/* * This code is generated by BioUML FrameWork * for BIOMD0000000147.xml diagram at 2008.03.20 15:09:36 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000147 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ private void __internalVarInitFunc_0(double time, double[] x) { Total_IkBalpha = x[4] + x[16] + x[1] + x[2] + x[3] + x[14]; Total_IkBbeta = x[8] + x[19] + x[5] + x[6] + x[7] + x[17]; Total_IkBeps = x[12] + x[22] + x[9] + x[10] + x[11] + x[20]; } /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_IKK_deg = cytoplasm*IKK_deg_IKK_deg*x[0]; rate_deg_a = cytoplasm*deg_a_deg1_c*x[4]; rate_deg_a_n = nucleus*deg_a_n_deg1_n*x[16]; rate_deg_ai = cytoplasm*deg_ai_r1*x[1]; rate_deg_ain = cytoplasm*deg_ain_r4*x[2]; rate_deg_an = cytoplasm*deg_an_deg4_c*x[3]; rate_deg_an_n = nucleus*deg_an_n_deg4_n*x[14]; rate_deg_b = cytoplasm*deg_b_deg2_c*x[8]; rate_deg_b_n = nucleus*deg_b_n_deg2_n*x[19]; rate_deg_bi = cytoplasm*deg_bi_r2*x[5]; rate_deg_bin = cytoplasm*deg_bin_r5*x[6]; rate_deg_bn = cytoplasm*deg_bn_deg5_c*x[7]; rate_deg_bn_n = nucleus*deg_bn_n_deg5_n*x[17]; rate_deg_e = cytoplasm*deg_e_deg3_c*x[12]; rate_deg_e_n = nucleus*deg_e_n_deg3_n*x[22]; rate_deg_ei = cytoplasm*deg_ei_r3*x[9]; rate_deg_ein = cytoplasm*deg_ein_r6*x[10]; rate_deg_en = cytoplasm*deg_en_deg6_c*x[11]; rate_deg_en_n = nucleus*deg_en_n_deg6_n*x[20]; rate_int_2ain = cytoplasm*(int_2ain_a4_3*x[1]*x[13] - int_2ain_d4_3*x[2]); rate_int_2ani = cytoplasm*(int_2ani_a7*x[3]*x[0] - int_2ani_d1_2*x[2]); rate_int_2bin = cytoplasm*(int_2bin_a5_3*x[5]*x[13] - int_2bin_d5_3*x[6]); rate_int_2bni = cytoplasm*(int_2bni_a8*x[7]*x[0] - int_2bni_d2_2*x[6]); rate_int_2ein = cytoplasm*(int_2ein_a6_3*x[9]*x[13] - int_2ein_d6_3*x[10]); rate_int_2eni = cytoplasm*(int_2eni_a9*x[11]*x[0] - int_2eni_d3_2*x[10]); rate_int_ai = cytoplasm*(int_ai_a1*x[4]*x[0] - int_ai_d1_1*x[1]); rate_int_an = cytoplasm*(int_an_a4_1*x[4]*x[13] - int_an_d4_1*x[3]); rate_int_an_n = nucleus*(int_an_n_a4_2*x[16]*x[23] - int_an_n_d4_2*x[14]); rate_int_bi = cytoplasm*(int_bi_a2*x[8]*x[0] - int_bi_d2_1*x[5]); rate_int_bn = cytoplasm*(int_bn_a5_1*x[8]*x[13] - int_bn_d5_1*x[7]); rate_int_bn_n = nucleus*(int_bn_n_a5_2*x[19]*x[23] - int_bn_n_d5_2*x[17]); rate_int_ei = cytoplasm*(int_ei_a3*x[12]*x[0] - int_ei_d3_1*x[9]); rate_int_en = cytoplasm*(int_en_a6_1*x[12]*x[13] - int_en_d6_1*x[11]); rate_int_en_n = nucleus*(int_en_n_a6_2*x[22]*x[23] - int_en_n_d6_2*x[20]); rate_itxn_a = nucleus*itxn_a_tr2a_i*Math.pow(x[23], 2); rate_loc_a = cytoplasm*loc_a_tp1a*x[4] - nucleus*loc_a_tp2a*x[16]; rate_loc_an = nucleus*loc_an_k2_a*x[14]; rate_loc_b = cytoplasm*loc_b_tp1b*x[8] - nucleus*loc_b_tp2b*x[19]; rate_loc_bn = nucleus*loc_bn_k2_b*x[17]; rate_loc_e = cytoplasm*loc_e_tp1e*x[12] - nucleus*loc_e_tp2e*x[22]; } public void __internalRateVarInitFunc_1(double time, double[] x) { rate_loc_en = nucleus*loc_en_k2_e*x[20]; rate_loc_n = cytoplasm*loc_n_k1_2*x[13] - nucleus*loc_n_k1_1*x[23]; rate_mdeg_a = nucleus*mdeg_a_tr3a*x[15]; rate_mdeg_b = nucleus*mdeg_b_tr3b*x[18]; rate_mdeg_e = nucleus*mdeg_e_tr3e*x[21]; rate_tsl_a = nucleus*tsl_a_tr1a*x[15]; rate_tsl_b = nucleus*tsl_b_tr1b*x[18]; rate_tsl_e = nucleus*tsl_e_tr1e*x[21]; rate_txn_a = nucleus*txn_a_tr2a; rate_txn_b = nucleus*txn_b_tr2b; rate_txn_e = nucleus*txn_e_tr2e; } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ cytoplasm = 1.0; // initial value of $cytoplasm nucleus = 1.0; // initial value of $nucleus deg_a_deg1_c = 0.12; // initial value of deg_a_deg1_c deg_a_n_deg1_n = 0.12; // initial value of deg_a_n_deg1_n deg_ai_r1 = 0.072; // initial value of deg_ai_r1 deg_ain_r4 = 0.36; // initial value of deg_ain_r4 deg_an_deg4_c = 6.0E-5; // initial value of deg_an_deg4_c deg_an_n_deg4_n = 6.0E-5; // initial value of deg_an_n_deg4_n deg_b_deg2_c = 0.18; // initial value of deg_b_deg2_c deg_b_n_deg2_n = 0.18; // initial value of deg_b_n_deg2_n deg_bi_r2 = 0.024; // initial value of deg_bi_r2 deg_bin_r5 = 0.12; // initial value of deg_bin_r5 deg_bn_deg5_c = 6.0E-5; // initial value of deg_bn_deg5_c deg_bn_n_deg5_n = 6.0E-5; // initial value of deg_bn_n_deg5_n deg_e_deg3_c = 0.18; // initial value of deg_e_deg3_c deg_e_n_deg3_n = 0.18; // initial value of deg_e_n_deg3_n deg_ei_r3 = 0.036; // initial value of deg_ei_r3 deg_ein_r6 = 0.18; // initial value of deg_ein_r6 deg_en_deg6_c = 6.0E-5; // initial value of deg_en_deg6_c deg_en_n_deg6_n = 6.0E-5; // initial value of deg_en_n_deg6_n int_2ain_a4_3 = 30.0; // initial value of int_2ain_a4_3 int_2ain_d4_3 = 6.0E-5; // initial value of int_2ain_d4_3 int_2ani_a7 = 11.1; // initial value of int_2ani_a7 int_2ani_d1_2 = 0.075; // initial value of int_2ani_d1_2 int_2bin_a5_3 = 30.0; // initial value of int_2bin_a5_3 int_2bin_d5_3 = 6.0E-5; // initial value of int_2bin_d5_3 int_2bni_a8 = 2.88; // initial value of int_2bni_a8 int_2bni_d2_2 = 0.105; // initial value of int_2bni_d2_2 int_2ein_a6_3 = 30.0; // initial value of int_2ein_a6_3 int_2ein_d6_3 = 6.0E-5; // initial value of int_2ein_d6_3 int_2eni_a9 = 4.2; // initial value of int_2eni_a9 int_2eni_d3_2 = 0.105; // initial value of int_2eni_d3_2 int_ai_a1 = 1.35; // initial value of int_ai_a1 int_ai_d1_1 = 0.075; // initial value of int_ai_d1_1 int_an_a4_1 = 30.0; // initial value of int_an_a4_1 int_an_d4_1 = 6.0E-5; // initial value of int_an_d4_1 int_an_n_a4_2 = 30.0; // initial value of int_an_n_a4_2 int_an_n_d4_2 = 6.0E-5; // initial value of int_an_n_d4_2 int_bi_a2 = 0.36; // initial value of int_bi_a2 int_bi_d2_1 = 0.105; // initial value of int_bi_d2_1 int_bn_a5_1 = 30.0; // initial value of int_bn_a5_1 int_bn_d5_1 = 6.0E-5; // initial value of int_bn_d5_1 int_bn_n_a5_2 = 30.0; // initial value of int_bn_n_a5_2 int_bn_n_d5_2 = 6.0E-5; // initial value of int_bn_n_d5_2 int_ei_a3 = 