/* * This code is generated by BioUML FrameWork * for BIOMD0000000049.xml diagram at 2008.03.20 15:04:28 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000049 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_J10 = compartment_c1*J10_J10_k*x[77]; rate_J100 = compartment_c1*J100_J100_k*x[31]; rate_J101 = compartment_c1*J101_J101_k*x[83]; rate_J102 = compartment_c1*J102_J102_k*x[54]; rate_J103 = compartment_c1*(J103_J103_k1*x[19]*x[73] - J103_J103_k2*x[23]); rate_J104 = compartment_c1*(J104_J104_k1*x[19]*x[74] - J104_J104_k2*x[24]); rate_J105 = compartment_c1*(J105_J105_k1*x[34]*x[91] - J105_J105_k2*x[38]); rate_J106 = compartment_c1*(J106_J106_k1*x[34]*x[85] - J106_J106_k2*x[39]); rate_J107 = compartment_c1*J107_J107_k*x[23]; rate_J108 = compartment_c1*J108_J108_k*x[24]; rate_J109 = compartment_c1*J109_J109_k*x[38]; rate_J11 = compartment_c1*J11_J11_k*x[78]; rate_J110 = compartment_c1*J110_J110_k*x[39]; rate_J112 = J112_J112_k*x[74]; rate_J113 = compartment*(J113_J113_k1*_compartment_c1_pro_TrkA_ - J113_J113_k2*x[5]); rate_J115 = compartment_c1*(J115_J115_k1*x[50]*x[63] - J115_J115_k2*x[52]); rate_J116 = compartment_c1*(J116_J116_k1*x[63]*x[79] - J116_J116_k2*x[81]); rate_J117 = compartment_c1*(J117_J117_k1*x[81]*x[49] - J117_J117_k2*x[36]); rate_J118 = compartment_c1*(J118_J118_k1*x[63]*x[27] - J118_J118_k2*x[29]); rate_J119 = compartment_c1*(J119_J119_k1*x[56]*x[20] - J119_J119_k2*x[21]); rate_J12 = compartment_c1*(J12_J12_k1*x[4]*x[50] - J12_J12_k2*x[51]); rate_J120 = compartment_c1*(J120_J120_k1*x[63]*x[69] - J120_J120_k2*x[71]); rate_J121 = compartment_c1*(J121_J121_Vmax*x[47]*x[68]/(J121_J121_Km1 + x[47])); rate_J122 = compartment_c1*(J122_J122_Vmax*x[44]*_compartment_c1_Rap1GAP_/(J122_J122_Km1 + x[44])); rate_J123 = compartment_c1*(J123_J123_Vmax*x[25]*(x[91] + x[54] + x[83] + x[38] + x[31] + x[73] + x[23])/(J123_J123_Km1 + x[25])); rate_J124 = compartment_c1*(J124_J124_Vmax*x[34]*x[65]/(J124_J124_Km1 + x[34])); rate_J13 = compartment_c1*J13_J13_k*x[51]; rate_J133 = compartment_c1*(J133_J133_k1*x[26]*x[40] - J133_J133_k2*x[41]); rate_J134 = compartment_c1*(J134_J134_k1*x[26]*x[75] - J134_J134_k2*x[76]); rate_J135 = compartment_c1*(J135_J135_k1*x[26]*x[88] - J135_J135_k2*x[89]); rate_J136 = compartment_c1*J136_J136_k*x[89]; rate_J137 = compartment_c1*(J137_J137_Vmax*x[58]*x[68]/(J137_J137_Km1 + x[58])); rate_J138 = compartment_c1*(J138_J138_Vmax*x[12]*x[68]/(J138_J138_Km1 + x[12])); rate_J139 = compartment_c1*(J139_J139_Vmax*x[7]*_compartment_c1_Rap1GAP_/(J139_J139_Km1 + x[7])); rate_J14 = compartment_c1*J14_J14_k*x[63]; rate_J140 = compartment_c1*(J140_J140_k1*x[58]*x[40] - J140_J140_k2*x[59]); rate_J141 = compartment_c1*(J141_J141_k1*x[58]*x[75] - J141_J141_k2*x[61]); rate_J142 = compartment_c1*(J142_J142_k1*x[58]*x[41] - J142_J142_k2*x[60]); rate_J143 = compartment_c1*(J143_J143_k1*x[58]*x[76] - J143_J143_k2*x[62]); rate_J144 = compartment_c1*(J144_J144_k1*x[12]*x[40] - J144_J144_k2*x[13]); } public void __internalRateVarInitFunc_1(double time, double[] x) { rate_J145 = compartment_c1*(J145_J145_k1*x[12]*x[75] - J145_J145_k2*x[15]); rate_J146 = compartment_c1*(J146_J146_k1*x[12]*x[41] - J146_J146_k2*x[14]); rate_J147 = compartment_c1*(J147_J147_k1*x[12]*x[76] - J147_J147_k2*x[16]); rate_J148 = compartment_c1*(J148_J148_k1*x[7]*x[40] - J148_J148_k2*x[8]); rate_J149 = compartment_c1*(J149_J149_k1*x[7]*x[75] - J149_J149_k2*x[10]); rate_J15 = compartment_c1*J15_J15_k*x[64]; rate_J150 = compartment_c1*(J150_J150_k1*x[7]*x[41] - J150_J150_k2*x[9]); rate_J151 = compartment_c1*(J151_J151_k1*x[7]*x[76] - J151_J151_k2*x[11]); rate_J152 = compartment_c1*J152_J152_k*x[59]; rate_J153 = compartment_c1*J153_J153_k*x[61]; rate_J154 = compartment_c1*J154_J154_k*x[60]; rate_J155 = compartment_c1*J155_J155_k*x[62]; rate_J156 = compartment_c1*J156_J156_k*x[13]; rate_J157 = compartment_c1*J157_J157_k*x[15]; rate_J158 = compartment_c1*J158_J158_k*x[14]; rate_J159 = compartment_c1*J159_J159_k*x[16]; rate_J16 = compartment_c1*(J16_J16_k1*x[56]*x[51] - J16_J16_k2*x[52]); rate_J160 = compartment_c1*J160_J160_k*x[8]; rate_J161 = compartment_c1*J161_J161_k*x[10]; rate_J162 = compartment_c1*J162_J162_k*x[9]; rate_J163 = compartment_c1*J163_J163_k*x[11]; rate_J164 = compartment_c1*J164_J164_k*x[22]; rate_J165 = compartment_c1*(J165_J165_k1*x[42]*x[65] - J165_J165_k2*x[66]); rate_J166 = compartment_c1*(J166_J166_k1*x[42]*x[86] - J166_J166_k2*x[87]); rate_J167 = compartment_c1*J167_J167_k*x[87]; rate_J168 = compartment_c1*J168_J168_k*x[66]; rate_J17 = compartment_c1*J17_J17_k*x[52]; rate_J18 = compartment_c1*J18_J18_k*x[53]; rate_J19 = compartment_c1*J19_J19_k*x[81]; rate_J20 = compartment_c1*J20_J20_k*x[82]; rate_J21 = compartment_c1*J21_J21_k*x[52]; rate_J22 = compartment_c1*(J22_J22_k1*x[79]*x[49] - J22_J22_k2*x[34]); rate_J23 = compartment_c1*(J23_J23_k1*x[4]*x[34] - J23_J23_k2*x[35]); rate_J24 = compartment_c1*(J24_J24_k1*x[80]*x[49] - J24_J24_k2*x[35]); rate_J25 = compartment_c1*(J25_J25_k1*x[56]*x[35] - J25_J25_k2*x[36]); rate_J27 = compartment_c1*(J27_J27_k1*x[63]*x[34] - J27_J27_k2*x[36]); rate_J28 = compartment_c1*J28_J28_k*x[36]; rate_J29 = compartment_c1*J29_J29_k*x[37]; rate_J3 = compartment_c1*(J3_J3_k1*x[48]*x[33] - J3_J3_k2*x[49]); rate_J30 = J30_J30_k*x[34]; } public void __internalRateVarInitFunc_2(double time, double[] x) { rate_J31 = compartment_c1*(J31_J31_Vmax*x[25]*(x[4] + x[51] + x[80] + x[35] + x[63] + x[52] + x[81] + x[36] + x[28] + x[70] + x[20] + x[29] + x[21])/(J31_J31_Km1 + x[25])); rate_J32 = compartment_c1*J32_J32_k*x[79]; rate_J33 = compartment_c1*J33_J33_k*x[69]; rate_J34 = compartment_c1*(J34_J34_k1*x[18]*x[17] - J34_J34_k2*x[19]); rate_J35 = compartment_c1*(J35_J35_k1*x[4]*x[27] - J35_J35_k2*x[28]); rate_J36 = compartment_c1*(J36_J36_k1*x[4]*x[69] - J36_J36_k2*x[70]); rate_J37 = compartment_c1*J37_J37_k*x[28]; rate_J38 = compartment_c1*(J38_J38_k1*x[70]*x[19] - J38_J38_k2*x[20]); rate_J39 = compartment_c1*(J39_J39_k1*x[28]*x[56] - J39_J39_k2*x[29]); rate_J4 = compartment_c1*(J4_J4_k1*x[33]*x[77] - J4_J4_k2*x[78]); rate_J40 = compartment_c1*(J40_J40_k1*x[56]*x[70] - J40_J40_k2*x[71]); rate_J41 = compartment_c1*J41_J41_k*x[71]; rate_J42 = compartment_c1*J42_J42_k*x[29]; rate_J43 = compartment_c1*J43_J43_k*x[29]; rate_J44 = compartment_c1*(J44_J44_k1*x[71]*x[19] - J44_J44_k2*x[21]); rate_J45 = compartment_c1*J45_J45_k*x[21]; rate_J46 = compartment_c1*J46_J46_k*x[30]; rate_J47 = compartment_c1*J47_J47_k*x[72]; rate_J49 = compartment_c1*(J49_J49_k1*x[67]*x[45] - J49_J49_k2*x[68]); rate_J5 = compartment*(J5_J5_k1*x[2] - J5_J5_k2*x[4]); rate_J50 = compartment_c1*(J50_J50_Vmax*x[49]*x[65]/(J50_J50_Km1 + x[49])); rate_J51 = compartment_c1*(J51_J51_Vmax*x[48]*x[65]/(J51_J51_Km1 + x[48])); rate_J52 = compartment_c1*(J52_J52_k1*x[57]*x[47] - J52_J52_k2*x[58]); rate_J53 = compartment_c1*(J53_J53_k1*x[44]*x[6] - J53_J53_k2*x[7]); rate_J54 = compartment_c1*(J54_J54_k1*x[47]*x[6] - J54_J54_k2*x[12]); rate_J57 = J57_J57_Vmax*x[88]*_compartment_c1_PP2A_/(J57_J57_Km1 + x[88]); rate_J58 = compartment_c1*(J58_J58_Vmax*x[75]*_compartment_c1_PP2A_/(J58_J58_Km1 + x[75])); rate_J6 = compartment_c1*(J6_J6_k1*x[4]*x[56] - J6_J6_k2*x[63]); rate_J61 = compartment_c1*(J61_J61_Vmax*x[89]*_compartment_c1_PP2A_/(J61_J61_Km1 + x[89])); rate_J62 = compartment_c1*(J62_J62_Vmax*x[76]*_compartment_c1_PP2A_/(J62_J62_Km1 + x[76])); rate_J63 = compartment_c1*(J63_J63_k1*x[86]*x[86] - J63_J63_k2*x[65]); rate_J66 = compartment_c1*J66_J66_k*x[47]; rate_J67 = compartment_c1*J67_J67_k*x[44]; rate_J68 = compartment_c1*(J68_J68_Vmax*x[43]*(x[20] + x[21] + x[24])/(J68_J68_Km1 + x[43])); rate_J69 = compartment_c1*(J69_J69_Vmax*x[46]*(x[35] + x[36] + x[38])/(J69_J69_Km1 + x[46])); rate_J7 = compartment_c1*(J7_J7_k1*x[4]*x[79] - J7_J7_k2*x[80]); rate_J70 = compartment*(J70_J70_k1*_compartment_NGF_*x[5] - J70_J70_k2*x[3]); rate_J71 = compartment*J71_J71_k*x[3]; rate_J72 = compartment_c1*J72_J72_k*x[91]; rate_J73 = compartment_c1*J73_J73_k*x[85]; } public void __internalRateVarInitFunc_3(double time, double[] x) { rate_J74 = compartment_c1*J74_J74_k*x[91]; rate_J75 = compartment_c1*(J75_J75_k1*x[50]*x[91] - J75_J75_k2*x[54]); rate_J76 = compartment_c1*(J76_J76_k1*x[79]*x[91] - J76_J76_k2*x[83]); rate_J77 = compartment_c1*(J77_J77_k1*x[27]*x[91] - J77_J77_k2*x[31]); rate_J78 = compartment_c1*(J78_J78_k1*x[69]*x[91] - J78_J78_k2*x[73]); rate_J79 = compartment_c1*(J79_J79_k1*x[85]*x[50] - J79_J79_k2*x[55]); rate_J8 = compartment_c1*(J8_J8_k1*x[67] - J8_J8_k2*x[25]); rate_J80 = compartment_c1*(J80_J80_k1*x[85]*x[79] - J80_J80_k2*x[84]); rate_J81 = compartment_c1*J81_J81_k*x[55]; rate_J82 = compartment_c1*J82_J82_k*x[54]; rate_J83 = compartment_c1*J83_J83_k*x[31]; rate_J84 = compartment_c1*(J84_J84_k1*x[85]*x[27] - J84_J84_k2*x[32]); rate_J85 = compartment_c1*(J85_J85_k1*x[85]*x[69] - J85_J85_k2*x[74]); rate_J86 = compartment_c1*J86_J86_k*x[32]; rate_J87 = compartment_c1*J87_J87_k*x[31]; rate_J88 = compartment_c1*J88_J88_k*x[73]; rate_J89 = compartment_c1*J89_J89_k*x[54]; rate_J9 = compartment_c1*(J9_J9_k1*x[56]*x[80] - J9_J9_k2*x[81]); rate_J90 = compartment_c1*J90_J90_k*x[83]; rate_J92 = compartment_c1*J92_J92_k*x[32]; rate_J93 = compartment_c1*J93_J93_k*x[55]; rate_J94 = compartment_c1*J94_J94_k*x[84]; rate_J95 = compartment_c1*(J95_J95_k1*x[49]*x[84] - J95_J95_k2*x[39]); rate_J96 = compartment_c1*(J96_J96_k1*x[49]*x[83] - J96_J96_k2*x[38]); rate_J97 = compartment_c1*J97_J97_k*x[38]; rate_J98 = compartment_c1*J98_J98_k*x[23]; rate_J99 = compartment_c1*J99_J99_k*x[73]; rate_re1 = compartment*(re1_re1_k1*_compartment_c1_pro_EGFR_ - re1_re1_k2*x[0]); rate_re2 = compartment*(re2_re2_k1*_compartment_EGF_*x[0] - re2_re2_k2*x[1]); rate_re8 = compartment*(re8_re8_k1*x[1]*x[1] - re8_re8_k2*x[2]); } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _compartment_EGF_ = 0.001613; // initial value of $"compartment.EGF" _compartment_c1_PP2A_ = 0.24; // initial value of $"compartment.c1.PP2A" _compartment_c1_Rap1GAP_ = 0.012; // initial value of $"compartment.c1.Rap1GAP" _compartment_c1_pro_EGFR_ = 0.3; // initial value of $"compartment.c1.pro_EGFR" _compartment_c1_pro_TrkA_ = 0.020631; // initial value of $"compartment.c1.pro_TrkA" compartment = 1.0; // initial value of $compartment compartment_c1 = 1.0; // initial value of $compartment.c1 J100_J100_k = 6.3E-4; // initial value of J100_J100_k J101_J101_k = 6.3E-4; // initial value of J101_J101_k J102_J102_k = 6.3E-4; // initial value of J102_J102_k J103_J103_k1 = 1.0; // initial value of J103_J103_k1 J103_J103_k2 = 0.2; // initial value of J103_J103_k2 J104_J104_k1 = 1.0; // initial value of J104_J104_k1 J104_J104_k2 = 0.2; // initial value of J104_J104_k2 J105_J105_k1 = 10.0; // initial value of J105_J105_k1 J105_J105_k2 = 0.2; // initial value of J105_J105_k2 J106_J106_k1 = 10.0; // initial value of J106_J106_k1 J106_J106_k2 = 0.2; // initial value of J106_J106_k2 J107_J107_k = 0.0022; // initial value of J107_J107_k J108_J108_k = 4.2E-4; // initial value of J108_J108_k J109_J109_k = 0.0022; // initial value of J109_J109_k J10_J10_k = 0.0020; // initial value of