/* * This code is generated by BioUML FrameWork * for BIOMD0000000061.xml diagram at 2008.03.20 15:04:46 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000061 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_vADH = _extracellular_cytosol_*(vADH_V12m*x[5]*x[19]/((vADH_K12NADH + x[19])*(vADH_K12ACA + x[5]))); rate_vAK = _extracellular_cytosol_*(vAK_k24f*x[7]*x[8] - vAK_k24r*Math.pow(x[6], 2)); rate_vALD = _extracellular_cytosol_*(vALD_V6f*x[13]/(vALD_K6FBP + x[13] + x[15]*vALD_K6DHAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6) + x[10]*vALD_K6GAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6) + x[13]*x[15]/vALD_K6IGAP + x[15]*x[10]*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6)) - vALD_V6f*x[15]*x[10]/vALD_K6eq/(vALD_K6FBP + x[13] + x[15]*vALD_K6DHAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6) + x[10]*vALD_K6GAP*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6) + x[13]*x[15]/vALD_K6IGAP + x[15]*x[10]*vALD_V6f/(vALD_K6eq*vALD_V6f*vALD_ratio6))); rate_vGAPDH = _extracellular_cytosol_*(vGAPDH_V8f*x[15]*x[18]/vGAPDH_K8GAP/vGAPDH_K8NAD/((1 + x[15]/vGAPDH_K8GAP + x[9]/vGAPDH_K8BPG)*(1 + x[18]/vGAPDH_K8NAD + x[19]/vGAPDH_K8NADH)) - vGAPDH_V8r*x[9]*x[19]/vGAPDH_K8eq/vGAPDH_K8GAP/vGAPDH_K8NAD/((1 + x[15]/vGAPDH_K8GAP + x[9]/vGAPDH_K8BPG)*(1 + x[18]/vGAPDH_K8NAD + x[19]/vGAPDH_K8NADH))); rate_vGlcTrans = extracellular*vGlcTrans_V2f/vGlcTrans_Yvol*(x[3]/vGlcTrans_K2Glc/(1 + x[3]/vGlcTrans_K2Glc + (vGlcTrans_P2*(x[3]/vGlcTrans_K2Glc) + 1)/(vGlcTrans_P2*(x[16]/vGlcTrans_K2Glc) + 1)*(1 + x[16]/vGlcTrans_K2Glc + x[14]/vGlcTrans_K2IG6P + x[16]*x[14]/(vGlcTrans_K2Glc*vGlcTrans_K2IIG6P)))) - _extracellular_cytosol_*vGlcTrans_V2r/vGlcTrans_Yvol*(x[16]/vGlcTrans_K2Glc/(1 + x[16]/vGlcTrans_K2Glc + (vGlcTrans_P2*(x[16]/vGlcTrans_K2Glc) + 1)/(vGlcTrans_P2*(x[3]/vGlcTrans_K2Glc) + 1)*(1 + x[3]/vGlcTrans_K2Glc) + x[14]/vGlcTrans_K2IG6P + x[16]*x[14]/(vGlcTrans_K2Glc*vGlcTrans_K2IIG6P))); rate_vHK = _extracellular_cytosol_*vHK_V3m*x[8]*x[16]/(vHK_K3DGlc*vHK_K3ATP + vHK_K3Glc*x[8] + vHK_K3ATP*x[16] + x[16]*x[8]); rate_vPDC = _extracellular_cytosol_*(vPDC_V11m*x[21]/(vPDC_K11 + x[21])); rate_vPFK = _extracellular_cytosol_*(vPFK_V5m*Math.pow(x[12], 2)/(vPFK_K5*(1 + vPFK_kappa5*(x[8]/x[7])*(x[8]/x[7])) + Math.pow(x[12], 2))); rate_vPGI = _extracellular_cytosol_*(vPGI_V4f*x[14]/(vPGI_K4G6P + x[14] + vPGI_K4G6P/vPGI_K4F6P*x[12]) - vPGI_V4r*(x[12]/vPGI_K4eq)/(vPGI_K4G6P + x[14] + vPGI_K4G6P/vPGI_K4F6P*x[12])); rate_vPK = _extracellular_cytosol_*(vPK_V10m*x[6]*x[20]/((vPK_K10PEP + x[20])*(vPK_K10ADP + x[6]))); rate_vTIM = _extracellular_cytosol_*(vTIM_V7f*x[10]/(vTIM_K7DHAP + x[10] + vTIM_K7DHAP/vTIM_K7GAP*x[15]) - vTIM_V7r*(x[15]/vTIM_K7eq)/(vTIM_K7DHAP + x[10] + vTIM_K7DHAP/vTIM_K7GAP*x[15])); rate_vconsum = _extracellular_cytosol_*vconsum_k23*x[8]; rate_vdifACA = vdifACA_k18/vdifACA_Yvol*(_extracellular_cytosol_*x[5] - extracellular*x[0]); rate_vdifEtOH = vdifEtOH_k13/vdifEtOH_Yvol*(_extracellular_cytosol_*x[11] - extracellular*x[2]); rate_vdifGlyc = vdifGlyc_k16/vdifGlyc_Yvol*(_extracellular_cytosol_*x[17] - extracellular*x[4]); rate_vinCN = extracellular*vinCN_k0*(_extracellular_CNX0_ - x[1]); rate_vinGlc = extracellular*vinGlc_k0*(_extracellular_GlcX0_ - x[3]); rate_vlacto = extracellular*vlacto_k20*x[0]*x[1]; rate_vlpGlyc = _extracellular_cytosol_*(vlpGlyc_V15m*x[10]/(vlpGlyc_K15DHAP*(1 + vlpGlyc_K15INADH/x[19]*(1 + x[18]/vlpGlyc_K15INAD)) + x[10]*(1 + vlpGlyc_K15NADH/x[19]*(1 + x[18]/vlpGlyc_K15INAD)))); rate_vlpPEP = _extracellular_cytosol_*(vlpPEP_k9f*x[9]*x[6] - vlpPEP_k9r*x[20]*x[8]); rate_voutACA = extracellular*voutACA_k0*x[0]; rate_voutEtOH = extracellular*voutEtOH_k0*x[2]; rate_voutGlyc = extracellular*voutGlyc_k0*x[4]; rate_vstorage = _extracellular_cytosol_*vstorage_k22*x[8]*x[14]; } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _extracellular_CNX0_ = 5.6; // initial value of $"extracellular.CNX0" _extracellular_GlcX0_ = 24.0; // initial value of $"extracellular.GlcX0" _extracellular_cytosol_ = 1.0; // initial value of $"extracellular.cytosol" extracellular = 1.0; // initial value of $extracellular vADH_K12ACA = 0.71; // initial value of vADH_K12ACA vADH_K12NADH = 0.1; // initial value of vADH_K12NADH vADH_V12m = 89.8023; // initial value of vADH_V12m vAK_k24f = 432.9; // initial value of vAK_k24f vAK_k24r = 133.333; // initial value of vAK_k24r vALD_K6DHAP = 2.0; // initial value of vALD_K6DHAP vALD_K6FBP = 0.3; // initial value of vALD_K6FBP vALD_K6GAP = 4.0; // initial value of vALD_K6GAP vALD_K6IGAP = 10.0; // initial value of vALD_K6IGAP vALD_K6eq = 0.081; // initial value of vALD_K6eq vALD_V6f = 2207.82; // initial value of vALD_V6f vALD_ratio6 = 5.0; // initial value of vALD_ratio6 vGAPDH_K8BPG = 0.01; // initial value of vGAPDH_K8BPG vGAPDH_K8GAP = 0.6; // initial value of vGAPDH_K8GAP vGAPDH_K8NAD = 0.1; // initial value of vGAPDH_K8NAD vGAPDH_K8NADH = 0.06; // initial value of vGAPDH_K8NADH vGAPDH_K8eq = 0.0055; // initial value of vGAPDH_K8eq vGAPDH_V8f = 833.858; // initial value of vGAPDH_V8f vGAPDH_V8r = 833.858; // initial value of vGAPDH_V8r vGlcTrans_K2Glc = 1.7; // initial value of vGlcTrans_K2Glc vGlcTrans_K2IG6P = 1.2; // initial value of vGlcTrans_K2IG6P vGlcTrans_K2IIG6P = 7.2; // initial value of vGlcTrans_K2IIG6P vGlcTrans_P2 = 1.0; // initial value of vGlcTrans_P2 vGlcTrans_V2f = 1014.96; // initial value of vGlcTrans_V2f vGlcTrans_V2r = 1014.96; // initial value of vGlcTrans_V2r vGlcTrans_Yvol = 59.0; // initial value of vGlcTrans_Yvol vHK_K3ATP = 0.1; // initial value of vHK_K3ATP vHK_K3DGlc = 0.37; // initial value of vHK_K3DGlc vHK_V3m = 51.7547; // initial value of vHK_V3m vPDC_K11 = 0.3; // initial value of vPDC_K11 vPDC_V11m = 53.1328; // initial value of vPDC_V11m vPFK_K5 = 0.021; // initial value of vPFK_K5 vPFK_V5m = 45.4327; // initial value of vPFK_V5m vPFK_kappa5 = 0.15; // initial value of vPFK_kappa5 vPGI_K4F6P = 0.15; // initial value of vPGI_K4F6P vPGI_K4G6P = 0.8; // initial value of vPGI_K4G6P vPGI_K4eq = 0.13; // initial value of vPGI_K4eq vPGI_V4f = 496.042; // initial value of vPGI_V4f vPGI_V4r = 496.042; // initial value of vPGI_V4r vPK_K10ADP = 0.17; // initial value of vPK_K10ADP vPK_K10PEP = 0.2; // initial value of vPK_K10PEP vPK_V10m = 343.096; // initial value of vPK_V10m vTIM_K7DHAP = 1.23; // initial value of vTIM_K7DHAP vTIM_K7GAP = 1.27; // initial value of vTIM_K7GAP vTIM_K7eq = 0.055; // initial value of vTIM_K7eq vTIM_V7f = 116.365; // initial value of vTIM_V7f vTIM_V7r = 116.365; // initial value of vTIM_V7r vconsum_k23 = 3.2076; // initial value of vconsum_k23 vdifACA_Yvol = 59.0; // initial