vRibPepi_Keqv21 vRibPepi_Vmaxv21 = 4634.0; // initial value of vRibPepi_Vmaxv21 vRibPiso_KR5Pv22 = 2.2; // initial value of vRibPiso_KR5Pv22 vRibPiso_KRu5Pv22 = 0.78; // initial value of vRibPiso_KRu5Pv22 vRibPiso_Keqv22 = 3.0; // initial value of vRibPiso_Keqv22 vRibPiso_Vmaxv22 = 730.0; // initial value of vRibPiso_Vmaxv22 vTPI_KDHAPv5 = 0.838; // initial value of vTPI_KDHAPv5 vTPI_KGraPv5 = 0.428; // initial value of vTPI_KGraPv5 vTPI_Keqv5 = 0.0407; // initial value of vTPI_Keqv5 vTPI_Vmaxv5 = 5456.600098; // initial value of vTPI_Vmaxv5 vTrAld_K1v24 = 0.00823; // initial value of vTrAld_K1v24 vTrAld_K2v24 = 0.04765; // initial value of vTrAld_K2v24 vTrAld_K3v24 = 0.1733; // initial value of vTrAld_K3v24 vTrAld_K4v24 = 0.006095; // initial value of vTrAld_K4v24 vTrAld_K5v24 = 0.8683; // initial value of vTrAld_K5v24 vTrAld_K6v24 = 0.4653; // initial value of vTrAld_K6v24 vTrAld_K7v24 = 2.524; // initial value of vTrAld_K7v24 vTrAld_Keqv24 = 1.05; // initial value of vTrAld_Keqv24 vTrAld_Vmaxv24 = 27.2; // initial value of vTrAld_Vmaxv24 vTrKet1_K1v23 = 0.4177; // initial value of vTrKet1_K1v23 vTrKet1_K2v23 = 0.3055; // initial value of vTrKet1_K2v23 vTrKet1_K3v23 = 12.432; // initial value of vTrKet1_K3v23 vTrKet1_K4v23 = 0.00496; // initial value of vTrKet1_K4v23 vTrKet1_K5v23 = 0.41139; // initial value of vTrKet1_K5v23 vTrKet1_K6v23 = 0.00774; // initial value of vTrKet1_K6v23 vTrKet1_K7v23 = 48.8; // initial value of vTrKet1_K7v23 vTrKet1_Keqv23 = 1.05; // initial value of vTrKet1_Keqv23 vTrKet1_Vmaxv23 = 23.5; // initial value of vTrKet1_Vmaxv23 vTrKet2_K1v26 = 0.00184; // initial value of vTrKet2_K1v26 vTrKet2_K2v26 = 0.3055; // initial value of vTrKet2_K2v26 vTrKet2_K3v26 = 0.0548; // initial value of vTrKet2_K3v26 vTrKet2_K4v26 = 3.0E-4; // initial value of vTrKet2_K4v26 vTrKet2_K5v26 = 0.0287; // initial value of vTrKet2_K5v26 vTrKet2_K6v26 = 0.122; // initial value of vTrKet2_K6v26 vTrKet2_K7v26 = 0.215; // initial value of vTrKet2_K7v26 vTrKet2_Keqv26 = 1.2; // initial value of vTrKet2_Keqv26 vTrKet2_Vmaxv26 = 23.5; // initial value of vTrKet2_Vmaxv26 } /* * Model variables initial values */ protected double _compartment_Glcout_; protected double _compartment_Lacex_; protected double _compartment_PRPP_; protected double _compartment_Phiex_; protected double _compartment_Pyrex_; protected double rate_vAK; protected double rate_vALD; protected double rate_vATPase; protected double rate_vBPGM; protected double rate_vBPGP; protected double rate_vENO; protected double rate_vG6PDH; protected double rate_vGAPDH; protected double rate_vGLT; protected double rate_vGPI; protected double rate_vGSHox; protected double rate_vGSSGRD; protected double rate_vHEX; protected double rate_vLDHNADH; protected double rate_vLDHNADPH; protected double rate_vLacexch; protected double rate_vMgADP; protected double rate_vMgAMP; protected double rate_vMgATP; protected double rate_vMgGri23P2; protected double rate_vP1NADP; protected double rate_vP1NADPH; protected double rate_vP2NADP; protected double rate_vP2NADPH; protected double rate_vPFK; protected double rate_vPGK; protected double rate_vPGLDH; protected double rate_vPGM; protected double rate_vPK; protected double rate_vPPRPPS; protected double rate_vPhiexch; protected double rate_vPyrexch; protected double rate_vRibPepi; protected double rate_vRibPiso; protected