J10_J10_k J110_J110_k = 4.2E-4; // initial value of J110_J110_k J112_J112_k = 4.2E-4; // initial value of J112_J112_k J113_J113_k1 = 8.333E-4; // initial value of J113_J113_k1 J113_J113_k2 = 2.7778E-4; // initial value of J113_J113_k2 J115_J115_k1 = 10.0; // initial value of J115_J115_k1 J115_J115_k2 = 0.2; // initial value of J115_J115_k2 J116_J116_k1 = 10.0; // initial value of J116_J116_k1 J116_J116_k2 = 0.2; // initial value of J116_J116_k2 J117_J117_k1 = 10.0; // initial value of J117_J117_k1 J117_J117_k2 = 0.2; // initial value of J117_J117_k2 J118_J118_k1 = 1.0; // initial value of J118_J118_k1 J118_J118_k2 = 0.2; // initial value of J118_J118_k2 J119_J119_k1 = 0.5; // initial value of J119_J119_k1 J119_J119_k2 = 0.2; // initial value of J119_J119_k2 J11_J11_k = 0.0020; // initial value of J11_J11_k J120_J120_k1 = 1.0; // initial value of J120_J120_k1 J120_J120_k2 = 0.2; // initial value of J120_J120_k2 J121_J121_Km1 = 1.0; // initial value of J121_J121_Km1 J121_J121_Vmax = 10.0; // initial value of J121_J121_Vmax J122_J122_Km1 = 1.0; // initial value of J122_J122_Km1 J122_J122_Vmax = 2.0; // initial value of J122_J122_Vmax J123_J123_Km1 = 0.1; // initial value of J123_J123_Km1 J123_J123_Vmax = 0.02; // initial value of J123_J123_Vmax J124_J124_Km1 = 25.641; // initial value of J124_J124_Km1 J124_J124_Vmax = 1.0; // initial value of J124_J124_Vmax J12_J12_k1 = 10.0; // initial value of J12_J12_k1 J12_J12_k2 = 0.2; // initial value of J12_J12_k2 J133_J133_k1 = 16.304; // initial value of J133_J133_k1 J133_J133_k2 = 0.6; // initial value of J133_J133_k2 J134_J134_k1 = 16.304; // initial value of J134_J134_k1 J134_J134_k2 = 0.6; // initial value of J134_J134_k2 J135_J135_k1 = 16.304; // initial value of J135_J135_k1 J135_J135_k2 = 0.6; // initial value of J135_J135_k2 J136_J136_k = 0.15; // initial value of J136_J136_k J137_J137_Km1 = 1.0; // initial value of J137_J137_Km1 J137_J137_Vmax = 10.0; // initial value of J137_J137_Vmax J138_J138_Km1 = 1.0; // initial value of J138_J138_Km1 J138_J138_Vmax = 10.0; // initial value of J138_J138_Vmax J139_J139_Km1 = 1.0; // initial value of J139_J139_Km1 J139_J139_Vmax = 2.0; // initial value of J139_J139_Vmax J13_J13_k = 1.0; // initial value of J13_J13_k J140_J140_k1 = 15.625; // initial value of J140_J140_k1 J140_J140_k2 = 2.0; // initial value of J140_J140_k2 J141_J141_k1 = 15.625; // initial value of J141_J141_k1 J141_J141_k2 = 2.0; // initial value of J141_J141_k2 J142_J142_k1 = 15.625; // initial value of J142_J142_k1 J142_J142_k2 = 2.0; // initial value of J142_J142_k2 J143_J143_k1 = 15.625; // initial value of J143_J143_k1 J143_J143_k2 = 2.0; // initial value of J143_J143_k2 J144_J144_k1 = 6.25; // initial value of J144_J144_k1 J144_J144_k2 = 0.8; // initial value of J144_J144_k2 J145_J145_k1 = 6.25; // initial value of J145_J145_k1 J145_J145_k2 = 0.8; // initial value of J145_J145_k2 J146_J146_k1 = 6.25; // initial value of J146_J146_k1 J146_J146_k2 = 0.8; // initial value of J146_J146_k2 J147_J147_k1 = 6.25; // initial value of J147_J147_k1 J147_J147_k2 = 0.8; // initial value of J147_J147_k2 J148_J148_k1 = 9.375; // initial value of J148_J148_k1 J148_J148_k2 = 1.2; // initial value of J148_J148_k2 J149_J149_k1 = 9.375; // initial value of J149_J149_k1 J149_J149_k2 = 1.2; // initial value of J149_J149_k2 J14_J14_k = 0.05; // initial value of J14_J14_k J150_J150_k1 = 9.375; // initial value of J150_J150_k1 J150_J150_k2 = 1.2; // initial value of J150_J150_k2 J151_J151_k1 = 9.375; // initial value of J151_J151_k1 J151_J151_k2 = 1.2; // initial value of J151_J151_k2 J152_J152_k = 0.5; // initial value of J152_J152_k J153_J153_k = 0.5; // initial value of J153_J153_k J154_J154_k = 0.5; // initial value of J154_J154_k J155_J155_k = 0.5; // initial value of J155_J155_k J156_J156_k = 0.2; // initial value of J156_J156_k J157_J157_k = 0.2; // initial value of J157_J157_k J158_J158_k = 0.2; // initial value of J158_J158_k J159_J159_k = 0.2; // initial value of J159_J159_k J15_J15_k = 0.0010; // initial value of J15_J15_k J160_J160_k = 0.3; // initial value of J160_J160_k J161_J161_k = 0.3; // initial value of J161_J161_k J162_J162_k = 0.3; // initial value of J162_J162_k J163_J163_k = 0.3; // initial value of J163_J163_k J164_J164_k = 0.0010; // initial value of J164_J164_k J165_J165_k1 = 15.0; // initial value of J165_J165_k1 J165_J165_k2 = 0.24; // initial value of J165_J165_k2 J166_J166_k1 = 15.0; // initial value of J166_J166_k1 J166_J166_k2 = 0.24; // initial value of J166_J166_k2 J167_J167_k = 0.06; // initial value of J167_J167_k J168_J168_k = 0.06; // initial value of J168_J168_k J16_J16_k1 = 0.5; // initial value of J16_J16_k1 J16_J16_k2 = 0.2; // initial value of J16_J16_k2 J17_J17_k = 0.05; // initial value of J17_J17_k J18_J18_k = 0.0010; // initial value of J18_J18_k J19_J19_k = 0.05; // initial value of J19_J19_k J20_J20_k = 0.0010; // initial value of J20_J20_k J21_J21_k = 1.0; // initial value of J21_J21_k J22_J22_k1 = 10.0; // initial value of J22_J22_k1 J22_J22_k2 = 0.2; // initial value of J22_J22_k2 J23_J23_k1 = 10.0; // initial value of J23_J23_k1 J23_J23_k2 = 0.2; // initial value of J23_J23_k2 J24_J24_k1 = 10.0; // initial value of J24_J24_k1 J24_J24_k2 = 0.2; // initial value of J24_J24_k2 J25_J25_k1 = 0.5; // initial value of J25_J25_k1 J25_J25_k2 = 0.2; // initial value of J25_J25_k2 J27_J27_k1 = 10.0; // initial value of J27_J27_k1 J27_J27_k2 = 0.2; // initial value of J27_J27_k2 J28_J28_k = 0.05; // initial value of J28_J28_k J29_J29_k = 0.0010; // initial value