value of vdifACA_Yvol vdifACA_k18 = 24.7; // initial value of vdifACA_k18 vdifEtOH_Yvol = 59.0; // initial value of vdifEtOH_Yvol vdifEtOH_k13 = 16.72; // initial value of vdifEtOH_k13 vdifGlyc_Yvol = 59.0; // initial value of vdifGlyc_Yvol vdifGlyc_k16 = 1.9; // initial value of vdifGlyc_k16 vinCN_k0 = 0.048; // initial value of vinCN_k0 vinGlc_k0 = 0.048; // initial value of vinGlc_k0 vlacto_k20 = 0.00283828; // initial value of vlacto_k20 vlpGlyc_K15DHAP = 25.0; // initial value of vlpGlyc_K15DHAP vlpGlyc_K15INAD = 0.13; // initial value of vlpGlyc_K15INAD vlpGlyc_K15INADH = 0.034; // initial value of vlpGlyc_K15INADH vlpGlyc_K15NADH = 0.13; // initial value of vlpGlyc_K15NADH vlpGlyc_V15m = 81.4797; // initial value of vlpGlyc_V15m vlpPEP_k9f = 443866.0; // initial value of vlpPEP_k9f vlpPEP_k9r = 1528.62; // initial value of vlpPEP_k9r voutACA_k0 = 0.048; // initial value of voutACA_k0 voutEtOH_k0 = 0.048; // initial value of voutEtOH_k0 voutGlyc_k0 = 0.048; // initial value of voutGlyc_k0 vstorage_k22 = 2.25932; // initial value of vstorage_k22 } /* * Model variables initial values */ protected double _extracellular_CNX0_; protected double _extracellular_GlcX0_; protected double _extracellular_P_; protected double _extracellular_cytosol_; protected double rate_vADH; protected double rate_vAK; protected double rate_vALD; protected double rate_vGAPDH; protected double rate_vGlcTrans; protected double rate_vHK; protected double rate_vPDC; protected double rate_vPFK; protected double rate_vPGI; protected double rate_vPK; protected double rate_vTIM; protected double rate_vconsum; protected double rate_vdifACA; protected double rate_vdifEtOH; protected double rate_vdifGlyc; protected double rate_vinCN; protected double rate_vinGlc; protected double rate_vlacto; protected double rate_vlpGlyc; protected double rate_vlpPEP; protected double rate_voutACA; protected double rate_voutEtOH; protected double rate_voutGlyc; protected double rate_vstorage; protected double extracellular; protected double vADH_K12ACA; protected double vADH_K12NADH; protected double vADH_V12m; protected double vAK_k24f; protected double vAK_k24r; protected double vALD_K6DHAP; protected double vALD_K6FBP; protected double vALD_K6GAP; protected double vALD_K6IGAP; protected double vALD_K6eq; protected double vALD_V6f; protected double vALD_ratio6; protected double vGAPDH_K8BPG; protected double vGAPDH_K8GAP; protected double vGAPDH_K8NAD; protected double vGAPDH_K8NADH; protected double vGAPDH_K8eq; protected double vGAPDH_V8f; protected double vGAPDH_V8r; protected double vGlcTrans_K2Glc; protected double vGlcTrans_K2IG6P; protected double vGlcTrans_K2IIG6P; protected double vGlcTrans_P2; protected double vGlcTrans_V2f; protected double vGlcTrans_V2r; protected double vGlcTrans_Yvol; protected double vHK_K3ATP; protected double vHK_K3DGlc; protected double vHK_K3Glc; protected double vHK_V3m; protected double vPDC_K11; protected double vPDC_V11m; protected double vPFK_K5; protected double vPFK_V5m; protected double vPFK_kappa5; protected double vPGI_K4F6P; protected double vPGI_K4G6P; protected double vPGI_K4eq; protected double vPGI_V4f; protected double vPGI_V4r; protected double vPK_K10ADP; protected double vPK_K10PEP; protected double vPK_V10m; protected double