/* * This code is generated by BioUML FrameWork * for BIOMD0000000151.xml diagram at 2008.03.20 15:09:40 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000151 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_R1 = cytosol*kf0*cytosol_x1*IL6; rate_R10 = cytosol*k10*x[15]; rate_R11 = cytosol*(kf5*x[64]*x[65] - kr5*x[10]); rate_R12 = cytosol*k6*x[10]; rate_R13 = cytosol*(kf7*x[64]*x[9] - kr7*x[11]); rate_R14 = cytosol*(kf9*x[64]*x[14] - kr9*x[15]); rate_R15 = cytosol*(kf21*x[19]*x[64] - kr21*x[20]); rate_R16 = cytosol*(kf37*x[29] - kr37*x[64]*x[36]); rate_R16a = cytosol*(kf39*x[30] - kr39*x[35]*x[64]); rate_R17 = cytosol*(kf32*x[31] - kr32*x[34]*x[64]); rate_R18 = cytosol*k12*x[17]; rate_R19 = cytosol*(kf13*x[65]*x[9] - kr13*x[13]); rate_R2 = cytosol*kr0*x[59]; rate_R20 = _cytosol_nucleus_*k17*x[2]; rate_R21 = cytosol*(kf5*x[65]*x[20] - kr5*x[21]); rate_R22 = cytosol*k10*x[22]; rate_R23 = cytosol*(2*kf8*Math.pow(x[9], 2) - 2*kr8*x[12]); rate_R24 = cytosol*(kf11*x[9]*x[16] - kr11*x[17]); rate_R25 = cytosol*(kf11*x[12]*x[16] - kr11*x[18]); rate_R26 = cytosol*k14*x[12]; rate_R27 = cytosol*k12*x[18]; rate_R28 = cytosol*(kf9*x[14]*x[21] - kr9*x[22]); rate_R29 = cytosol*Vm*x[36]/(Km + x[36]); rate_R3 = cytosol*(kr2*x[62] - kf2*x[59]*x[61]); rate_R30 = cytosol*(kf34*x[15] - kr34*x[29]); rate_R31 = _cytosol_nucleus_*(kr8*x[0] - kf8*Math.pow(x[1], 2)); rate_R32 = _cytosol_nucleus_*(kf15*x[3]*x[0] - kr15*x[7]); rate_R33 = _cytosol_nucleus_*(kf15*x[3]*x[1] - kr15*x[8]); rate_R34 = _cytosol_nucleus_*(kr13*x[4] - kf13*x[1]*x[2]); rate_R35 = _cytosol_nucleus_*k16*x[8]; rate_R36 = _cytosol_nucleus_*k16*x[7]; rate_R37 = _cytosol_nucleus_*(k18a*x[0]/(k18b + x[0])); rate_R38 = _cytosol_nucleus_*k19*x[5]; rate_R39 = _cytosol_nucleus_*k22*x[6]; rate_R40 = _cytosol_nucleus_*k20*x[6]; rate_R41 = cytosol*k23*x[19]; rate_R42 = cytosol*k23*x[22]; rate_R43 = cytosol*(kf38*x[24]*x[36] - kr38*x[35]); rate_R44 = cytosol*(kf35*x[28] - kr35*x[24]*x[25]); rate_R45 = cytosol*(kf24*x[29]*x[24] - kr24*x[30]); } public void __internalRateVarInitFunc_1(double time, double[] x) { rate_R46 = cytosol*(kf25*x[25]*x[30] - kr25*x[31]); rate_R47 = cytosol*(kf40*x[25]*x[35] - kr40*x[34]); rate_R48 = cytosol*(kf26*x[26]*x[31] - kr26*x[32]); rate_R49 = cytosol*(kf31*x[33] - kr31*x[26]*x[31]); rate_R5 = cytosol*(kf1*cytosol_x3*x[60] - kr1*x[61]); rate_R50 = cytosol*(kf27*x[32] - kr27*x[27]*x[31]); rate_R51 = cytosol*(kf28*x[27]*x[37] - kr28*x[38]); rate_R52 = cytosol*(kf41*x[28]*x[29] - kr41*x[31]); rate_R53 = cytosol*(kf33*x[34] - kr33*x[28]*x[36]); rate_R54 = cytosol*(kf30*x[39]*x[31] - kr30*x[33]); rate_R55 = cytosol*k43*x[42]; rate_R56 = cytosol*(kf29*x[38] - kr29*x[39]*x[41]); rate_R57 = cytosol*(kf42*x[40]*x[41] - kr42*x[42]); rate_R58 = cytosol*(kf44*x[41]*x[43] - kr44*x[44]); rate_R59 = cytosol*k45*x[44]; rate_R60 = cytosol*(kf46*x[45]*x[41] - kr46*x[46]); rate_R61 = cytosol*k51*x[50]; rate_R62 = cytosol*k49*x[48]; rate_R63 = cytosol*(kf50*x[45]*x[49] - kr50*x[50]); rate_R64 = cytosol*k47*x[46]; rate_R65 = cytosol*(kf48*x[47]*x[49] - kr48*x[48]); rate_R66 = cytosol*(kf52*x[47]*x[51] - kr52*x[52]); rate_R67 = cytosol*k53*x[52]; rate_R68 = cytosol*(kr54*x[54] - kf54*x[47]*x[53]); rate_R69 = cytosol*k55*x[54]; rate_R7 = cytosol*kf3*Math.pow(x[62], 2); rate_R70 = cytosol*k59*x[58]; rate_R71 = cytosol*k57*x[57]; rate_R72 = cytosol*(kf58*x[53]*x[56] - kr58*x[58]); rate_R73 = cytosol*(kf56*x[55]*x[56] - kr56*x[57]); rate_R8 = cytosol*kr3*x[63]; rate_R9 = cytosol*k4*x[63]; } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _cytosol_nucleus_ = 