double rate_vTPI; protected double rate_vTrAld; protected double rate_vTrKet1; protected double rate_vTrKet2; protected double compartment; protected double vAK_KADPv16; protected double vAK_KAMPv16; protected double vAK_KATPv16; protected double vAK_Keqv16; protected double vAK_Vmaxv16; protected double vALD_KDHAPv4; protected double vALD_KFru16P2v4; protected double vALD_KGraPv4; protected double vALD_Keqv4; protected double vALD_KiGraPv4; protected double vALD_KiiGraPv4; protected double vALD_Vmaxv4; protected double vATPase_kATPasev15; protected double vBPGM_K23P2Gv8; protected double vBPGM_Keqv8; protected double vBPGM_kDPGMv8; protected double vBPGP_K23P2Gv9; protected double vBPGP_Keqv9; protected double vBPGP_Vmaxv9; protected double vENO_K2PGv11; protected double vENO_KPEPv11; protected double vENO_Keqv11; protected double vENO_Vmaxv11; protected double vG6PDH_KATPv17; protected double vG6PDH_KG6Pv17; protected double vG6PDH_KNADPHv17; protected double vG6PDH_KNADPv17; protected double vG6PDH_KPGA23v17; protected double vG6PDH_Keqv17; protected double vG6PDH_Vmaxv17; protected double vGAPDH_K13P2Gv6; protected double vGAPDH_KGraPv6; protected double vGAPDH_KNADHv6; protected double vGAPDH_KNADv6; protected double vGAPDH_KPv6; protected double vGAPDH_Keqv6; protected double vGAPDH_Vmaxv6; protected double vGLT_KMinv0; protected double vGLT_KMoutv0; protected double vGLT_Keqv0; protected double vGLT_Vmaxv0; protected double vGLT_alfav0; protected double vGPI_KFru6Pv2; protected double vGPI_KGlc6Pv2; protected double vGPI_Keqv2; protected double vGPI_Vmaxv2; protected double vGSHox_Kv20; protected double vGSSGRD_KGSHv19; protected double vGSSGRD_KGSSGv19; protected double vGSSGRD_KNADPHv19; protected double vGSSGRD_KNADPv19; protected double vGSSGRD_Keqv19; protected double vGSSGRD_Vmaxv19; protected double vHEX_Inhibv1; protected double vHEX_K23P2Gv1; protected double vHEX_KGlc6Pv1; protected double vHEX_KMGlcv1; protected double vHEX_KMg23P2Gv1; protected double vHEX_KMgATPMgv1; protected double vHEX_KMgATPv1; protected double vHEX_KMgv1; protected double vHEX_Keqv1; protected double vHEX_Vmax1v1; protected double vHEX_Vmax2v1; protected double vLDHNADH_Keqv13; protected double vLDHNADH_Vmaxv13; protected double vLDHNADPH_Keqv14; protected double vLDHNADPH_kLDHv14; protected double vLacexch_Keqv28; protected double vLacexch_Vmaxv28; protected double vMgADP_EqMult; protected double vMgADP_KdADP; protected double vMgAMP_EqMult; protected double vMgAMP_KdAMP; protected double vMgATP_EqMult; protected double vMgATP_KdATP; protected double vMgGri23P2_EqMult; protected double vMgGri23P2_Kd23P2G; protected double vP1NADPH_EqMult; protected double vP1NADPH_Kd3; protected double vP1NADP_EqMult; protected double vP1NADP_Kd1; protected double vP2NADPH_EqMult; protected double vP2NADPH_Kd4; protected double vP2NADP_EqMult; protected double vP2NADP_Kd2; protected double vPFK_KAMPv3; protected double vPFK_KATPv3; protected double vPFK_KFru6Pv3; protected double vPFK_KMgATPv3; protected double vPFK_KMgv3; protected double vPFK_Keqv3; protected double vPFK_L0v3; protected double vPFK_Vmaxv3; protected double vPGK_K13P2Gv7; protected double vPGK_K3PGv7; protected double vPGK_KMgADPv7; protected double vPGK_KMgATPv7; protected double vPGK_Keqv7; protected double vPGK_Vmaxv7; protected double