/* * This code is generated by BioUML FrameWork * for BIOMD0000000110.xml diagram at 2008.03.20 15:08:46 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000110 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ private void __internalVarInitFunc_0(double time, double[] x) { _compartment_0000001_c_ = (compartment_0000001_c0 - x[3] - x[8] - x[5] - x[1])/compartment_0000001_c0; _compartment_0000001_totalCyclin_ = x[3] + x[8] + x[4]; } /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_reaction_0000001 = k1*compartment_0000001; rate_reaction_0000002 = compartment_0000001*(k3*_compartment_0000001_c_*x[4] - x[8]*k4); rate_reaction_0000003 = compartment_0000001*(k2 + k2u*x[2])*x[4]; rate_reaction_0000004 = compartment_0000001*((bz + cz*x[3])*x[9] - x[10]*az); rate_reaction_0000005 = compartment_0000001*((k6 + x[6])*x[3] - (k5 + x[11])*x[8]); rate_reaction_0000006 = compartment_0000001*((bz + cz*x[3])*x[10] - az*x[11]); rate_reaction_0000007 = k10*compartment_0000001; rate_reaction_0000010 = k12*compartment_0000001; rate_reaction_0000011 = (k14*x[3]*x[0] - k15*x[5])*compartment_0000001; rate_reaction_0000013 = compartment_0000001*x[2]/Tau; rate_reaction_0000014 = compartment_0000001*((bi + ci*x[3])*x[5] - ai*x[1]); rate_reaction_0000015 = compartment_0000001*k13*x[0]; rate_reaction_0000016 = compartment_0000001*k16*k16u*x[1]; rate_reaction_0000017 = compartment_0000001*x[6]*k11; rate_reaction_0000018 = compartment_0000001*k11*x[7]; rate_reaction_0000019 = compartment_0000001*k9*x[9]; rate_reaction_0000020 = compartment_0000001*k9*x[10]; rate_reaction_0000021 = compartment_0000001*k9*x[11]; rate_reaction_0000022 = compartment_0000001*k8; rate_reaction_0000023 = compartment_0000001*(k7 + k7u*x[2])*x[3]; rate_reaction_000008 = compartment_0000001*((bw + cw*x[3])*x[6] - aw*x[7]); rate_reaction_000009 = compartment_0000001*Math.pow(x[3], 2)/(Math.pow(a, 2) + Math.pow(x[3], 2))/Tau; } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ compartment_0000001 = 1.0; // initial value of $compartment_0000001 compartment_0000001_c0 = 200.0; // initial value of $compartment_0000001.c0 Tau = 25.0; // initial value of Tau a = 4.0; // initial value of a ai = 10.0; // initial value of ai aw = 10.0; // initial value of aw az = 10.0; // initial value of az bi = 0.1; // initial value of bi bw = 0.1; // initial value of bw bz = 0.1; // initial value of bz ci = 1.0; // initial value of ci cw = 1.0; // initial value of cw cz = 1.0; // initial value of cz k1 = 300.0; // initial value of k1 k10 = 10.0; // initial value of k10 k11 = 1.0; // initial value of k11 k13 = 1.0; // initial value of k13 k14 = 1.0; // initial value of k14 k15 = 1.0; // initial value of k15 k16 = 2.0; // initial value of k16 k16u = 25.0; // initial value of k16u k2 = 5.0; // initial value of k2 k2u = 50.0; // initial value of k2u k3 = 30.0; // initial value of k3 k4 = 30.0; // initial value of k4 k5 = 0.1; // initial value of k5 k6 = 1.0; // initial value of k6 k7 = 10.0; // initial value of k7 k8 = 100.0; // initial value of k8 k9 = 1.0; // initial value of k9 } /* * Model variables initial values */ protected double _compartment_0000001_c_; protected double _compartment_0000001_totalCyclin_; protected double rate_reaction_0000001; protected double rate_reaction_0000002; protected double rate_reaction_0000003; protected double rate_reaction_0000004; protected double rate_reaction_0000005; protected double rate_reaction_0000006; protected double rate_reaction_0000007; protected double rate_reaction_0000010; protected double rate_reaction_0000011; protected double rate_reaction_0000013; protected double rate_reaction_0000014; protected double rate_reaction_0000015; protected double rate_reaction_0000016; protected double rate_reaction_0000017; protected double rate_reaction_0000018; protected double rate_reaction_0000019; protected double rate_reaction_0000020; protected double rate_reaction_0000021; protected double rate_reaction_0000022; protected double rate_reaction_0000023; protected double rate_reaction_000008; protected double rate_reaction_000009; protected double compartment_0000001; protected double compartment_0000001_c0; protected double Tau; protected double a; protected double ai; protected double aw; protected double az; protected double bi; protected double bw; protected double bz; protected double ci; protected double cw; protected double cz; protected double k1; protected double k10; protected double k11; protected double k12; protected double k13; protected double k14; protected double k15; protected double k16; protected double k16u; protected double k2; protected double k2u; protected double k3; protected double k4; protected double k5; protected double k6; protected double k7; protected double k7u; protected double k8; protected double k9; public double[] extendResult(double time,double [] x) { this.time = time; __internalVarInitFunc_0(time, x); double[] y = new double[14]; y[0] = _compartment_0000001_c_; y[1] = x[0]; y[2] = x[1]; y[3] = _compartment_0000001_totalCyclin_; y[4] = x[2]; y[5] = x[3]; y[6] = x[4]; y[7] = x[5]; y[8] = x[6]; y[9] = x[7]; y[10] = x[8]; y[11] = x[9]; y[12] = x[10]; y[13] = x[11]; return y; } public double[] getInitialValues() { double [] x = new double[12]; this.time = 0.0; x[0] = 0.0; // - $"compartment_0000001.i" x[1] = 0.0; // - $"compartment_0000001.ixp" x[2] = 0.0; // - $"compartment_0000001.u" x[3] = 0.1; // - $"compartment_0000001.x" x[4] = 0.0; // - $"compartment_0000001.y" x[5] = 0.0; // - $compartment_0000001.ix x[6] = 0.0; // - $compartment_0000001.w0 x[7] = 0.0; // - $compartment_0000001.w1 x[8] = 0.1; // - $compartment_0000001.x1 x[9] = 0.0; // - $compartment_0000001.z0 x[10] = 0.0; // - $compartment_0000001.z1 x[11] = 0.0; // - $compartment_0000001.z2 __internalVarInitFunc_0(time, x); __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) { __internalVarInitFunc_0(time, x); __internalRateVarInitFunc_0(time, x); } /* * calculate dy/dt for 'BIOMD0000000110.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = +rate_reaction_0000010-rate_reaction_0000011-rate_reaction_0000015; result[1] = +rate_reaction_0000014-rate_reaction_0000016; result[2] = -rate_reaction_0000013+rate_reaction_000009; result[3] = -rate_reaction_0000005-rate_reaction_0000011+rate_reaction_0000016-rate_reaction_0000023; result[4] = +rate_reaction_0000001-rate_reaction_0000002-rate_reaction_0000003; result[5] = +rate_reaction_0000011-rate_reaction_0000014; result[6] = +rate_reaction_0000007-rate_reaction_0000017-rate_reaction_000008; result[7] = -rate_reaction_0000018+rate_reaction_000008; result[8] = +rate_reaction_0000002+rate_reaction_0000005; result[9] = -rate_reaction_0000004-rate_reaction_0000019+rate_reaction_0000022; result[10] = +rate_reaction_0000004-rate_reaction_0000006-rate_reaction_0000020; result[11] = +rate_reaction_0000006-rate_reaction_0000021; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[12]; __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 ...