1.0; // initial value of $"cytosol.nucleus" cytosol = 1.0; // initial value of $cytosol cytosol_x1 = 8.0; // initial value of $cytosol.x1 cytosol_x3 = 0.8; // initial value of $cytosol.x3 IL6 = 0.38; // initial value of IL6 Km = 340.0; // initial value of Km Vm = 1.7; // initial value of Vm k10 = 0.0030; // initial value of k10 k12 = 0.0030; // initial value of k12 k14 = 0.0050; // initial value of k14 k16 = 0.0050; // initial value of k16 k17 = 0.05; // initial value of k17 k18a = 0.01; // initial value of k18a k18b = 400.0; // initial value of k18b k19 = 0.0010; // initial value of k19 k20 = 0.01; // initial value of k20 k22 = 5.0E-4; // initial value of k22 k23 = 5.0E-4; // initial value of k23 k4 = 0.0050; // initial value of k4 k43 = 1.0; // initial value of k43 k45 = 3.5; // initial value of k45 k47 = 2.9; // initial value of k47 k49 = 0.058; // initial value of k49 k51 = 0.058; // initial value of k51 k53 = 16.0; // initial value of k53 k55 = 6.7; // initial value of k55 k57 = 0.27; // initial value of k57 k59 = 0.3; // initial value of k59 k6 = 0.4; // initial value of k6 kf0 = 0.1; // initial value of kf0 kf1 = 0.1; // initial value of kf1 kf11 = 0.0010; // initial value of kf11 kf13 = 2.0E-7; // initial value of kf13 kf15 = 0.0010; // initial value of kf15 kf2 = 0.02; // initial value of kf2 kf21 = 0.02; // initial value of kf21 kf24 = 0.01; // initial value of kf24 kf25 = 0.01; // initial value of kf25 kf26 = 0.015; // initial value of kf26 kf27 = 0.5; // initial value of kf27 kf28 = 0.0010; // initial value of kf28 kf29 = 1.0; // initial value of kf29 kf3 = 0.04; // initial value of kf3 kf30 = 0.0079; // initial value of kf30 kf31 = 0.023; // initial value of kf31 kf32 = 0.1; // initial value of kf32 kf33 = 0.3; // initial value of kf33 kf34 = 6.0; // initial value of kf34 kf35 = 0.0015; // initial value of kf35 kf37 = 0.3; // initial value of kf37 kf38 = 0.01; // initial value of kf38 kf39 = 0.3; // initial value of kf39 kf40 = 0.03; // initial value of kf40 kf41 = 0.03; // initial value of kf41 kf42 = 0.0717; // initial value of kf42 kf44 = 0.011; // initial value of kf44 kf46 = 0.011; // initial value of kf46 kf48 = 0.0143; // initial value of kf48 kf5 = 0.0080; // initial value of kf5 kf50 = 2.5E-4; // initial value of kf50 kf52 = 1.1E-4; // initial value of kf52 kf54 = 1.1E-4; // initial value of kf54 kf56 = 0.014; // initial value of kf56 kf58 = 0.0050; // initial value of kf58 kf7 = 0.0050; // initial value of kf7 kf8 = 0.02; // initial value of kf8 kf9 = 0.0010; // initial value of kf9 kr0 = 0.05; // initial value of kr0 kr1 = 0.05; // initial value of kr1 kr11 = 0.2; // initial value of kr11 kr13 = 0.2; // initial value of kr13 kr15 = 0.2; // initial value of kr15 kr2 = 0.02; // initial value of kr2 kr21 = 0.1; // initial value of kr21 kr24 = 0.55; // initial value of kr24 kr25 = 0.0214; // initial value of kr25 kr26 = 1.3; // initial value of kr26 kr27 = 1.0E-4; // initial value of kr27 kr28 = 0.0053; // initial value of kr28 kr29 = 7.0E-4; // initial value of kr29 kr3 = 0.2; // initial value of kr3 kr30 = 0.4; // initial value of kr30 kr31 = 2.2E-4; // initial value of kr31 kr32 = 2.45E-4; // initial value of kr32 kr33 = 0.021; // initial value of kr33 kr34 = 0.06; // initial value of kr34 kr35 = 0.0045; // initial value of kr35 kr37 = 9.0E-4; // initial value of kr37 kr38 = 0.55; // initial value of kr38 kr39 = 9.0E-4; // initial value of kr39 kr40 = 0.064; // initial value of kr40 kr41 = 0.0429; // initial value of kr41 kr42 = 0.2; // initial value of kr42 kr44 = 0.001833; // initial value of kr44 