vPGLDH_K6PG1v18; protected double vPGLDH_K6PG2v18; protected double vPGLDH_KATPv18; protected double vPGLDH_KNADPHv18; protected double vPGLDH_KNADPv18; protected double vPGLDH_KPGA23v18; protected double vPGLDH_Keqv18; protected double vPGLDH_Vmaxv18; protected double vPGM_K2PGv10; protected double vPGM_K3PGv10; protected double vPGM_Keqv10; protected double vPGM_Vmaxv10; protected double vPK_KATPv12; protected double vPK_KFru16P2v12; protected double vPK_KMgADPv12; protected double vPK_KPEPv12; protected double vPK_Keqv12; protected double vPK_L0v12; protected double vPK_Vmaxv12; protected double vPPRPPS_KATPv25; protected double vPPRPPS_KR5Pv25; protected double vPPRPPS_Keqv25; protected double vPPRPPS_Vmaxv25; protected double vPhiexch_Keqv27; protected double vPhiexch_Vmaxv27; protected double vPyrexch_Keqv29; protected double vPyrexch_Vmaxv29; protected double vRibPepi_KRu5Pv21; protected double vRibPepi_KX5Pv21; protected double vRibPepi_Keqv21; protected double vRibPepi_Vmaxv21; protected double vRibPiso_KR5Pv22; protected double vRibPiso_KRu5Pv22; protected double vRibPiso_Keqv22; protected double vRibPiso_Vmaxv22; protected double vTPI_KDHAPv5; protected double vTPI_KGraPv5; protected double vTPI_Keqv5; protected double vTPI_Vmaxv5; protected double vTrAld_K1v24; protected double vTrAld_K2v24; protected double vTrAld_K3v24; protected double vTrAld_K4v24; protected double vTrAld_K5v24; protected double vTrAld_K6v24; protected double vTrAld_K7v24; protected double vTrAld_Keqv24; protected double vTrAld_Vmaxv24; protected double vTrKet1_K1v23; protected double vTrKet1_K2v23; protected double vTrKet1_K3v23; protected double vTrKet1_K4v23; protected double vTrKet1_K5v23; protected double vTrKet1_K6v23; protected double vTrKet1_K7v23; protected double vTrKet1_Keqv23; protected double vTrKet1_Vmaxv23; protected double vTrKet2_K1v26; protected double vTrKet2_K2v26; protected double vTrKet2_K3v26; protected double vTrKet2_K4v26; protected double vTrKet2_K5v26; protected double vTrKet2_K6v26; protected double vTrKet2_K7v26; protected double vTrKet2_Keqv26; protected double vTrKet2_Vmaxv26; public double[] extendResult(double time,double [] x) { this.time = time; double[] y = new double[40]; 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] = x[18]; y[19] = x[19]; y[20] = x[20]; y[21] = x[21]; y[22] = x[22]; y[23] = x[23]; y[24] = x[24]; y[25] = x[25]; y[26] = x[26]; y[27] = x[27]; y[28] = x[28]; y[29] = x[29]; y[30] = x[30]; y[31] = x[31]; y[32] = x[32]; y[33] = x[33]; y[34] = x[34]; y[35] = x[35]; y[36] = x[36]; y[37] = x[37]; y[38] = x[38]; y[39] = x[39]; return y; } public double[] getInitialValues() { double [] x = new double[40]; this.time = 0.0; x[0] = 0.25; // - $"compartment.ADPf" x[1] = 0.0; // - $"compartment.AMPf" x[2] = 0.25; // - $"compartment.ATPf" x[3] = 0.1492; // - $"compartment.DHAP" x[4] = 0.0063; // - $"compartment.E4P" x[5] = 0.0097; // - $"compartment.Fru16P2" x[6] = 0.0153; // - $"compartment.Fru6P" x[7] = 3.1136; // - $"compartment.GSH" x[8] = 4.0E-4; // - $"compartment.GSSG" x[9] = 0.0394; // - $"compartment.Glc6P" x[10] = 0.025; // - $"compartment.GlcA6P" x[11] = 4.5663; // - $"compartment.Glcin" x[12] = 0.0061; // - $"compartment.GraP" x[13] = 5.0E-4; // - $"compartment.Gri13P2" x[14] = 2.0601; // - $"compartment.Gri23P2f" x[15] = 0.0084; // - $"compartment.Gri2P" x[16] = 