/* * This code is generated by BioUML FrameWork * for BIOMD0000000109.xml diagram at 2008.03.20 15:08:45 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000109 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ private void __internalVarInitFunc_0(double time, double[] x) { _X_totalYCyclinYD_ = x[38] + x[32] + x[36]; _X_hyperphosphorylatedYpRb_ = x[47] + x[48]; _X_activeYCdk2_ = x[19] + x[22]; _X_totalYEmi1_ = x[41] + x[8]; _X_ksYCyclinE_ = ks0YCyclinE + ks1YCyclinE*x[40]/(ksMYCyclinE + x[40]); _X_ksYCyclinA_ = ks0YCyclinA + ks1YCyclinA*x[40]/(ksMYCyclinA + x[40]); _X_ksYEmi1_ = ks0YEmi1 + ks1YEmi1*x[40]/(ksMYEmi1 + x[40]); _X_ksYE2F_ = ks0YE2F + ks1YE2F*x[40]/(ksMYE2F + x[40]); _X_totalYCyclinYE_ = x[39] + x[16] + x[19] + x[26] + x[29]; _X_totalYCyclinYA_ = x[37] + x[10] + x[12] + x[17] + x[22] + x[27] + x[30]; _X_totalYp27_ = x[42] + x[35] + x[36] + x[25] + x[26] + x[27] + x[28] + x[29] + x[30]; _X_hypophosphorylatedYpRb_ = x[45] + x[46]; } /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_rxnY001 = ksYCyclinD*X; rate_rxnY002 = kdYCyclinD*x[38]*X; rate_rxnY003 = kdYCyclinD*x[32]*X; rate_rxnY004 = kdYCyclinD*x[36]*X; rate_rxnY005 = ksYp27*X; rate_rxnY006 = kdYp27*x[42]*X; rate_rxnY007 = kdYp27*x[35]*X; rate_rxnY008 = kdYp27*x[36]*X; rate_rxnY009 = kdYp27*x[25]*X; rate_rxnY010 = kdYp27*x[26]*X; rate_rxnY011 = kdYp27*x[27]*X; rate_rxnY012 = kdYp27*x[28]*X; rate_rxnY013 = kd1Yp27*x[29]*X; rate_rxnY014 = kdYp27*x[30]*X; rate_rxnY015 = _X_ksYCyclinE_*X; rate_rxnY016 = kdYCyclinE*x[39]*X; rate_rxnY017 = kdYCyclinE*x[16]*X; rate_rxnY018 = kdYCyclinE*x[26]*X; rate_rxnY019 = kdYCyclinE*x[19]*X; rate_rxnY020 = kdYCyclinE*x[29]*X; rate_rxnY021 = _X_ksYCyclinA_*X; rate_rxnY022 = kdYCyclinA*x[37]*X; rate_rxnY023 = kdYCyclinA*x[10]*X; rate_rxnY024 = kdYCyclinA*x[12]*X; rate_rxnY025 = kdYCyclinA*x[17]*X; rate_rxnY026 = kdYCyclinA*x[27]*X; rate_rxnY027 = kdYCyclinA*x[22]*X; rate_rxnY028 = kdYCyclinA*x[30]*X; rate_rxnY029 = _X_ksYE2F_*X; rate_rxnY030 = kd0YE2F*x[40]*X; rate_rxnY031 = kdYE2F*x[44]*X; rate_rxnY032 = kdYE2F*x[46]*X; rate_rxnY033 = kdYE2F*x[48]*X; rate_rxnY034 = _X_ksYEmi1_*X; rate_rxnY035 = kdYEmi1*x[41]*X; rate_rxnY036 = kdYEmi1*x[8]*X; rate_rxnY037 = kbYCyclinDYYCdk4*x[31]*x[38]*X; rate_rxnY038 = kuYCyclinDYYCdk4*x[32]*X; rate_rxnY039 = kbYCyclinDYYCdk4*x[35]*x[38]*X; rate_rxnY040 = kuYCyclinDYYCdk4*x[36]*X; } public void __internalRateVarInitFunc_1(double time, double[] x) { rate_rxnY041 = kbYp27YYCdk4*x[31]*x[42]*X; rate_rxnY042 = kuYp27YYCdk4*x[35]*X; rate_rxnY043 = kbYp27YYCdk4*x[32]*x[42]*X; rate_rxnY044 = kuYp27YYCdk4*x[36]*X; rate_rxnY045 = kbYp27YYCdk2*x[15]*x[42]*X; rate_rxnY046 = kuYp27YYCdk2*x[25]*X; rate_rxnY047 = kbYp27YYCdk2*x[16]*x[42]*X; rate_rxnY048 = kuYp27YYCdk2*x[26]*X; rate_rxnY049 = kbYp27YYCdk2*x[17]*x[42]*X; rate_rxnY050 = kuYp27YYCdk2*x[27]*X; rate_rxnY051 = kbYp27YYCdk2*x[18]*x[42]*X; rate_rxnY052 = kuYp27YYCdk2*x[28]*X; rate_rxnY053 = kbYp27YYCdk2*x[19]*x[42]*X; rate_rxnY054 = kuYp27YYCdk2*x[29]*X; rate_rxnY055 = kbYp27YYCdk2*x[22]*x[42]*X; rate_rxnY056 = kuYp27YYCdk2*x[30]*X; rate_rxnY057 = kYact*x[15]*X; rate_rxnY058 = kYact*x[25]*X; rate_rxnY059 = kYact*x[16]*X; rate_rxnY060 = kYact*x[26]*X; rate_rxnY061 = kYact*x[17]*X; rate_rxnY062 = kYact*x[27]*X; rate_rxnY063 = kbYCyclinEYYCdk2*x[15]*x[39]*X; rate_rxnY064 = kuYCyclinEYYCdk2*x[16]*X; rate_rxnY065 = kbYCyclinEYYCdk2*x[25]*x[39]*X; rate_rxnY066 = kuYCyclinEYYCdk2*x[26]*X; rate_rxnY067 = kbYCyclinEYYCdk2*x[18]*x[39]*X; rate_rxnY068 = kuYCyclinEYYCdk2*x[19]*X; rate_rxnY069 = kbYCyclinEYYCdk2*x[28]*x[39]*X; rate_rxnY070 = kuYCyclinEYYCdk2*x[29]*X; rate_rxnY071 = kbYCyclinAYYCdk2*x[15]*x[37]*X; rate_rxnY072 = kuYCyclinAYYCdk2*x[17]*X; rate_rxnY073 = kbYCyclinAYYCdk2*x[25]*x[37]*X; rate_rxnY074 = X*kuYCyclinAYYCdk2*x[27]; rate_rxnY075 = X*kbYCyclinAYYCdk2*x[18]*x[37]; rate_rxnY076 = X*kuYCyclinAYYCdk2*x[22]; rate_rxnY077 = X*kbYCyclinAYYCdk2*x[28]*x[37]; rate_rxnY078 = X*kuYCyclinAYYCdk2*x[30]; rate_rxnY079 = X*kYact*x[9]; rate_rxnY080 = X*kYact*x[10]; } public void __internalRateVarInitFunc_2(double time, double[] x) { rate_rxnY081 = X*kbYCyclinAYYCdk1*x[9]*x[37]; rate_rxnY082 = X*kuYCyclinAYYCdk1*x[10]; rate_rxnY083 = X*kbYCyclinAYYCdk1*x[11]*x[37]; rate_rxnY084 = X*kuYCyclinAYYCdk1*x[12]; rate_rxnY085 = X*kbYD4YYpRb*x[43]*x[32]; rate_rxnY086 = X*kuYD4YYpRb*x[33]; rate_rxnY087 = X*kupYD4YYpRb*x[33]; rate_rxnY088 = X*kbYD4YYpRb*x[44]*x[32]; rate_rxnY089 = X*kuYD4YYpRb*x[34]; rate_rxnY090 = X*kupYD4YYpRb*x[34]; rate_rxnY091 = X*kbYE2YYpRb*x[45]*x[19]; rate_rxnY092 = X*kuYE2YYpRb*x[20]; rate_rxnY093 = X*kupYE2YYpRb*x[20]; rate_rxnY094 = X*kbYE2YYpRb*x[46]*x[19]; rate_rxnY095 = X*kuYE2YYpRb*x[21]; rate_rxnY096 = X*kupYE2YYpRb*x[21]; rate_rxnY097 = X*kbYA2YYpRb*x[45]*x[22]; rate_rxnY098 = X*kuYA2YYpRb*x[23]; rate_rxnY099 = X*kupYA2YYpRb*x[23]; rate_rxnY100 = X*kbYA2YYpRb*x[46]*x[22]; rate_rxnY101 = X*kuYA2YYpRb*x[24]; rate_rxnY102 = X*kupYA2YYpRb*x[24]; rate_rxnY103 = X*kbYA1YYpRb*x[45]*x[12]; rate_rxnY104 = X*kuYA1YYpRb*x[13]; rate_rxnY105 = X*kupYA1YYpRb*x[13]; rate_rxnY106 = X*kbYA1YYpRb*x[45]*x[12]; rate_rxnY107 = X*kuYA1YYpRb*x[14]; rate_rxnY108 = X*kupYA1YYpRb*x[14]; rate_rxnY109 = X*ktYpRbYYDephos*x[47]; rate_rxnY110 = X*ktYpRbYYDephos*x[48]; rate_rxnY111 = X*kbYE2FYYpRb*x[43]*x[40]; rate_rxnY112 = X*kuYE2FYYpRb*x[44]; rate_rxnY113 = X*kbYE2FYYpRb*x[45]*x[40]; rate_rxnY114 = X*kuYE2FYYpRb*x[46]; rate_rxnY115 = X*kuYE2FYYpRb*x[48]; rate_rxnY116 = X*kbYEmi1YYAPCC*x[0]*x[41]; rate_rxnY117 = X*kuYEmi1YYAPCC*x[8]; rate_rxnY118 = X*kbYAPCCYYCyclinA*x[37]*x[0]; rate_rxnY119 = X*kuYAPCCYYCyclinA*x[7]; rate_rxnY120 = X*kudYAPCCYYCyclinA*x[7]; } public void __internalRateVarInitFunc_3(double time, double[] x) { rate_rxnY121 = X*kbYAPCCYYCyclinA*x[17]*x[0]; rate_rxnY122 = X*kuYAPCCYYCyclinA*x[3]; rate_rxnY123 = X*kudYAPCCYYCyclinA*x[3]; rate_rxnY124 = X*kbYAPCCYYCyclinA*x[27]*x[0]; rate_rxnY125 = X*kuYAPCCYYCyclinA*x[5]; rate_rxnY126 = X*kudYAPCCYYCyclinA*x[5]; rate_rxnY127 = X*kbYAPCCYYCyclinA*x[27]*x[0]; rate_rxnY128 = X*kuYAPCCYYCyclinA*x[4]; rate_rxnY129 = X*kudYAPCCYYCyclinA*x[4]; rate_rxnY130 = X*kbYAPCCYYCyclinA*x[30]*x[0]; rate_rxnY131 = X*kuYAPCCYYCyclinA*x[6]; rate_rxnY132 = X*kudYAPCCYYCyclinA*x[6]; rate_rxnY133 = X*kbYAPCCYYCyclinA*x[10]*x[0]; rate_rxnY134 = X*kuYAPCCYYCyclinA*x[1]; rate_rxnY135 = X*kudYAPCCYYCyclinA*x[1]; rate_rxnY136 = X*kbYAPCCYYCyclinA*x[12]*x[0]; rate_rxnY137 = X*kuYAPCCYYCyclinA*x[2]; rate_rxnY138 = X*kudYAPCCYYCyclinA*x[2]; } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ X = 1.0; // initial value of $X k1Yact = 0.01075; // initial value of k1Yact kbYA1YYpRb = 6.73E-5; // initial value of kbYA1YYpRb kbYA2YYpRb = 6.25E-5; // initial value of kbYA2YYpRb kbYAPCCYYCyclinA = 1.61E-5; // initial value of kbYAPCCYYCyclinA kbYCyclinAYYCdk1 = 6.48E-5; // initial value of kbYCyclinAYYCdk1 kbYCyclinAYYCdk2 = 9.52E-5; // initial value of kbYCyclinAYYCdk2 kbYCyclinDYYCdk4 = 1.43E-6; // initial value of kbYCyclinDYYCdk4 kbYCyclinEYYCdk2 = 5.01E-5; // initial value of kbYCyclinEYYCdk2 kbYD4YYpRb = 3.15E-5; // initial value of kbYD4YYpRb kbYE2FYYpRb = 9.66E-6; // initial value of kbYE2FYYpRb kbYE2YYpRb = 5.74E-5; // initial value of kbYE2YYpRb kbYEmi1YYAPCC = 1.0E-4; // initial value of kbYEmi1YYAPCC kbYp27YYCdk2 = 1.23E-5; // initial value of kbYp27YYCdk2 kbYp27YYCdk4 = 6.34E-6; // initial value of kbYp27YYCdk4 kd0YE2F = 0.002229; // initial value of kd0YE2F kd1Yp27 = 0.071149; // initial value of kd1Yp27 kdYCyclinA = 0.05; // initial value of kdYCyclinA kdYCyclinD = 0.05; // initial value of kdYCyclinD kdYCyclinE = 0.05; // initial value of kdYCyclinE kdYE2F = 0.006465; // initial value of kdYE2F kdYEmi1 = 0.018158; // initial value of kdYEmi1 kdYp27 = 0.001575; // initial value of kdYp27 ks0YCyclinA = 499.9437; // initial value of ks0YCyclinA ks0YCyclinE = 254.0742; // initial value of ks0YCyclinE ks0YE2F = 6.927086; // initial value of ks0YE2F ks0YEmi1 = 2.004744; // initial value of ks0YEmi1 ks1YCyclinA = 7999.996; // initial value of ks1YCyclinA ks1YCyclinE = 980.611; // initial value of ks1YCyclinE ks1YE2F = 65.44282; // initial value of ks1YE2F ks1YEmi1 = 1788.517; // initial value of ks1YEmi1 ksMYCyclinA = 4064.384; // initial value of ksMYCyclinA ksMYCyclinE = 9992.647; // initial value of ksMYCyclinE ksMYE2F = 9818.78; // initial value of ksMYE2F ksMYEmi1 = 9608.162; // initial value of ksMYEmi1 ksYCyclinD = 1354.231; // initial value of ksYCyclinD ksYp27 = 195.4716; // initial value of ksYp27 ktYpRbYYDephos = 0.023194; // initial value of ktYpRbYYDephos kuYA1YYpRb = 0.1; // initial value of kuYA1YYpRb kuYA2YYpRb = 0.1; // initial value of kuYA2YYpRb kuYAPCCYYCyclinA = 0.1; // initial value of kuYAPCCYYCyclinA kuYCyclinAYYCdk1 = 0.1; // initial value of kuYCyclinAYYCdk1 kuYCyclinAYYCdk2 = 0.1; // initial value of kuYCyclinAYYCdk2 kuYCyclinDYYCdk4 = 0.1; // initial value of kuYCyclinDYYCdk4 kuYCyclinEYYCdk2 = 0.1; // initial value of kuYCyclinEYYCdk2 kuYD4YYpRb = 0.1; // initial value of kuYD4YYpRb kuYE2FYYpRb = 0.1; // initial value of kuYE2FYYpRb kuYE2YYpRb = 0.1; // initial value of kuYE2YYpRb kuYEmi1YYAPCC = 0.1; // initial value of kuYEmi1YYAPCC kuYp27YYCdk2 = 0.1; // initial value of kuYp27YYCdk2 kuYp27YYCdk4 = 0.1; // initial value of kuYp27YYCdk4 kudYAPCCYYCyclinA = 4.999555; // initial value of kudYAPCCYYCyclinA kupYA1YYpRb = 0.202132; // initial value of