0.54; // initial value of int_ei_a3 int_ei_d3_1 = 0.105; // initial value of int_ei_d3_1 int_en_a6_1 = 30.0; // initial value of int_en_a6_1 int_en_d6_1 = 6.0E-5; // initial value of int_en_d6_1 int_en_n_a6_2 = 30.0; // initial value of int_en_n_a6_2 int_en_n_d6_2 = 6.0E-5; // initial value of int_en_n_d6_2 itxn_a_tr2a_i = 1.98; // initial value of itxn_a_tr2a_i loc_a_tp1a = 0.018; // initial value of loc_a_tp1a loc_a_tp2a = 0.012; // initial value of loc_a_tp2a loc_an_k2_a = 0.828; // initial value of loc_an_k2_a loc_b_tp1b = 0.018; // initial value of loc_b_tp1b loc_b_tp2b = 0.012; // initial value of loc_b_tp2b loc_bn_k2_b = 0.414; // initial value of loc_bn_k2_b loc_e_tp1e = 0.018; // initial value of loc_e_tp1e loc_e_tp2e = 0.012; // initial value of loc_e_tp2e loc_en_k2_e = 0.414; // initial value of loc_en_k2_e loc_n_k1_1 = 0.0048; // initial value of loc_n_k1_1 loc_n_k1_2 = 5.4; // initial value of loc_n_k1_2 mdeg_a_tr3a = 0.0168; // initial value of mdeg_a_tr3a mdeg_b_tr3b = 0.0168; // initial value of mdeg_b_tr3b mdeg_e_tr3e = 0.0168; // initial value of mdeg_e_tr3e tsl_a_tr1a = 0.2448; // initial value of tsl_a_tr1a tsl_b_tr1b = 0.2448; // initial value of tsl_b_tr1b tsl_e_tr1e = 0.2448; // initial value of tsl_e_tr1e txn_a_tr2a = 1.848E-4; // initial value of txn_a_tr2a txn_b_tr2b = 4.272E-5; // initial value of txn_b_tr2b txn_e_tr2e = 3.048E-5; // initial value of txn_e_tr2e } /* * Model variables initial values */ protected double rate_IKK_deg; protected double rate_deg_a; protected double rate_deg_a_n; protected double rate_deg_ai; protected double rate_deg_ain; protected double rate_deg_an; protected double rate_deg_an_n; protected double rate_deg_b; protected double rate_deg_b_n; protected double rate_deg_bi; protected double rate_deg_bin; protected double rate_deg_bn; protected double rate_deg_bn_n; protected double rate_deg_e; protected double rate_deg_e_n; protected double rate_deg_ei; protected double rate_deg_ein; protected double rate_deg_en; protected double rate_deg_en_n; protected double rate_int_2ain; protected double rate_int_2ani; protected double rate_int_2bin; protected double rate_int_2bni; protected double rate_int_2ein; protected double rate_int_2eni; protected double rate_int_ai; protected double rate_int_an; protected double rate_int_an_n; protected double rate_int_bi; protected double rate_int_bn; protected double rate_int_bn_n; protected double rate_int_ei; protected double rate_int_en; protected double rate_int_en_n; protected double rate_itxn_a; protected double rate_loc_a; protected double rate_loc_an; protected double rate_loc_b; protected double rate_loc_bn; protected double rate_loc_e; protected double rate_loc_en; protected double rate_loc_n; protected double rate_mdeg_a; protected double rate_mdeg_b; protected double rate_mdeg_e; protected double rate_tsl_a; protected double