kr46 = 0.001833; // initial value of kr46 kr48 = 0.8; // initial value of kr48 kr5 = 0.8; // initial value of kr5 kr50 = 0.5; // initial value of kr50 kr52 = 0.033; // initial value of kr52 kr54 = 0.033; // initial value of kr54 kr56 = 0.6; // initial value of kr56 kr58 = 0.5; // initial value of kr58 kr7 = 0.5; // initial value of kr7 kr8 = 0.1; // initial value of kr8 kr9 = 0.2; // initial value of kr9 } /* * Model variables initial values */ protected double _cytosol_nucleus_; protected double rate_R1; protected double rate_R10; protected double rate_R11; protected double rate_R12; protected double rate_R13; protected double rate_R14; protected double rate_R15; protected double rate_R16; protected double rate_R16a; protected double rate_R17; protected double rate_R18; protected double rate_R19; protected double rate_R2; protected double rate_R20; protected double rate_R21; protected double rate_R22; protected double rate_R23; protected double rate_R24; protected double rate_R25; protected double rate_R26; protected double rate_R27; protected double rate_R28; protected double rate_R29; protected double rate_R3; protected double rate_R30; protected double rate_R31; protected double rate_R32; protected double rate_R33; protected double rate_R34; protected double rate_R35; protected double rate_R36; protected double rate_R37; protected double rate_R38; protected double rate_R39; protected double rate_R40; protected double rate_R41; protected double rate_R42; protected double rate_R43; protected double rate_R44; protected double rate_R45; protected double rate_R46; protected double rate_R47; protected double rate_R48; protected double rate_R49; protected double rate_R5; protected double rate_R50; protected double rate_R51; protected double rate_R52; protected double rate_R53; protected double rate_R54; protected double rate_R55; protected double rate_R56; protected double rate_R57; protected double rate_R58; protected double rate_R59; protected double rate_R60; protected double rate_R61; protected double rate_R62; protected double rate_R63; protected double rate_R64; protected double rate_R65; protected double rate_R66; protected double rate_R67; protected double rate_R68; protected double rate_R69; protected double rate_R7; protected double rate_R70; protected double rate_R71; protected double rate_R72; protected double rate_R73; protected double rate_R8; protected double rate_R9; protected double cytosol; protected double cytosol_x1; protected double cytosol_x3; protected double IL6; protected double Km; protected double Vm; protected double k10; protected double k12; protected double k14; protected double k16; protected double k17; protected double k18a; protected double k18b; protected double k19; protected double k20; protected double k22; protected double k23; protected double k4; protected double k43; protected double k45; protected double k47; protected double k49; protected double k51; protected double k53; protected double k55; protected double k57; protected double k59; protected double k6; protected double kf0; protected double kf1; protected double kf11; protected double kf13; protected double kf15; protected double kf2; protected double kf21; protected double kf24; protected double kf25; protected double kf26; protected double kf27; protected double kf28; protected double kf29; protected double kf3; protected double kf30; protected double kf31; protected double kf32; protected double kf33; protected double kf34; protected double kf35; protected double kf37; protected double kf38; protected double