kupYA1YYpRb kupYA2YYpRb = 0.200091; // initial value of kupYA2YYpRb kupYD4YYpRb = 1.694662; // initial value of kupYD4YYpRb kupYE2YYpRb = 4.78271; // initial value of kupYE2YYpRb } /* * Model variables initial values */ protected double _X_activeYCdk2_; protected double _X_hyperphosphorylatedYpRb_; protected double _X_hypophosphorylatedYpRb_; protected double _X_ksYCyclinA_; protected double _X_ksYCyclinE_; protected double _X_ksYE2F_; protected double _X_ksYEmi1_; protected double _X_totalYCyclinYA_; protected double _X_totalYCyclinYD_; protected double _X_totalYCyclinYE_; protected double _X_totalYEmi1_; protected double _X_totalYp27_; protected double rate_rxnY001; protected double rate_rxnY002; protected double rate_rxnY003; protected double rate_rxnY004; protected double rate_rxnY005; protected double rate_rxnY006; protected double rate_rxnY007; protected double rate_rxnY008; protected double rate_rxnY009; protected double rate_rxnY010; protected double rate_rxnY011; protected double rate_rxnY012; protected double rate_rxnY013; protected double rate_rxnY014; protected double rate_rxnY015; protected double rate_rxnY016; protected double rate_rxnY017; protected double rate_rxnY018; protected double rate_rxnY019; protected double rate_rxnY020; protected double rate_rxnY021; protected double rate_rxnY022; protected double rate_rxnY023; protected double rate_rxnY024; protected double rate_rxnY025; protected double rate_rxnY026; protected double rate_rxnY027; protected double rate_rxnY028; protected double rate_rxnY029; protected double rate_rxnY030; protected double rate_rxnY031; protected double rate_rxnY032; protected double rate_rxnY033; protected double rate_rxnY034; protected double rate_rxnY035; protected double rate_rxnY036; protected double rate_rxnY037; protected double rate_rxnY038; protected double rate_rxnY039; protected double rate_rxnY040; protected double rate_rxnY041; protected double rate_rxnY042; protected double rate_rxnY043; protected double rate_rxnY044; protected double rate_rxnY045; protected double rate_rxnY046; protected double rate_rxnY047; protected double rate_rxnY048; protected double rate_rxnY049; protected double rate_rxnY050; protected double rate_rxnY051; protected double rate_rxnY052; protected double rate_rxnY053; protected double rate_rxnY054; protected double rate_rxnY055; protected double rate_rxnY056; protected double rate_rxnY057; protected double rate_rxnY058; protected double rate_rxnY059; protected double rate_rxnY060; protected double rate_rxnY061; protected double rate_rxnY062; protected double rate_rxnY063; protected double rate_rxnY064; protected double rate_rxnY065; protected double rate_rxnY066; protected double rate_rxnY067; protected double rate_rxnY068; protected double rate_rxnY069; protected double rate_rxnY070; protected double rate_rxnY071; protected double rate_rxnY072; protected double rate_rxnY073; protected double rate_rxnY074; protected double rate_rxnY075; protected double rate_rxnY076; protected double rate_rxnY077; protected double rate_rxnY078; protected double rate_rxnY079; protected double