of J29_J29_k J30_J30_k = 0.0050; // initial value of J30_J30_k J31_J31_Km1 = 0.1; // initial value of J31_J31_Km1 J31_J31_Vmax = 0.2; // initial value of J31_J31_Vmax J32_J32_k = 0.0050; // initial value of J32_J32_k J33_J33_k = 0.0050; // initial value of J33_J33_k J34_J34_k1 = 1.0; // initial value of J34_J34_k1 J34_J34_k2 = 0.0020; // initial value of J34_J34_k2 J35_J35_k1 = 1.0; // initial value of J35_J35_k1 J35_J35_k2 = 0.2; // initial value of J35_J35_k2 J36_J36_k1 = 1.0; // initial value of J36_J36_k1 J36_J36_k2 = 0.2; // initial value of J36_J36_k2 J37_J37_k = 1.0; // initial value of J37_J37_k J38_J38_k1 = 1.0; // initial value of J38_J38_k1 J38_J38_k2 = 0.2; // initial value of J38_J38_k2 J39_J39_k1 = 0.5; // initial value of J39_J39_k1 J39_J39_k2 = 0.2; // initial value of J39_J39_k2 J3_J3_k1 = 0.03; // initial value of J3_J3_k1 J3_J3_k2 = 0.0168; // initial value of J3_J3_k2 J40_J40_k1 = 0.5; // initial value of J40_J40_k1 J40_J40_k2 = 0.2; // initial value of J40_J40_k2 J41_J41_k = 0.05; // initial value of J41_J41_k J42_J42_k = 0.05; // initial value of J42_J42_k J43_J43_k = 1.0; // initial value of J43_J43_k J44_J44_k1 = 1.0; // initial value of J44_J44_k1 J44_J44_k2 = 0.2; // initial value of J44_J44_k2 J45_J45_k = 0.05; // initial value of J45_J45_k J46_J46_k = 0.0010; // initial value of J46_J46_k J47_J47_k = 0.0010; // initial value of J47_J47_k J49_J49_k1 = 0.12; // initial value of J49_J49_k1 J49_J49_k2 = 0.01; // initial value of J49_J49_k2 J4_J4_k1 = 0.03; // initial value of J4_J4_k1 J4_J4_k2 = 0.0168; // initial value of J4_J4_k2 J50_J50_Km1 = 25.641; // initial value of J50_J50_Km1 J50_J50_Vmax = 1.0; // initial value of J50_J50_Vmax J51_J51_Km1 = 25.641; // initial value of J51_J51_Km1 J51_J51_Vmax = 1.0; // initial value of J51_J51_Vmax J52_J52_k1 = 60.0; // initial value of J52_J52_k1 J52_J52_k2 = 0.5; // initial value of J52_J52_k2 J53_J53_k1 = 60.0; // initial value of J53_J53_k1 J53_J53_k2 = 0.5; // initial value of J53_J53_k2 J54_J54_k1 = 60.0; // initial value of J54_J54_k1 J54_J54_k2 = 0.5; // initial value of J54_J54_k2 J57_J57_Km1 = 15.657; // initial value of J57_J57_Km1 J57_J57_Vmax = 3.0; // initial value of J57_J57_Vmax J58_J58_Km1 = 15.657; // initial value of J58_J58_Km1 J58_J58_Vmax = 3.0; // initial value of J58_J58_Vmax J5_J5_k1 = 4.0; // initial value of J5_J5_k1 J5_J5_k2 = 0.0010; // initial value of J5_J5_k2 J61_J61_Km1 = 15.657; // initial value of J61_J61_Km1 J61_J61_Vmax = 3.0; // initial value of J61_J61_Vmax J62_J62_Km1 = 15.657; // initial value of J62_J62_Km1 J62_J62_Vmax = 3.0; // initial value of J62_J62_Vmax J63_J63_k1 = 10.0; // initial value of J63_J63_k1 J63_J63_k2 = 0.075; // initial value of J63_J63_k2 J66_J66_k = 1.667E-4; // initial value of J66_J66_k J67_J67_k = 1.166E-4; // initial value of J67_J67_k J68_J68_Km1 = 0.01; // initial value of J68_J68_Km1 J68_J68_Vmax = 0.024; // initial value of J68_J68_Vmax J69_J69_Km1 = 0.02; // initial value of J69_J69_Km1 J69_J69_Vmax = 2.0; // initial value of J69_J69_Vmax J6_J6_k1 = 0.5; // initial value of J6_J6_k1 J6_J6_k2 = 0.2; // initial value of J6_J6_k2 J70_J70_k1 = 6.2; // initial value of J70_J70_k1 J70_J70_k2 = 6.4E-5; // initial value of J70_J70_k2 J71_J71_k = 1.0; // initial value of J71_J71_k J72_J72_k = 6.3E-4; // initial value of J72_J72_k J73_J73_k = 4.2E-4; // initial value of J73_J73_k J74_J74_k = 0.0022; // initial value of J74_J74_k J75_J75_k1 = 10.0; // initial value of J75_J75_k1 J75_J75_k2 = 0.2; // initial value of J75_J75_k2 J76_J76_k1 = 10.0; // initial value of J76_J76_k1 J76_J76_k2 = 0.2; // initial value of J76_J76_k2 J77_J77_k1 = 5.0; // initial value of J77_J77_k1 J77_J77_k2 = 0.1; // initial value of J77_J77_k2 J78_J78_k1 = 5.0; // initial value of J78_J78_k1 J78_J78_k2 = 0.1; // initial value of J78_J78_k2 J79_J79_k1 = 10.0; // initial value of J79_J79_k1 J79_J79_k2 = 0.2; // initial value of J79_J79_k2 J7_J7_k1 = 10.0; // initial value of J7_J7_k1 J7_J7_k2 = 0.2; // initial value of J7_J7_k2 J80_J80_k1 = 10.0; // initial value of J80_J80_k1 J80_J80_k2 = 0.2; // initial value of J80_J80_k2 J81_J81_k = 0.1; // initial value of J81_J81_k J82_J82_k = 0.1; // initial value of J82_J82_k J83_J83_k = 2.0; // initial value of J83_J83_k J84_J84_k1 = 5.0; // initial value of J84_J84_k1 J84_J84_k2 = 0.1; // initial value of J84_J84_k2 J85_J85_k1 = 5.0; // initial value of J85_J85_k1 J85_J85_k2 = 0.1; // initial value of J85_J85_k2 J86_J86_k = 2.0; // initial value of J86_J86_k J87_J87_k = 0.0022; // initial value of J87_J87_k J88_J88_k = 0.0022; // initial value of J88_J88_k J89_J89_k = 0.0022; // initial value of J89_J89_k J8_J8_k1 = 0.0020; // initial value of J8_J8_k1 J8_J8_k2 = 1.0E-5; // initial value of J8_J8_k2 J90_J90_k = 0.0022; // initial value of J90_J90_k J92_J92_k = 4.2E-4; // initial value of J92_J92_k J93_J93_k = 4.2E-4; // initial value of J93_J93_k J94_J94_k = 4.2E-4; // initial value of J94_J94_k J95_J95_k1 = 10.0; // initial value of J95_J95_k1 J95_J95_k2 = 0.2; // initial value of J95_J95_k2 J96_J96_k1 = 10.0; // initial value of J96_J96_k1 J96_J96_k2 = 0.2; // initial value of J96_J96_k2 J97_J97_k = 6.3E-4; // initial value of J97_J97_k J98_J98_k = 6.3E-4; // initial value of J98_J98_k J99_J99_k = 6.3E-4; // initial value of J99_J99_k J9_J9_k1 = 0.5; // initial value of J9_J9_k1 J9_J9_k2 = 0.2; // initial value of J9_J9_k2 re1_re1_k1 = 1.0E-4; // initial value of re1_re1_k1 re1_re1_k2 = 1.0E-4; // initial value of re1_re1_k2 re2_re2_k1 = 2.2833; // initial value of re2_re2_k1 re2_re2_k2 = 