kf39; protected double kf40; protected double kf41; protected double kf42; protected double kf44; protected double kf46; protected double kf48; protected double kf5; protected double kf50; protected double kf52; protected double kf54; protected double kf56; protected double kf58; protected double kf7; protected double kf8; protected double kf9; protected double kr0; protected double kr1; protected double kr11; protected double kr13; protected double kr15; protected double kr2; protected double kr21; protected double kr24; protected double kr25; protected double kr26; protected double kr27; protected double kr28; protected double kr29; protected double kr3; protected double kr30; protected double kr31; protected double kr32; protected double kr33; protected double kr34; protected double kr35; protected double kr37; protected double kr38; protected double kr39; protected double kr40; protected double kr41; protected double kr42; protected double kr44; protected double kr46; protected double kr48; protected double kr5; protected double kr50; protected double kr52; protected double kr54; protected double kr56; protected double kr58; protected double kr7; protected double kr8; protected double kr9; public double[] extendResult(double time,double [] x) { this.time = time; double[] y = new double[66]; 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]; y[40] = x[40]; y[41] = x[41]; y[42] = x[42]; y[43] = x[43]; y[44] = x[44]; y[45] = x[45]; y[46] = x[46]; y[47] = x[47]; y[48] = x[48]; y[49] = x[49]; y[50] = x[50]; y[51] = x[51]; y[52] = x[52]; y[53] = x[53]; y[54] = x[54]; y[55] = x[55]; y[56] = x[56]; y[57] = x[57]; y[58] = x[58]; y[59] = x[59]; y[60] = x[60]; y[61] = x[61]; y[62] = x[62]; y[63] = x[63]; y[64] = x[64]; y[65] = x[65]; return y; } public double[] getInitialValues() { double [] x = new double[66]; this.time = 0.0; x[0] = 0.0; // - $"cytosol.nucleus.x20" x[1] = 0.0; // - $"cytosol.nucleus.x21" x[2] = 0.0; // - $"cytosol.nucleus.x22" x[3] = 60.0; // - $"cytosol.nucleus.x23" x[4] = 0.0; // - $"cytosol.nucleus.x24" x[5] = 0.0; // - $"cytosol.nucleus.x25" x[6] = 0.0; // - $"cytosol.nucleus.x26" x[7] = 0.0; // - $"cytosol.nucleus.x27" x[8] = 0.0; // - $"cytosol.nucleus.x28" x[9] = 0.0; // - $"cytosol.x10" x[10] = 0.0; // - $"cytosol.x11" x[11] = 0.0; // - $"cytosol.x12" x[12] = 0.0; // - $"cytosol.x13" x[13] = 0.0; // - $"cytosol.x14" x[14] = 100.0; // - $"cytosol.x15" x[15] = 0.0; // - $"cytosol.x16" x[16] = 50.0; // - $"cytosol.x17" x[17] = 0.0; // - $"cytosol.x18" x[18] = 0.0; // - $"cytosol.x19" x[19] = 0.0; // - $"cytosol.x29" x[20] = 0.0; // - $"cytosol.x30" x[21] = 0.0; // - $"cytosol.x31" x[22] = 0.0; // - $"cytosol.x32" x[23] = 0.0; // - $"cytosol.x33" x[24] = 85.0; // - $"cytosol.x34" x[25] = 34.0; // - $"cytosol.x35" x[26] = 19000.0; // - $"cytosol.x36" x[27] = 0.0; // - $"cytosol.x37" x[28] = 0.0; // - $"cytosol.x38" x[29] = 0.0; // - $"cytosol.x39" x[30] = 0.0; // - $"cytosol.x40" x[31] = 0.0; // - $"cytosol.x41" x[32] = 0.0; // - $"cytosol.x42" x[33] = 0.0; // - $"cytosol.x43" x[34] = 0.0; // - $"cytosol.x44" x[35] = 0.0; // - $"cytosol.x45" x[36] = 0.0; // - $"cytosol.x46" x[37] = 67.0; // - $"cytosol.x47" x[38] = 0.0; // - $"cytosol.x48" x[39] = 0.0; // - $"cytosol.x49" x[40] = 67.0; // - $"cytosol.x50" x[41] = 0.0; // - $"cytosol.x51" x[42] = 0.0; // - $"cytosol.x52" x[43] = 41667.0; // - $"cytosol.x53" x[44] = 0.0; // - $"cytosol.x54" x[45] = 0.0; // - $"cytosol.x55" x[46] = 0.0; // - $"cytosol.x56" x[47] = 0.0; // - $"cytosol.x57" x[48] = 0.0; // - $"cytosol.x58" x[49] = 67.0; // - $"cytosol.x59" x[50] = 