rate_tsl_b; protected double rate_tsl_e; protected double rate_txn_a; protected double rate_txn_b; protected double rate_txn_e; protected double cytoplasm; protected double nucleus; protected double IKK_deg_IKK_deg; protected double Total_IkBalpha; protected double Total_IkBbeta; protected double Total_IkBeps; protected double deg_a_deg1_c; protected double deg_a_n_deg1_n; protected double deg_ai_r1; protected double deg_ain_r4; protected double deg_an_deg4_c; protected double deg_an_n_deg4_n; protected double deg_b_deg2_c; protected double deg_b_n_deg2_n; protected double deg_bi_r2; protected double deg_bin_r5; protected double deg_bn_deg5_c; protected double deg_bn_n_deg5_n; protected double deg_e_deg3_c; protected double deg_e_n_deg3_n; protected double deg_ei_r3; protected double deg_ein_r6; protected double deg_en_deg6_c; protected double deg_en_n_deg6_n; protected double int_2ain_a4_3; protected double int_2ain_d4_3; protected double int_2ani_a7; protected double int_2ani_d1_2; protected double int_2bin_a5_3; protected double int_2bin_d5_3; protected double int_2bni_a8; protected double int_2bni_d2_2; protected double int_2ein_a6_3; protected double int_2ein_d6_3; protected double int_2eni_a9; protected double int_2eni_d3_2; protected double int_ai_a1; protected double int_ai_d1_1; protected double int_an_a4_1; protected double int_an_d4_1; protected double int_an_n_a4_2; protected double int_an_n_d4_2; protected double int_bi_a2; protected double int_bi_d2_1; protected double int_bn_a5_1; protected double int_bn_d5_1; protected double int_bn_n_a5_2; protected double int_bn_n_d5_2; protected double int_ei_a3; protected double int_ei_d3_1; protected double int_en_a6_1; protected double int_en_d6_1; protected double int_en_n_a6_2; protected double int_en_n_d6_2; protected double itxn_a_tr2a_i; protected double loc_a_tp1a; protected double loc_a_tp2a; protected double loc_an_k2_a; protected double loc_b_tp1b; protected double loc_b_tp2b; protected double loc_bn_k2_b; protected double loc_e_tp1e; protected double loc_e_tp2e; protected double loc_en_k2_e; protected double loc_n_k1_1; protected double loc_n_k1_2; protected double mdeg_a_tr3a; protected double mdeg_b_tr3b; protected double mdeg_e_tr3e; protected double tsl_a_tr1a; protected double tsl_b_tr1b; protected double tsl_e_tr1e; protected double txn_a_tr2a; protected double txn_b_tr2b; protected double txn_e_tr2e; public double[] extendResult(double time,double [] x) { this.time = time; __internalVarInitFunc_0(time, x); double[] y = new double[27]; 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] = Total_IkBalpha; y[25] = Total_IkBbeta; y[26] = Total_IkBeps; return y; } public double[] getInitialValues() { double [] x = new double[24]; this.time = 0.0; x[0] = 0.0010; // - $"cytoplasm.IKK" x[1] = 0.0; // - $"cytoplasm.IkBaIKK" x[2] = 0.0; // - $"cytoplasm.IkBaIKKNFkB" x[3] = 