0.0029666; // initial value of re2_re2_k2 re8_re8_k1 = 10.0; // initial value of re8_re8_k1 re8_re8_k2 = 0.02; // initial value of re8_re8_k2 } /* * Model variables initial values */ protected double _compartment_EGF_; protected double _compartment_NGF_; protected double _compartment_c1_PP2A_; protected double _compartment_c1_Rap1GAP_; protected double _compartment_c1_degradation_; protected double _compartment_c1_pro_EGFR_; protected double _compartment_c1_pro_TrkA_; protected double rate_J10; protected double rate_J100; protected double rate_J101; protected double rate_J102; protected double rate_J103; protected double rate_J104; protected double rate_J105; protected double rate_J106; protected double rate_J107; protected double rate_J108; protected double rate_J109; protected double rate_J11; protected double rate_J110; protected double rate_J112; protected double rate_J113; protected double rate_J115; protected double rate_J116; protected double rate_J117; protected double rate_J118; protected double rate_J119; protected double rate_J12; protected double rate_J120; protected double rate_J121; protected double rate_J122; protected double rate_J123; protected double rate_J124; protected double rate_J13; protected double rate_J133; protected double rate_J134; protected double rate_J135; protected double rate_J136; protected double rate_J137; protected double rate_J138; protected double rate_J139; protected double rate_J14; protected double rate_J140; protected double rate_J141; protected double rate_J142; protected double rate_J143; protected double rate_J144; protected double rate_J145; protected double rate_J146; protected double rate_J147; protected double rate_J148; protected double rate_J149; protected double rate_J15; protected double rate_J150; protected double rate_J151; protected double rate_J152; protected double rate_J153; protected double rate_J154; protected double rate_J155; protected double rate_J156; protected double rate_J157; protected double rate_J158; protected double rate_J159; protected double rate_J16; protected double rate_J160; protected double rate_J161; protected double rate_J162; protected double rate_J163; protected double rate_J164; protected double rate_J165; protected double rate_J166; protected double rate_J167; protected double rate_J168; protected double rate_J17; protected double rate_J18; protected double rate_J19; protected double rate_J20; protected double rate_J21; protected double rate_J22; protected double rate_J23; protected double rate_J24; protected double rate_J25; protected double rate_J27; protected double rate_J28; protected double rate_J29; protected double rate_J3; protected double rate_J30; protected double rate_J31; protected double rate_J32; protected double rate_J33; protected double rate_J34; protected double rate_J35; protected double rate_J36; protected double rate_J37; protected double rate_J38; protected double rate_J39; protected double rate_J4; protected double rate_J40; protected double rate_J41; protected double rate_J42; protected double rate_J43; protected double rate_J44; protected double rate_J45; protected double rate_J46; protected double rate_J47; protected double rate_J49; protected double rate_J5; protected double rate_J50; protected double rate_J51; protected double rate_J52; protected double rate_J53; protected double rate_J54; protected double rate_J57; protected double rate_J58; protected double rate_J6; protected double rate_J61; protected double rate_J62; protected double rate_J63; protected double rate_J66; protected double rate_J67; protected double rate_J68; protected double rate_J69; protected double rate_J7; protected double rate_J70; protected double rate_J71; protected double rate_J72; protected double rate_J73; protected double rate_J74; protected double rate_J75; protected double rate_J76; protected double rate_J77; protected double rate_J78; protected double rate_J79; protected double rate_J8; protected double rate_J80; protected double rate_J81; protected double rate_J82; protected double rate_J83; protected double rate_J84; protected double rate_J85; protected double rate_J86; protected double rate_J87; protected double rate_J88; protected double rate_J89; protected double rate_J9; protected double rate_J90; protected double rate_J92; protected double rate_J93; protected double rate_J94; protected double rate_J95; protected double rate_J96; protected double rate_J97; protected double rate_J98; protected double rate_J99; protected double rate_re1; protected double rate_re2; protected double rate_re8; protected double compartment; protected double compartment_c1; protected double J100_J100_k; protected double J101_J101_k; protected double J102_J102_k; protected double J103_J103_k1; protected double J103_J103_k2; protected double J104_J104_k1; protected double J104_J104_k2; protected double J105_J105_k1; protected double J105_J105_k2; protected double J106_J106_k1; protected double J106_J106_k2; protected double J107_J107_k; protected double J108_J108_k; protected double J109_J109_k; protected double J10_J10_k; protected double J110_J110_k; protected double J112_J112_k; protected double J113_J113_k1; protected double J113_J113_k2; protected double J115_J115_k1; protected double J115_J115_k2; protected double J116_J116_k1; protected double J116_J116_k2; protected double J117_J117_k1; protected double J117_J117_k2; protected double J118_J118_k1; protected double J118_J118_k2; protected double J119_J119_k1; protected double J119_J119_k2; protected double