rate_rxnY080; protected double rate_rxnY081; protected double rate_rxnY082; protected double rate_rxnY083; protected double rate_rxnY084; protected double rate_rxnY085; protected double rate_rxnY086; protected double rate_rxnY087; protected double rate_rxnY088; protected double rate_rxnY089; protected double rate_rxnY090; protected double rate_rxnY091; protected double rate_rxnY092; protected double rate_rxnY093; protected double rate_rxnY094; protected double rate_rxnY095; protected double rate_rxnY096; protected double rate_rxnY097; protected double rate_rxnY098; protected double rate_rxnY099; protected double rate_rxnY100; protected double rate_rxnY101; protected double rate_rxnY102; protected double rate_rxnY103; protected double rate_rxnY104; protected double rate_rxnY105; protected double rate_rxnY106; protected double rate_rxnY107; protected double rate_rxnY108; protected double rate_rxnY109; protected double rate_rxnY110; protected double rate_rxnY111; protected double rate_rxnY112; protected double rate_rxnY113; protected double rate_rxnY114; protected double rate_rxnY115; protected double rate_rxnY116; protected double rate_rxnY117; protected double rate_rxnY118; protected double rate_rxnY119; protected double rate_rxnY120; protected double rate_rxnY121; protected double rate_rxnY122; protected double rate_rxnY123; protected double rate_rxnY124; protected double rate_rxnY125; protected double rate_rxnY126; protected double rate_rxnY127; protected double rate_rxnY128; protected double rate_rxnY129; protected double rate_rxnY130; protected double rate_rxnY131; protected double rate_rxnY132; protected double rate_rxnY133; protected double rate_rxnY134; protected double rate_rxnY135; protected double rate_rxnY136; protected double rate_rxnY137; protected double rate_rxnY138; protected double X; protected double k1Yact; protected double kYact; protected double kbYA1YYpRb; protected double kbYA2YYpRb; protected double kbYAPCCYYCyclinA; protected double kbYCyclinAYYCdk1; protected double kbYCyclinAYYCdk2; protected double kbYCyclinDYYCdk4; protected double kbYCyclinEYYCdk2; protected double kbYD4YYpRb; protected double kbYE2FYYpRb; protected double kbYE2YYpRb; protected double kbYEmi1YYAPCC; protected double kbYp27YYCdk2; protected double kbYp27YYCdk4; protected double kd0YE2F; protected double kd1Yp27; protected double kdYCyclinA; protected double kdYCyclinD; protected double kdYCyclinE; protected double kdYE2F; protected double kdYEmi1; protected double kdYp27; protected double ks0YCyclinA; protected double ks0YCyclinE; protected double ks0YE2F; protected double ks0YEmi1; protected double ks1YCyclinA; protected double ks1YCyclinE; protected double ks1YE2F; protected double ks1YEmi1; protected double ksMYCyclinA; protected double ksMYCyclinE; protected double ksMYE2F; protected double ksMYEmi1; protected double ksYCyclinD; protected double ksYp27; protected double ktYpRbYYDephos; protected double kuYA1YYpRb; protected double kuYA2YYpRb; protected double kuYAPCCYYCyclinA; protected double kuYCyclinAYYCdk1; protected double kuYCyclinAYYCdk2; protected double