0.0; // - $"cytosol.x60" x[51] = 35000.0; // - $"cytosol.x61" x[52] = 0.0; // - $"cytosol.x62" x[53] = 0.0; // - $"cytosol.x63" x[54] = 0.0; // - $"cytosol.x64" x[55] = 0.0; // - $"cytosol.x65" x[56] = 16667.0; // - $"cytosol.x66" x[57] = 0.0; // - $"cytosol.x67" x[58] = 0.0; // - $"cytosol.x68" x[59] = 0.0; // - $cytosol.x2 x[60] = 12.0; // - $cytosol.x4 x[61] = 0.0; // - $cytosol.x5 x[62] = 0.0; // - $cytosol.x6 x[63] = 0.0; // - $cytosol.x7 x[64] = 0.0; // - $cytosol.x8 x[65] = 1000.0; // - $cytosol.x9 __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) { __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); } /* * calculate dy/dt for 'BIOMD0000000151.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = +rate_R26-rate_R31-rate_R32; result[1] = +rate_R31*2-rate_R33+rate_R34; result[2] = -rate_R20+rate_R34+rate_R35; result[3] = -rate_R32-rate_R33+rate_R35+rate_R36; result[4] = -rate_R34+rate_R36; result[5] = +rate_R37-rate_R38; result[6] = +rate_R38-rate_R39; result[7] = +rate_R32-rate_R36; result[8] = +rate_R33-rate_R35; result[9] = +rate_R12-rate_R13-rate_R19-rate_R23-rate_R24; result[10] = +rate_R11-rate_R12; result[11] = +rate_R13; result[12] = +rate_R23*0.5-rate_R25-rate_R26; result[13] = +rate_R19+rate_R27; result[14] = +rate_R10-rate_R14+rate_R22-rate_R28+rate_R29; result[15] = -rate_R10+rate_R14-rate_R30; result[16] = +rate_R18-rate_R24-rate_R25+rate_R27; result[17] = -rate_R18+rate_R24; result[18] = +rate_R25-rate_R27; result[19] = -rate_R15+rate_R22+rate_R40-rate_R41+rate_R42; result[20] = +rate_R15-rate_R21; result[21] = +rate_R21-rate_R28; result[22] = -rate_R22+rate_R28-rate_R42; result[23] = +rate_R42; result[24] = -rate_R43+rate_R44-rate_R45; result[25] = +rate_R44-rate_R46-rate_R47; result[26] = -rate_R48+rate_R49; result[27] = +rate_R50-rate_R51; result[28] = -rate_R44-rate_R52+rate_R53; result[29] = -rate_R16+rate_R30-rate_R45-rate_R52; result[30] = -rate_R16a+rate_R45-rate_R46; result[31] = -rate_R17+rate_R46-rate_R48+rate_R49+rate_R50+rate_R52-rate_R54; result[32] = +rate_R48-rate_R50; result[33] = -rate_R49+rate_R54; result[34] = +rate_R17+rate_R47-rate_R53; result[35] = +rate_R16a+rate_R43-rate_R47; result[36] = +rate_R16-rate_R29-rate_R43+rate_R53; result[37] = -rate_R51+rate_R55; result[38] = +rate_R51-rate_R56; result[39] = -rate_R54+rate_R56; result[40] = +rate_R55-rate_R57; result[41] = +rate_R56-rate_R57-rate_R58+rate_R59-rate_R60+rate_R64; result[42] = -rate_R55+rate_R57; result[43] = -rate_R58+rate_R61; result[44] = +rate_R58-rate_R59; result[45] = +rate_R59-rate_R60+rate_R62-rate_R63; result[46] = +rate_R60-rate_R64; result[47] = +rate_R64-rate_R65-rate_R66+rate_R67+rate_R68+rate_R69; result[48] = -rate_R62+rate_R65; result[49] = +rate_R61+rate_R62-rate_R63-rate_R65; result[50] = -rate_R61+rate_R63; result[51] = -rate_R66+rate_R70; result[52] = +rate_R66-rate_R67; result[53] = +rate_R67+rate_R68+rate_R71-rate_R72; result[54] = -rate_R68-rate_R69; result[55] = +rate_R69-rate_R73; result[56] = +rate_R70+rate_R71-rate_R72-rate_R73; result[57] = -rate_R71+rate_R73; result[58] = -rate_R70+rate_R72; result[59] = +rate_R1-rate_R2+rate_R3; result[60] = -rate_R5; result[61] = +rate_R3+rate_R5; result[62] = -rate_R3-rate_R7*2+rate_R8*2; result[63] = +rate_R10+rate_R22+rate_R7-rate_R8-rate_R9; result[64] = -rate_R11+rate_R12-rate_R13-rate_R14-rate_R15+rate_R16+rate_R16a+rate_R17+rate_R9; result[65] = -rate_R11+rate_R18-rate_R19+rate_R20-rate_R21+rate_R22; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[66]; __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 ...