J11_J11_k; protected double J120_J120_k1; protected double J120_J120_k2; protected double J121_J121_Km1; protected double J121_J121_Vmax; protected double J122_J122_Km1; protected double J122_J122_Vmax; protected double J123_J123_Km1; protected double J123_J123_Vmax; protected double J124_J124_Km1; protected double J124_J124_Vmax; protected double J12_J12_k1; protected double J12_J12_k2; protected double J133_J133_k1; protected double J133_J133_k2; protected double J134_J134_k1; protected double J134_J134_k2; protected double J135_J135_k1; protected double J135_J135_k2; protected double J136_J136_k; protected double J137_J137_Km1; protected double J137_J137_Vmax; protected double J138_J138_Km1; protected double J138_J138_Vmax; protected double J139_J139_Km1; protected double J139_J139_Vmax; protected double J13_J13_k; protected double J140_J140_k1; protected double J140_J140_k2; protected double J141_J141_k1; protected double J141_J141_k2; protected double J142_J142_k1; protected double J142_J142_k2; protected double J143_J143_k1; protected double J143_J143_k2; protected double J144_J144_k1; protected double J144_J144_k2; protected double J145_J145_k1; protected double J145_J145_k2; protected double J146_J146_k1; protected double J146_J146_k2; protected double J147_J147_k1; protected double J147_J147_k2; protected double J148_J148_k1; protected double J148_J148_k2; protected double J149_J149_k1; protected double J149_J149_k2; protected double J14_J14_k; protected double J150_J150_k1; protected double J150_J150_k2; protected double J151_J151_k1; protected double J151_J151_k2; protected double J152_J152_k; protected double J153_J153_k; protected double J154_J154_k; protected double J155_J155_k; protected double J156_J156_k; protected double J157_J157_k; protected double J158_J158_k; protected double J159_J159_k; protected double J15_J15_k; protected double J160_J160_k; protected double J161_J161_k; protected double J162_J162_k; protected double J163_J163_k; protected double J164_J164_k; protected double J165_J165_k1; protected double J165_J165_k2; protected double J166_J166_k1; protected double J166_J166_k2; protected double J167_J167_k; protected double J168_J168_k; protected double J16_J16_k1; protected double J16_J16_k2; protected double J17_J17_k; protected double J18_J18_k; protected double J19_J19_k; protected double J20_J20_k; protected double J21_J21_k; protected double J22_J22_k1; protected double J22_J22_k2; protected double J23_J23_k1; protected double J23_J23_k2; protected double J24_J24_k1; protected double J24_J24_k2; protected double J25_J25_k1; protected double J25_J25_k2; protected double J27_J27_k1; protected double J27_J27_k2; protected double J28_J28_k; protected double J29_J29_k; protected double J30_J30_k; protected double J31_J31_Km1; protected double J31_J31_Vmax; protected double J32_J32_k; protected double J33_J33_k; protected double J34_J34_k1; protected double J34_J34_k2; protected double J35_J35_k1; protected double J35_J35_k2; protected double J36_J36_k1; protected double J36_J36_k2; protected double J37_J37_k; protected double J38_J38_k1; protected double J38_J38_k2; protected double J39_J39_k1; protected double J39_J39_k2; protected double J3_J3_k1; protected double J3_J3_k2; protected double J40_J40_k1; protected double J40_J40_k2; protected double J41_J41_k; protected double J42_J42_k; protected double J43_J43_k; protected double J44_J44_k1; protected double J44_J44_k2; protected double J45_J45_k; protected double J46_J46_k; protected double J47_J47_k; protected double J49_J49_k1; protected double J49_J49_k2; protected double J4_J4_k1; protected double J4_J4_k2; protected double J50_J50_Km1; protected double J50_J50_Vmax; protected double J51_J51_Km1; protected double J51_J51_Vmax; protected double J52_J52_k1; protected double J52_J52_k2; protected double J53_J53_k1; protected double J53_J53_k2; protected double J54_J54_k1; protected double J54_J54_k2; protected double J57_J57_Km1; protected double J57_J57_Vmax; protected double J58_J58_Km1; protected double J58_J58_Vmax; protected double J5_J5_k1; protected double J5_J5_k2; protected double J61_J61_Km1; protected double J61_J61_Vmax; protected double J62_J62_Km1; protected double J62_J62_Vmax; protected double J63_J63_k1; protected double J63_J63_k2; protected double J66_J66_k; protected double J67_J67_k; protected double J68_J68_Km1; protected double J68_J68_Vmax; protected double J69_J69_Km1; protected double J69_J69_Vmax; protected double J6_J6_k1; protected double J6_J6_k2; protected double J70_J70_k1; protected double J70_J70_k2; protected double J71_J71_k; protected double J72_J72_k; protected double J73_J73_k; protected double J74_J74_k; protected double J75_J75_k1; protected double J75_J75_k2; protected double J76_J76_k1; protected double J76_J76_k2; protected double J77_J77_k1; protected double J77_J77_k2; protected double J78_J78_k1; protected double J78_J78_k2; protected double J79_J79_k1; protected double J79_J79_k2; protected double J7_J7_k1; protected double J7_J7_k2; protected double J80_J80_k1; protected double J80_J80_k2; protected double J81_J81_k; protected double J82_J82_k; protected double J83_J83_k; protected double J84_J84_k1; protected double J84_J84_k2; protected double J85_J85_k1; protected double J85_J85_k2; protected double J86_J86_k; protected double J87_J87_k; protected double J88_J88_k; protected double J89_J89_k; protected double J8_J8_k1; protected double J8_J8_k2; protected double J90_J90_k; protected double J92_J92_k; protected