kuYCyclinDYYCdk4; protected double kuYCyclinEYYCdk2; protected double kuYD4YYpRb; protected double kuYE2FYYpRb; protected double kuYE2YYpRb; protected double kuYEmi1YYAPCC; protected double kuYp27YYCdk2; protected double kuYp27YYCdk4; protected double kudYAPCCYYCyclinA; protected double kupYA1YYpRb; protected double kupYA2YYpRb; protected double kupYD4YYpRb; protected double kupYE2YYpRb; protected double time; public double[] extendResult(double time,double [] x) { this.time = time; __internalVarInitFunc_0(time, x); double[] y = new double[62]; 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_activeYCdk2_; y[43] = _X_hyperphosphorylatedYpRb_; y[44] = _X_hypophosphorylatedYpRb_; y[45] = _X_ksYCyclinA_; y[46] = _X_ksYCyclinE_; y[47] = _X_ksYE2F_; y[48] = _X_ksYEmi1_; y[49] = x[42]; y[50] = x[43]; y[51] = x[44]; y[52] = x[45]; y[53] = x[46]; y[54] = x[47]; y[55] = x[48]; y[56] = _X_totalYCyclinYA_; y[57] = _X_totalYCyclinYD_; y[58] = _X_totalYCyclinYE_; y[59] = _X_totalYEmi1_; y[60] = _X_totalYp27_; y[61] = kYact; return y; } public double[] getInitialValues() { double [] x = new double[49]; this.time = 0.0; x[0] = 24582.9; // - $"X.APCC" x[1] = 104.388; // - $"X.APCCYCdk1Y00YCdk1Y01YInt" x[2] = 0.0; // - $"X.APCCYCdk1Y10YCdk1Y11YInt" x[3] = 52.8191; // - $"X.APCCYCdk2Y000YCdk2Y002YInt" x[4] = 0.0; // - $"X.APCCYCdk2Y010YCdk2Y012YInt" x[5] = 90.5091; // - $"X.APCCYCdk2Y100YCdk2Y102YInt" x[6] = 0.0; // - $"X.APCCYCdk2Y110YCdk2Y112YInt" x[7] = 8.79462; // - $"X.APCCYCyclinAYInt" x[8] = 5160.61; // - $"X.APCCYEmi1" x[9] = 98550.6; // - $"X.Cdk1Y00" x[10] = 1345.01; // - $"X.Cdk1Y01" x[11] = 0.0; // - $"X.Cdk1Y10" x[12] = 0.0; // - $"X.Cdk1Y11" x[13] = 0.0; // - $"X.Cdk1Y11YpRbY10YpRbY20YInt" x[14] = 0.0; // - $"X.Cdk1Y11YpRbY11YpRbY21YInt" x[15] = 33942.0; // - $"X.Cdk2Y000" x[16] = 2176.46; // - $"X.Cdk2Y001" x[17] = 680.557; // - $"X.Cdk2Y002" x[18] = 0.0; // - $"X.Cdk2Y010" x[19] = 0.0; // - $"X.Cdk2Y011" x[20] = 0.0; // - $"X.Cdk2Y011YpRbY10YpRbY20YInt" x[21] = 0.0; // - $"X.Cdk2Y011YpRbY11YpRbY21YInt" x[22] = 0.0; // - $"X.Cdk2Y012" x[23] = 0.0; // - $"X.Cdk2Y012YpRbY10YpRbY20YInt" x[24] = 0.0; // - $"X.Cdk2Y012YpRbY11YpRbY21YInt" x[25] = 58162.0; // - $"X.Cdk2Y100" x[26] = 3729.51; // - $"X.Cdk2Y101" x[27] = 1166.18; // - $"X.Cdk2Y102" x[28] = 0.0; // - $"X.Cdk2Y110" x[29] = 0.0; // - $"X.Cdk2Y111" x[30] = 0.0; // - $"X.Cdk2Y112" x[31] = 46551.9; // - $"X.Cdk4Y00" x[32] = 6547.64; // - $"X.Cdk4Y01" x[33] = 0.0; // - $"X.Cdk4Y01YpRbY00YpRbY10YInt" x[34] = 0.0; // - $"X.Cdk4Y01YpRbY01YpRbY11YInt" x[35] = 41117.2; // - $"X.Cdk4Y10" x[36] = 5783.23; // - $"X.Cdk4Y11" x[37] = 113.316; // - $"X.CyclinA" x[38] = 14753.7; // - $"X.CyclinD" x[39] = 191.985; // - $"X.CyclinE" x[40] = 546.211; // - $"X.E2F" x[41] = 248.046; // - $"X.Emi1" x[42] = 14150.9; // - $"X.p27" x[43] = 30000.0; // - $"X.pRbY00" x[44] = 0.0; // - $"X.pRbY01" x[45] = 28583.4; // - $"X.pRbY10" x[46] = 1416.59; // - $"X.pRbY11" x[47] = 0.0; // - $"X.pRbY20" x[48] = 0.0; // - $"X.pRbY21" __internalVarInitFunc_0(time, x); __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); __internalRateVarInitFunc_2(time, x); __internalRateVarInitFunc_3(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); __internalRateVarInitFunc_2(time, x); __internalRateVarInitFunc_3(time, x); } /* * calculate dy/dt for 'BIOMD0000000109.