0.06; // - $"cytoplasm.IkBaNFkB_cytoplasm" x[4] = 0.0; // - $"cytoplasm.IkBa_cytoplasm" x[5] = 0.0; // - $"cytoplasm.IkBbIKK" x[6] = 0.0; // - $"cytoplasm.IkBbIKKNFkB" x[7] = 0.03; // - $"cytoplasm.IkBbNFkB_cytoplasm" x[8] = 0.0; // - $"cytoplasm.IkBb_cytoplasm" x[9] = 0.0; // - $"cytoplasm.IkBeIKK" x[10] = 0.0; // - $"cytoplasm.IkBeIKKNFkB" x[11] = 0.01; // - $"cytoplasm.IkBeNFkB_cytoplasm" x[12] = 0.0; // - $"cytoplasm.IkBe_cytoplasm" x[13] = 0.0; // - $"cytoplasm.NFkB_cytoplasm" x[14] = 0.0; // - $"nucleus.IkBaNFkB_nucleus" x[15] = 0.0; // - $"nucleus.IkBa_mRNA" x[16] = 0.0; // - $"nucleus.IkBa_nucleus" x[17] = 0.0; // - $"nucleus.IkBbNFkB_nucleus" x[18] = 0.0; // - $"nucleus.IkBb_mRNA" x[19] = 0.0; // - $"nucleus.IkBb_nucleus" x[20] = 0.0; // - $"nucleus.IkBeNFkB_nucleus" x[21] = 0.0; // - $"nucleus.IkBe_mRNA" x[22] = 0.0; // - $"nucleus.IkBe_nucleus" x[23] = 0.0; // - $"nucleus.NFkB_nucleus" __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 'BIOMD0000000147.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = -rate_IKK_deg+rate_deg_ai+rate_deg_ain+rate_deg_bi+rate_deg_bin+rate_deg_ei+rate_deg_ein-rate_int_2ani-rate_int_2bni-rate_int_2eni-rate_int_ai-rate_int_bi-rate_int_ei; result[1] = -rate_deg_ai-rate_int_2ain+rate_int_ai; result[2] = -rate_deg_ain+rate_int_2ain+rate_int_2ani; result[3] = -rate_deg_an-rate_int_2ani+rate_int_an+rate_loc_an; result[4] = -rate_deg_a-rate_int_ai-rate_int_an-rate_loc_a+rate_tsl_a; result[5] = -rate_deg_bi-rate_int_2bin+rate_int_bi; result[6] = -rate_deg_bin+rate_int_2bin+rate_int_2bni; result[7] = -rate_deg_bn-rate_int_2bni+rate_int_bn+rate_loc_bn; result[8] = -rate_deg_b-rate_int_bi-rate_int_bn-rate_loc_b+rate_tsl_b; result[9] = -rate_deg_ei-rate_int_2ein+rate_int_ei; result[10] = -rate_deg_ein+rate_int_2ein+rate_int_2eni; result[11] = -rate_deg_en-rate_int_2eni+rate_int_en+rate_loc_en; result[12] = -rate_deg_e-rate_int_ei-rate_int_en-rate_loc_e+rate_tsl_e; result[13] = +rate_deg_ain+rate_deg_an+rate_deg_bin+rate_deg_bn+rate_deg_ein+rate_deg_en-rate_int_2ain-rate_int_2bin-rate_int_2ein-rate_int_an-rate_int_bn-rate_int_en-rate_loc_n; result[14] = -rate_deg_an_n+rate_int_an_n-rate_loc_an; result[15] = +rate_itxn_a-rate_mdeg_a+rate_tsl_a-rate_tsl_a+rate_txn_a; result[16] = -rate_deg_a_n-rate_int_an_n+rate_loc_a; result[17] = -rate_deg_bn_n+rate_int_bn_n-rate_loc_bn; result[18] = -rate_mdeg_b+rate_tsl_b-rate_tsl_b+rate_txn_b; result[19] = -rate_deg_b_n-rate_int_bn_n+rate_loc_b; result[20] = -rate_deg_en_n+rate_int_en_n-rate_loc_en; result[21] = -rate_mdeg_e+rate_tsl_e-rate_tsl_e+rate_txn_e; result[22] = -rate_deg_e_n-rate_int_en_n+rate_loc_e; result[23] = +rate_deg_an_n+rate_deg_bn_n+rate_deg_en_n-rate_int_an_n-rate_int_bn_n-rate_int_en_n+rate_loc_n; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[24]; __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 ...