vTIM_K7DHAP; protected double vTIM_K7GAP; protected double vTIM_K7eq; protected double vTIM_V7f; protected double vTIM_V7r; protected double vconsum_k23; protected double vdifACA_Yvol; protected double vdifACA_k18; protected double vdifEtOH_Yvol; protected double vdifEtOH_k13; protected double vdifGlyc_Yvol; protected double vdifGlyc_k16; protected double vinCN_k0; protected double vinGlc_k0; protected double vlacto_k20; protected double vlpGlyc_K15DHAP; protected double vlpGlyc_K15INAD; protected double vlpGlyc_K15INADH; protected double vlpGlyc_K15NADH; protected double vlpGlyc_V15m; protected double vlpPEP_k9f; protected double vlpPEP_k9r; protected double voutACA_k0; protected double voutEtOH_k0; protected double voutGlyc_k0; protected double vstorage_k22; public double[] extendResult(double time,double [] x) { this.time = time; double[] y = new double[22]; 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]; return y; } public double[] getInitialValues() { double [] x = new double[22]; this.time = 0.0; x[0] = 1.28836; // - $"extracellular.ACAX" x[1] = 5.20358; // - $"extracellular.CNX" x[2] = 16.4514; // - $"extracellular.EtOHX" x[3] = 6.7; // - $"extracellular.GlcX" x[4] = 1.68478; // - $"extracellular.GlycX" x[5] = 1.48153; // - $"extracellular.cytosol.ACA" x[6] = 1.5; // - $"extracellular.cytosol.ADP" x[7] = 0.33; // - $"extracellular.cytosol.AMP" x[8] = 2.1; // - $"extracellular.cytosol.ATP" x[9] = 2.7E-4; // - $"extracellular.cytosol.BPG" x[10] = 2.95; // - $"extracellular.cytosol.DHAP" x[11] = 19.2379; // - $"extracellular.cytosol.EtOH" x[12] = 0.49; // - $"extracellular.cytosol.F6P" x[13] = 4.64; // - $"extracellular.cytosol.FBP" x[14] = 4.2; // - $"extracellular.cytosol.G6P" x[15] = 0.115; // - $"extracellular.cytosol.GAP" x[16] = 0.573074; // - $"extracellular.cytosol.Glc" x[17] = 4.196; // - $"extracellular.cytosol.Glyc" x[18] = 0.65; // - $"extracellular.cytosol.NAD" x[19] = 0.33; // - $"extracellular.cytosol.NADH" x[20] = 0.04; // - $"extracellular.cytosol.PEP" x[21] = 8.7; // - $"extracellular.cytosol.Pyr" __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 'BIOMD0000000061.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = +rate_vdifACA-rate_vlacto-rate_voutACA; result[1] = +rate_vinCN-rate_vlacto; result[2] = +rate_vdifEtOH-rate_voutEtOH; result[3] = -rate_vGlcTrans+rate_vinGlc; result[4] = +rate_vdifGlyc-rate_voutGlyc; result[5] = -rate_vADH+rate_vPDC-rate_vdifACA*59; result[6] = +rate_vAK*2+rate_vHK+rate_vPFK-rate_vPK+rate_vconsum-rate_vlpPEP+rate_vstorage; result[7] = -rate_vAK; result[8] = -rate_vAK-rate_vHK-rate_vPFK+rate_vPK-rate_vconsum+rate_vlpPEP-rate_vstorage; result[9] = +rate_vGAPDH-rate_vlpPEP; result[10] = +rate_vALD-rate_vTIM-rate_vlpGlyc; result[11] = +rate_vADH-rate_vdifEtOH*59; result[12] = -rate_vPFK+rate_vPGI; result[13] = -rate_vALD+rate_vPFK; result[14] = +rate_vHK-rate_vPGI-rate_vstorage; result[15] = +rate_vALD-rate_vGAPDH+rate_vTIM; result[16] = +rate_vGlcTrans*59-rate_vHK; result[17] = -rate_vdifGlyc*59+rate_vlpGlyc; result[18] = +rate_vADH-rate_vGAPDH+rate_vlpGlyc; result[19] = -rate_vADH+rate_vGAPDH-rate_vlpGlyc; result[20] = -rate_vPK+rate_vlpPEP; result[21] = -rate_vPDC+rate_vPK; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[22]; __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 ...