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = +rate_rxnY036-rate_rxnY116+rate_rxnY117-rate_rxnY118+rate_rxnY119+rate_rxnY120-rate_rxnY121+rate_rxnY122+rate_rxnY123-rate_rxnY124+rate_rxnY125+rate_rxnY126-rate_rxnY127+rate_rxnY128+rate_rxnY129-rate_rxnY130+rate_rxnY131+rate_rxnY132-rate_rxnY133-rate_rxnY134+rate_rxnY135-rate_rxnY136-rate_rxnY137+rate_rxnY138; result[1] = +rate_rxnY133-rate_rxnY134-rate_rxnY135; result[2] = +rate_rxnY136-rate_rxnY137-rate_rxnY138; result[3] = +rate_rxnY121-rate_rxnY122-rate_rxnY123; result[4] = +rate_rxnY127-rate_rxnY128-rate_rxnY129; result[5] = +rate_rxnY124-rate_rxnY125-rate_rxnY126; result[6] = +rate_rxnY130-rate_rxnY131-rate_rxnY132; result[7] = +rate_rxnY118-rate_rxnY119-rate_rxnY120; result[8] = -rate_rxnY036+rate_rxnY116-rate_rxnY117; result[9] = +rate_rxnY023-rate_rxnY079-rate_rxnY081+rate_rxnY082+rate_rxnY135; result[10] = -rate_rxnY023-rate_rxnY080+rate_rxnY081-rate_rxnY082-rate_rxnY133+rate_rxnY134; result[11] = +rate_rxnY024+rate_rxnY079-rate_rxnY083+rate_rxnY084+rate_rxnY138; result[12] = -rate_rxnY024+rate_rxnY080+rate_rxnY083-rate_rxnY084-rate_rxnY103+rate_rxnY104+rate_rxnY105-rate_rxnY106+rate_rxnY107+rate_rxnY108-rate_rxnY136+rate_rxnY137; result[13] = +rate_rxnY103-rate_rxnY104-rate_rxnY105; result[14] = +rate_rxnY106-rate_rxnY107-rate_rxnY108; result[15] = +rate_rxnY009+rate_rxnY017+rate_rxnY025-rate_rxnY045+rate_rxnY046-rate_rxnY057-rate_rxnY063+rate_rxnY064-rate_rxnY071+rate_rxnY072+rate_rxnY123; result[16] = +rate_rxnY010-rate_rxnY017-rate_rxnY047+rate_rxnY048-rate_rxnY059+rate_rxnY063-rate_rxnY064; result[17] = +rate_rxnY011-rate_rxnY025-rate_rxnY049+rate_rxnY050-rate_rxnY061+rate_rxnY071-rate_rxnY072-rate_rxnY121+rate_rxnY122; result[18] = +rate_rxnY012+rate_rxnY019+rate_rxnY027-rate_rxnY051+rate_rxnY052+rate_rxnY057-rate_rxnY067+rate_rxnY068-rate_rxnY075+rate_rxnY076+rate_rxnY129; result[19] = +rate_rxnY013-rate_rxnY019-rate_rxnY053+rate_rxnY054+rate_rxnY059+rate_rxnY067-rate_rxnY068-rate_rxnY091+rate_rxnY092+rate_rxnY093-rate_rxnY094+rate_rxnY095+rate_rxnY096; result[20] = +rate_rxnY091-rate_rxnY092-rate_rxnY093; result[21] = +rate_rxnY094-rate_rxnY095-rate_rxnY096; result[22] = +rate_rxnY014-rate_rxnY027-rate_rxnY055+rate_rxnY056+rate_rxnY061+rate_rxnY075-rate_rxnY076-rate_rxnY097+rate_rxnY098+rate_rxnY099-rate_rxnY100+rate_rxnY101+rate_rxnY102-rate_rxnY127+rate_rxnY128; result[23] = +rate_rxnY097-rate_rxnY098-rate_rxnY099; result[24] = +rate_rxnY100-rate_rxnY101-rate_rxnY102; result[25] = -rate_rxnY009+rate_rxnY018+rate_rxnY026+rate_rxnY045-rate_rxnY046-rate_rxnY058-rate_rxnY065+rate_rxnY066-rate_rxnY073+rate_rxnY074+rate_rxnY126; result[26] = -rate_rxnY010-rate_rxnY018+rate_rxnY047-rate_rxnY048-rate_rxnY060+rate_rxnY065-rate_rxnY066; result[27] = -rate_rxnY011-rate_rxnY026+rate_rxnY049-rate_rxnY050-rate_rxnY062+rate_rxnY073-rate_rxnY074-rate_rxnY124+rate_rxnY125; result[28] = -rate_rxnY012