0.0658; // - $"compartment.Gri3P" x[17] = 1.6803; // - $"compartment.Lac" x[18] = 0.1; // - $"compartment.MgADP" x[19] = 0.0; // - $"compartment.MgAMP" x[20] = 1.4; // - $"compartment.MgATP" x[21] = 0.5; // - $"compartment.MgGri23P2" x[22] = 0.8; // - $"compartment.Mgf" x[23] = 0.0653; // - $"compartment.NAD" x[24] = 2.0E-4; // - $"compartment.NADH" x[25] = 0.0040; // - $"compartment.NADPHf" x[26] = 0.0; // - $"compartment.NADPf" x[27] = 0.0; // - $"compartment.P1NADP" x[28] = 0.024; // - $"compartment.P1NADPH" x[29] = 0.0; // - $"compartment.P1f" x[30] = 0.0; // - $"compartment.P2NADP" x[31] = 0.024; // - $"compartment.P2NADPH" x[32] = 0.0; // - $"compartment.P2f" x[33] = 0.0109; // - $"compartment.PEP" x[34] = 0.9992; // - $"compartment.Phi" x[35] = 0.084; // - $"compartment.Pyr" x[36] = 0.014; // - $"compartment.Rib5P" x[37] = 0.0047; // - $"compartment.Rul5P" x[38] = 0.0154; // - $"compartment.Sed7P" x[39] = 0.0127; // - $"compartment.Xul5P" __internalRateVarInitFunc_0(time, x); return x; } /* * code for algebraic rules calculations */ /* * end of code for algebraic rules calculations */ protected void calculateRates(double time, double[] x) { __internalRateVarInitFunc_0(time, x); } /* * calculate dy/dt for 'BIOMD0000000070.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = +rate_vAK+rate_vMgADP; result[1] = -rate_vAK+rate_vMgAMP; result[2] = +rate_vMgATP; result[3] = +rate_vALD-rate_vTPI; result[4] = +rate_vTrAld-rate_vTrKet2; result[5] = -rate_vALD+rate_vPFK; result[6] = +rate_vGPI-rate_vPFK+rate_vTrAld+rate_vTrKet2; result[7] = -rate_vGSHox*2+rate_vGSSGRD*2; result[8] = +rate_vGSHox-rate_vGSSGRD; result[9] = -rate_vG6PDH-rate_vGPI+rate_vHEX; result[10] = +rate_vG6PDH-rate_vPGLDH; result[11] = +rate_vGLT-rate_vHEX; result[12] = +rate_vALD-rate_vGAPDH+rate_vTPI-rate_vTrAld+rate_vTrKet1+rate_vTrKet2; result[13] = -rate_vBPGM+rate_vGAPDH-rate_vPGK; result[14] = +rate_vBPGM-rate_vBPGP+rate_vMgGri23P2; result[15] = -rate_vENO+rate_vPGM; result[16] = +rate_vBPGP+rate_vPGK-rate_vPGM; result[17] = +rate_vLDHNADH+rate_vLDHNADPH+rate_vLacexch; result[18] = +rate_vAK+rate_vATPase+rate_vHEX-rate_vMgADP+rate_vPFK-rate_vPGK-rate_vPK; result[19] = -rate_vMgAMP+rate_vPPRPPS; result[20] = -rate_vAK-rate_vATPase-rate_vHEX-rate_vMgATP-rate_vPFK+rate_vPGK+rate_vPK-rate_vPPRPPS; result[21] = -rate_vMgGri23P2; result[22] = +rate_vMgADP+rate_vMgAMP+rate_vMgATP+rate_vMgGri23P2; result[23] = -rate_vGAPDH+rate_vLDHNADH; result[24] = +rate_vGAPDH-rate_vLDHNADH; result[25] = +rate_vG6PDH-rate_vGSSGRD-rate_vLDHNADPH+rate_vP1NADPH+rate_vP2NADPH+rate_vPGLDH; result[26] = -rate_vG6PDH+rate_vGSSGRD+rate_vLDHNADPH+rate_vP1NADP+rate_vP2NADP-rate_vPGLDH; result[27] = -rate_vP1NADP; result[28] = -rate_vP1NADPH; result[29] = +rate_vP1NADP+rate_vP1NADPH; result[30] = -rate_vP2NADP; result[31] = -rate_vP2NADPH; result[32] = +rate_vP2NADP+rate_vP2NADPH; result[33] = +rate_vENO-rate_vPK; result[34] = +rate_vATPase+rate_vBPGP-rate_vGAPDH+rate_vPhiexch; result[35] = -rate_vLDHNADH-rate_vLDHNADPH+rate_vPK+rate_vPyrexch; result[36] = -rate_vPPRPPS+rate_vRibPiso-rate_vTrKet1; result[37] = +rate_vPGLDH-rate_vRibPepi-rate_vRibPiso; result[38] = -rate_vTrAld+rate_vTrKet1; result[39] = +rate_vRibPepi-rate_vTrKet1-rate_vTrKet2; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[40]; __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 ...