double J93_J93_k; protected double J94_J94_k; protected double J95_J95_k1; protected double J95_J95_k2; protected double J96_J96_k1; protected double J96_J96_k2; protected double J97_J97_k; protected double J98_J98_k; protected double J99_J99_k; protected double J9_J9_k1; protected double J9_J9_k2; protected double re1_re1_k1; protected double re1_re1_k2; protected double re2_re2_k1; protected double re2_re2_k2; protected double re8_re8_k1; protected double re8_re8_k2; public double[] extendResult(double time,double [] x) { this.time = time; double[] y = new double[92]; 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]; y[66] = x[66]; y[67] = x[67]; y[68] = x[68]; y[69] = x[69]; y[70] = x[70]; y[71] = x[71]; y[72] = x[72]; y[73] = x[73]; y[74] = x[74]; y[75] = x[75]; y[76] = x[76]; y[77] = x[77]; y[78] = x[78]; y[79] = x[79]; y[80] = x[80]; y[81] = x[81]; y[82] = x[82]; y[83] = x[83]; y[84] = x[84]; y[85] = x[85]; y[86] = x[86]; y[87] = x[87]; y[88] = x[88]; y[89] = x[89]; y[90] = x[90]; y[91] = x[91]; return y; } public double[] getInitialValues() { double [] x = new double[92]; this.time = 0.0; x[0] = 0.3; // - $"compartment.EGFR" x[1] = 0.0; // - $"compartment.L_EGFR" x[2] = 0.0; // - $"compartment.L_EGFR_dimer" x[3] = 0.0; // - $"compartment.L_NGFR" x[4] = 0.0; // - $"compartment.L_dpEGFR" x[5] = 0.061894; // - $"compartment.NGFR" x[6] = 0.2; // - $"compartment.c1.B_Raf" x[7] = 0.0; // - $"compartment.c1.B_Raf_Rap1_GTP" x[8] = 0.0; // - $"compartment.c1.B_Raf_Rap1_GTP_MEK" x[9] = 0.0; // - $"compartment.c1.B_Raf_Rap1_GTP_MEK_ERK" x[10] = 0.0; // - $"compartment.c1.B_Raf_Rap1_GTP_pMEK" x[11] = 0.0; // - $"compartment.c1.B_Raf_Rap1_GTP_pMEK_ERK" x[12] = 0.0; // - $"compartment.c1.B_Raf_Ras_GTP" x[13] = 0.0; // - $"compartment.c1.B_Raf_Ras_GTP_MEK" x[14] = 0.0; // - $"compartment.c1.B_Raf_Ras_GTP_MEK_ERK" x[15] = 0.0; // - $"compartment.c1.B_Raf_Ras_GTP_pMEK" x[16] = 0.0; // - $"compartment.c1.B_Raf_Ras_GTP_pMEK_ERK" x[17] = 0.5; // - $"compartment.c1.C3G" x[18] = 1.0; // - $"compartment.c1.Crk" x[19] = 0.0; // - $"compartment.c1.Crk_C3G" x[20] = 0.0; // - $"compartment.c1.Crk_C3G_pFRS2_dpEGFR" x[21] = 0.0; // - $"compartment.c1.Crk_C3G_pFRS2_dpEGFR_c_Cbl" x[22] = 0.0; // - $"compartment.c1.Crk_C3G_pFRS2_dpEGFR_c_Cbl_ubiq" x[23] = 0.0; // - $"compartment.c1.Crk_C3G_pFRS2_pTrkA" x[24] = 0.0; // - $"compartment.c1.Crk_C3G_pFRS2_pTrkA_endo" x[25] = 0.3; // - $"compartment.c1.Dok" x[26] = 0.26; // - $"compartment.c1.ERK" x[27] = 1.0; // - $"compartment.c1.FRS2" x[28] = 0.0; // - $"compartment.c1.FRS2_dpEGFR" x[29] = 0.0; // - $"compartment.c1.FRS2_dpEGFR_c_Cbl" x[30] = 0.0; // - $"compartment.c1.FRS2_dpEGFR_c_Cbl_ubiq" x[31] = 0.0; // - $"compartment.c1.FRS2_pTrkA" x[32] = 0.0; // - $"compartment.c1.FRS2_pTrkA_endo" x[33] = 1.0; // - $"compartment.c1.Grb2" x[34] = 0.0; // - $"compartment.c1.Grb2_SOS_pShc" x[35] = 0.0; // - $"compartment.c1.Grb2_SOS_pShc_dpEGFR" x[36] = 0.0; // - $"compartment.c1.Grb2_SOS_pShc_dpEGFR_c_Cbl" x[37] = 0.0; // - $"compartment.c1.Grb2_SOS_pShc_dpEGFR_c_Cbl_ubiq" x[38] = 0.0; // - $"compartment.c1.Grb2_SOS_pShc_pTrkA" x[39] = 0.0; // - $"compartment.c1.Grb2_SOS_pShc_pTrkA_endo" x[40] = 0.68; // - $"compartment.c1.MEK" x[41] = 0.0; // - $"compartment.c1.MEK_ERK" x[42] = 0.018; // - $"compartment.c1.MKP3" x[43] = 0.2; // - $"compartment.c1.Rap1_GDP" x[44] = 0.0; // - $"compartment.c1.Rap1_GTP" x[45] = 0.1; // - $"compartment.c1.RasGAP" x[46] = 0.1; // - $"compartment.c1.Ras_GDP" x[47] = 0.0; // - $"compartment.c1.Ras_GTP" x[48] = 0.1; // - $"compartment.c1.SOS" x[49] = 0.0; // - $"compartment.c1.SOS_Grb2" x[50] = 1.0; // - $"compartment.c1.Shc" x[51] = 0.0; // - $"compartment.c1.Shc_dpEGFR" x[52] = 0.0; // - $"compartment.c1.Shc_dpEGFR_c_Cbl" x[53] = 0.0; // - $"compartment.c1.Shc_dpEGFR_c_Cbl_ubiq" x[54] = 0.0; // - $"compartment.c1.Shc_pTrkA" x[55] = 0.0; // - $"compartment.c1.Shc_pTrkA_endo" x[56] = 0.5; // - $"compartment.c1.c_Cbl" x[57] = 0.5; // - $"compartment.c1.c_Raf" x[58] = 0.0; // - $"compartment.c1.c_Raf_Ras_GTP" x[59] = 0.0; // - $"compartment.c1.c_Raf_Ras_GTP_MEK" x[60] = 0.0; // - $"compartment.c1.c_Raf_Ras_GTP_MEK_ERK" x[61] = 0.0; // - $"compartment.c1.c_Raf_Ras_GTP_pMEK" x[62] = 0.0; // - $"compartment.c1.c_Raf_Ras_GTP_pMEK_ERK" x[63] = 0.0; // - $"compartment.c1.dpEGFR_c_Cbl" x[64] = 0.0; // - $"compartment.c1.dpEGFR_c_Cbl_ubiq" x[65] = 0.0; // - $"compartment.c1.dppERK" x[66] = 0.0; // - $"compartment.c1.dppERK_MKP3" x[67] = 0.0; // - $"compartment.c1.pDok" x[68] = 0.0; // - $"compartment.c1.pDok_RasGAP" x[69] = 0.0; // - $"compartment.c1.pFRS2" x[70] = 0.0; // - $"compartment.c1.pFRS2_dpEGFR" x[71] = 0.0; // - $"compartment.c1.pFRS2_dpEGFR_c_Cbl" x[72] = 0.0; // - $"compartment.c1.pFRS2_dpEGFR_c_Cbl_ubiq" x[73] = 0.0; // - $"compartment.c1.pFRS2_pTrkA" x[74] = 0.0; // - $"compartment.c1.pFRS2_pTrkA_endo" x[75] = 0.0; // - $"compartment.c1.pMEK" x[76] = 0.0; // - $"compartment.c1.pMEK_ERK" x[77] = 0.0; // - $"compartment.c1.pSOS" x[78] = 0.0; // - $"compartment.c1.pSOS_Grb2" x[79] = 0.0; // - $"compartment.c1.pShc" x[80] = 0.0; // - $"compartment.c1.pShc_dpEGFR" x[81] = 0.0; // - $"compartment.c1.pShc_dpEGFR_c_Cbl" x[82] = 0.0; // - $"compartment.c1.pShc_dpEGFR_c_Cbl_ubiq" x[83] = 0.0; // - $"compartment.c1.pShc_pTrkA" x[84] = 0.0; // - $"compartment.c1.pShc_pTrkA_endo" x[85] = 0.0; // - $"compartment.c1.pTrkA_endo" x[86] = 0.0; // - $"compartment.c1.ppERK" x[87] = 0.0; // - $"compartment.c1.ppERK_MKP3" x[88] = 0.0; // - $"compartment.c1.ppMEK" x[89] = 0.0; // - $"compartment.c1.ppMEK_ERK" x[90] = 0.0; // - $"compartment.c1.proteosome" x[91] = 0.0; // - $"compartment.pTrkA" __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) { __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); __internalRateVarInitFunc_2(time, x); __internalRateVarInitFunc_3(time, x); } /* * calculate dy/dt for 'BIOMD0000000049.