+rate_rxnY020+rate_rxnY028+rate_rxnY051-rate_rxnY052+rate_rxnY058-rate_rxnY069+rate_rxnY070-rate_rxnY077+rate_rxnY078+rate_rxnY132; result[29] = -rate_rxnY013-rate_rxnY020+rate_rxnY053-rate_rxnY054+rate_rxnY060+rate_rxnY069-rate_rxnY070; result[30] = -rate_rxnY014-rate_rxnY028+rate_rxnY055-rate_rxnY056+rate_rxnY062+rate_rxnY077-rate_rxnY078-rate_rxnY130+rate_rxnY131; result[31] = +rate_rxnY003+rate_rxnY007-rate_rxnY037+rate_rxnY038-rate_rxnY041+rate_rxnY042; result[32] = -rate_rxnY003+rate_rxnY008+rate_rxnY037-rate_rxnY038-rate_rxnY043+rate_rxnY044-rate_rxnY085+rate_rxnY086+rate_rxnY087-rate_rxnY088+rate_rxnY089+rate_rxnY090; result[33] = +rate_rxnY085-rate_rxnY086-rate_rxnY087; result[34] = +rate_rxnY088-rate_rxnY089-rate_rxnY090; result[35] = +rate_rxnY004-rate_rxnY007-rate_rxnY039+rate_rxnY040+rate_rxnY041-rate_rxnY042; result[36] = -rate_rxnY004-rate_rxnY008+rate_rxnY039-rate_rxnY040+rate_rxnY043-rate_rxnY044; result[37] = +rate_rxnY021-rate_rxnY022-rate_rxnY071+rate_rxnY072-rate_rxnY073+rate_rxnY074-rate_rxnY075+rate_rxnY076-rate_rxnY077+rate_rxnY078-rate_rxnY081+rate_rxnY082-rate_rxnY083+rate_rxnY084-rate_rxnY118+rate_rxnY119; result[38] = +rate_rxnY001-rate_rxnY002-rate_rxnY037+rate_rxnY038-rate_rxnY039+rate_rxnY040; result[39] = +rate_rxnY015-rate_rxnY016-rate_rxnY063+rate_rxnY064-rate_rxnY065+rate_rxnY066-rate_rxnY067+rate_rxnY068-rate_rxnY069+rate_rxnY070; result[40] = +rate_rxnY029-rate_rxnY030-rate_rxnY111+rate_rxnY112-rate_rxnY113+rate_rxnY114+rate_rxnY115; result[41] = +rate_rxnY034-rate_rxnY035-rate_rxnY116+rate_rxnY117; result[42] = +rate_rxnY005-rate_rxnY006-rate_rxnY041+rate_rxnY042-rate_rxnY043+rate_rxnY044-rate_rxnY045+rate_rxnY046-rate_rxnY047+rate_rxnY048-rate_rxnY049+rate_rxnY050-rate_rxnY051+rate_rxnY052-rate_rxnY053+rate_rxnY054-rate_rxnY055+rate_rxnY056; result[43] = +rate_rxnY031-rate_rxnY085+rate_rxnY086+rate_rxnY109-rate_rxnY111+rate_rxnY112; result[44] = -rate_rxnY031-rate_rxnY088+rate_rxnY089+rate_rxnY110+rate_rxnY111-rate_rxnY112; result[45] = +rate_rxnY032+rate_rxnY087-rate_rxnY091+rate_rxnY092-rate_rxnY097+rate_rxnY098-rate_rxnY103+rate_rxnY104-rate_rxnY113+rate_rxnY114; result[46] = -rate_rxnY032+rate_rxnY090-rate_rxnY094+rate_rxnY095-rate_rxnY100+rate_rxnY101-rate_rxnY106+rate_rxnY107+rate_rxnY113-rate_rxnY114; result[47] = +rate_rxnY033+rate_rxnY093+rate_rxnY099+rate_rxnY105-rate_rxnY109+rate_rxnY115; result[48] = -rate_rxnY033+rate_rxnY096+rate_rxnY102+rate_rxnY108-rate_rxnY110-rate_rxnY115; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[49]; __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 ); } public double[] checkEvent(double time, double[] x) { this.time = time; __internalVarInitFunc_0(time, x); __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); __internalRateVarInitFunc_2(time, x); __internalRateVarInitFunc_3(time, x); double [] flags = new double[1]; flags[0] = (time > 240.0637) ? +1 : -1; //event_1 return flags; } public void processEvent(int __internalVar12060041255150, double time, double[] x) { this.time = time; if ( __internalVar12060041255150 == 0) //event_1 { kYact = k1Yact; } } } // class ...