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = +rate_re1-rate_re2; result[1] = +rate_re2-rate_re8*2; result[2] = -rate_J5+rate_re8; result[3] = +rate_J70-rate_J71; result[4] = -rate_J12-rate_J23-rate_J35-rate_J36+rate_J5-rate_J6-rate_J7; result[5] = +rate_J113-rate_J70; result[6] = +rate_J138+rate_J139-rate_J53-rate_J54; result[7] = -rate_J139-rate_J148-rate_J149-rate_J150-rate_J151+rate_J160+rate_J161+rate_J162+rate_J163+rate_J53; result[8] = +rate_J148-rate_J160; result[9] = +rate_J150-rate_J162; result[10] = +rate_J149-rate_J161; result[11] = +rate_J151-rate_J163; result[12] = -rate_J138-rate_J144-rate_J145-rate_J146-rate_J147+rate_J156+rate_J157+rate_J158+rate_J159+rate_J54; result[13] = +rate_J144-rate_J156; result[14] = +rate_J146-rate_J158; result[15] = +rate_J145-rate_J157; result[16] = +rate_J147-rate_J159; result[17] = -rate_J34; result[18] = -rate_J34; result[19] = -rate_J103-rate_J104+rate_J107+rate_J108+rate_J164+rate_J34-rate_J38-rate_J44; result[20] = -rate_J119+rate_J38; result[21] = +rate_J119+rate_J44-rate_J45; result[22] = -rate_J164+rate_J45; result[23] = +rate_J103-rate_J107-rate_J98; result[24] = +rate_J104-rate_J108+rate_J98; result[25] = -rate_J123-rate_J31+rate_J8; result[26] = -rate_J133-rate_J134-rate_J135+rate_J167+rate_J168; result[27] = -rate_J118+rate_J33-rate_J35+rate_J46-rate_J77-rate_J84+rate_J87+rate_J92; result[28] = +rate_J35-rate_J37-rate_J39; result[29] = +rate_J118+rate_J39-rate_J42-rate_J43; result[30] = +rate_J42-rate_J46; result[31] = -rate_J100+rate_J77-rate_J83-rate_J87; result[32] = +rate_J100+rate_J84-rate_J86-rate_J92; result[33] = -rate_J3-rate_J4; result[34] = -rate_J105-rate_J106+rate_J109+rate_J110-rate_J124+rate_J22-rate_J23-rate_J27+rate_J29-rate_J30; result[35] = +rate_J23+rate_J24-rate_J25; result[36] = +rate_J117+rate_J25+rate_J27-rate_J28; result[37] = +rate_J28-rate_J29; result[38] = +rate_J105-rate_J109+rate_J96-rate_J97; result[39] = +rate_J106-rate_J110+rate_J95+rate_J97; result[40] = -rate_J133-rate_J140-rate_J144-rate_J148+rate_J58; result[41] = +rate_J133-rate_J142-rate_J146-rate_J150+rate_J62; result[42] = -rate_J165-rate_J166+rate_J167+rate_J168; result[43] = +rate_J122+rate_J139+rate_J67-rate_J68; result[44] = -rate_J122-rate_J53-rate_J67+rate_J68; result[45] = -rate_J49; result[46] = +rate_J121+rate_J137+rate_J138+rate_J66-rate_J69; result[47] = -rate_J121-rate_J52-rate_J54-rate_J66+rate_J69; result[48] = +rate_J10-rate_J3-rate_J51; result[49] = -rate_J117+rate_J11-rate_J22-rate_J24+rate_J30+rate_J3-rate_J50-rate_J95-rate_J96; result[50] = -rate_J115-rate_J12+rate_J18+rate_J30+rate_J32-rate_J75-rate_J79+rate_J89+rate_J93; result[51] = +rate_J12-rate_J13-rate_J16; result[52] = +rate_J115+rate_J16-rate_J17-rate_J21; result[53] = +rate_J17-rate_J18; result[54] = -rate_J102+rate_J75-rate_J82-rate_J89; result[55] = +rate_J102+rate_J79-rate_J81-rate_J93; result[56] = -rate_J119+rate_J15+rate_J164-rate_J16+rate_J18+rate_J20-rate_J25+rate_J29-rate_J39-rate_J40+rate_J46+rate_J47-rate_J6-rate_J9; result[57] = +rate_J137-rate_J52; result[58] = -rate_J137-rate_J140-rate_J141-rate_J142-rate_J143+rate_J152+rate_J153+rate_J154+rate_J155+rate_J52; result[59] = +rate_J140-rate_J152; result[60] = +rate_J142-rate_J154; result[61] = +rate_J141-rate_J153; result[62] = +rate_J143-rate_J155; result[63] = -rate_J115-rate_J116-rate_J118-rate_J120-rate_J14-rate_J27+rate_J6; result[64] = +rate_J14-rate_J15; result[65] = -rate_J165+rate_J63; result[66] = +rate_J165-rate_J168; result[67] = +rate_J123+rate_J31-rate_J49-rate_J8; result[68] = +rate_J49; result[69] = +rate_J107+rate_J108+rate_J112-rate_J120+rate_J164-rate_J33-rate_J36+rate_J47-rate_J78-rate_J85+rate_J88; result[70] = +rate_J36+rate_J37-rate_J38-rate_J40; result[71] = +rate_J120+rate_J40-rate_J41+rate_J43-rate_J44; result[72] = +rate_J41-rate_J47; result[73] = -rate_J103+rate_J78+rate_J83-rate_J88-rate_J99; result[74] = -rate_J104-rate_J112+rate_J85+rate_J86+rate_J99; result[75] = -rate_J134-rate_J141-rate_J145-rate_J149+rate_J152+rate_J156+rate_J160+rate_J57-rate_J58; result[76] = +rate_J134-rate_J143-rate_J147-rate_J151+rate_J154+rate_J158+rate_J162+rate_J61-rate_J62; result[77] = -rate_J10-rate_J4+rate_J51; result[78] = -rate_J11+rate_J124+rate_J4+rate_J50; result[79] = -rate_J116+rate_J124+rate_J20-rate_J22-rate_J32-rate_J76-rate_J7-rate_J80+rate_J90+rate_J94; result[80] = +rate_J13-rate_J24+rate_J7-rate_J9; result[81] = +rate_J116-rate_J117-rate_J19+rate_J21+rate_J9; result[82] = +rate_J19-rate_J20; result[83] = -rate_J101+rate_J76+rate_J82-rate_J90-rate_J96; result[84] = +rate_J101+rate_J80+rate_J81-rate_J94-rate_J95; result[85] = -rate_J106+rate_J72-rate_J73-rate_J79-rate_J80-rate_J84-rate_J85; result[86] = +rate_J136-rate_J166+rate_J168-rate_J63*2; result[87] = +rate_J166-rate_J167; result[88] = -rate_J135+rate_J136+rate_J153+rate_J157+rate_J161-rate_J57; result[89] = +rate_J135-rate_J136+rate_J155+rate_J159+rate_J163-rate_J61; result[90] = +rate_J15+rate_J18+rate_J20+rate_J29+rate_J46+rate_J47; result[91] = -rate_J105+rate_J71-rate_J72-rate_J74-rate_J75-rate_J76-rate_J77-rate_J78; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[92]; __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 ...