/* * This code is generated by BioUML FrameWork * for BIOMD0000000056.xml diagram at 2008.03.20 15:04:41 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000056 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ private void __internalVarInitFunc_0(double time, double[] x) { _cell_0_BCK2_1_ = b0_75*_cell_0_MASS_37_; Vaiep_59 = kaiep_128*x[14]; Vacdh_58 = kacdh_126 + kacdh_127*x[5]; Vicdh_67 = kicdh_174 + kicdh_175*(eicdhn3_97*_cell_0_CLN3_25_ + eicdhn2_96*x[16] + eicdhb5_95*x[15] + eicdhb2_94*x[14]); Vkpnet_71 = (kkpnet_181 + kkpnet_182*x[6])*_cell_0_MASS_37_; Vppnet_74 = kppnet_185 + kppnet_186*x[29]; Vasbf_60 = kasbf_132*(esbfn2_101*x[16] + esbfn3_102*(_cell_0_CLN3_25_ + _cell_0_BCK2_1_) + esbfb5_100*x[15]); _cell_0_SBF_49_ = GK_219(Vasbf_60, Visbf_68, Jasbf_109, Jisbf_116); _cell_0_MCM1_38_ = GK_219(kamcm_129*x[14], kimcm_177, Jamcm_108, Jimcm_115); mu_39 = 0.6931471805599453/mdt_216; D_26 = 1.026/mu_39 - 32.0; Visbf_68 = kisbf_178 + kisbf_179*x[14]; F_28 = Math.exp(-mu_39*D_26); Vd2c1_61 = kd2c1_144*(ec1n3_88*_cell_0_CLN3_25_ + ec1k2_86*_cell_0_BCK2_1_ + ec1n2_87*x[16] + ec1b5_85*x[15] + ec1b2_84*x[14]); Vd2f6_62 = kd2f6_145*(ef6n3_93*_cell_0_CLN3_25_ + ef6k2_91*_cell_0_BCK2_1_ + ef6n2_92*x[16] + ef6b5_90*x[15] + ef6b2_89*x[14]); Vkpc1_69 = kd1c1_140 + Vd2c1_61/(Jd2c1_111 + x[33] + x[2] + x[4] + x[32] + x[1] + x[3]); Vkpf6_70 = kd1f6_141 + Vd2f6_62/(Jd2f6_112 + x[11] + x[19] + x[21] + x[10] + x[18] + x[20]); Vdb2_63 = kdb_150 + kdb_151*x[12] + kdb2p_152*x[8]; Vdb5_64 = kdb_153 + kdb_154*x[8]; Vdpds_65 = kdpds_142 + kdpds_146*x[8] + kdpds_149*x[12]; Vdppx_66 = kdppx_167 + kdppx_168*(J20ppx_105 + x[8])*Jpds_119/(Jpds_119 + x[27]); _cell_0_CLB2T_21_ = x[14] + x[2] + x[1] + x[19] + x[18]; _cell_0_CLN3_25_ = C0_78*Dn3_80*_cell_0_MASS_37_/(Jn3_118 + Dn3_80*_cell_0_MASS_37_); _cell_0_CLB5T_23_ = x[15] + x[4] + x[3] + x[21] + x[20]; _cell_0_CDC14T_9_ = x[5] + x[31] + x[30]; _cell_0_NET1T_42_ = x[25] + x[24] + x[31] + x[30]; _cell_0_SIC1T_52_ = x[33] + x[2] + x[4] + x[32] + x[1] + x[3]; _cell_0_CDC6T_16_ = x[11] + x[19] + x[21] + x[10] + x[18] + x[20]; _cell_0_CKIT_19_ = _cell_0_SIC1T_52_ + _cell_0_CDC6T_16_; Vppc1_72 = kppc1_183*x[5]; Vppf6_73 = kppf6_184*x[5]; } /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_Activation_282 = MichaelisMenten_220(Vacdh_58, Jacdh_106, 1.0, x[13]); rate_ActivationofCDC_278 = Mass_Action_1_222(ka_124 + ka_125*x[22], x[9]); rate_ActivationofIEP_273 = MichaelisMenten_220(Vaiep_59, Jaiep_107, 1.0, x[23]); rate_ActivationofSWI_271 = Mass_Action_1_222(kaswi_138*x[5], x[35]); rate_AssocofCLBandSIC_236 = Mass_Action_2_221(kasb2_130, x[14], x[33]); rate_AssocofCLBandSIC_238 = Mass_Action_2_221(kasb5_131, x[15], x[33]); rate_AssocwithESPtoformPE_306 = Mass_Action_2_221(kasesp_133, x[27], x[17]); rate_AssocwithNETPtoformRENTP_287 = Mass_Action_2_221(kasrentp_137, x[5], x[24]); rate_AssocwithNETtoformRENT_285 = Mass_Action_2_221(kasrent_136, x[5], x[25]); rate_CDCactivation_301 = Mass_Action_1_222(ka_121*x[37] + ka_122*x[38] + ka15p_123*x[5], x[7]); rate_DegradationofCDCinRENTP_298 = Mass_Action_1_222(kd14_139, x[30]); rate_DegradationofCDCinRENT_297 = Mass_Action_1_222(kd14_139, x[31]); rate_DegradationofCLB_229 = Mass_Action_1_222(Vdb2_63, x[14]); rate_DegradationofCLB_231 = Mass_Action_1_222(Vdb5_64, x[15]); rate_DegradationofCLBinCP_248 = Mass_Action_1_222(Vdb2_63, x[1]); rate_DegradationofCLBinC_244 = Mass_Action_1_222(Vdb2_63, x[2]); rate_DegradationofCLN_227 = Mass_Action_1_222(kdn2_164, x[16]); rate_DegradationofNETPinRENTP_296 = Mass_Action_1_222(kdnet_165, x[30]); rate_DegradationofNETinRENT_295 = Mass_Action_1_222(kdnet_165, x[31]); rate_DegradationofPDSinPE_305 = Mass_Action_1_222(Vdpds_65, x[28]); rate_DegradationofSICinCP_246 = Mass_Action_1_222(kd3c1_147, x[1]); rate_DegradationofSWIP_270 = Mass_Action_1_222(kdswi_170, x[35]); rate_DegradationofSWI_269 = Mass_Action_1_222(kdswi_170, x[36]); rate_DegradationofactiveCDC_277 = Mass_Action_1_222(kd20_143, x[8]); rate_DegradationofinactiveCDC_276 = Mass_Action_1_222(kd20_143, x[9]); rate_DephosphorylationofCP_241 = Mass_Action_1_222(Vppc1_72, x[1]); rate_DephosphorylationofSIC_234 = Mass_Action_1_222(Vppc1_72, x[32]); rate_DissocfromRENP_288 = Mass_Action_1_222(kdirentp_163, x[30]); rate_DissocfromRENT_286 = Mass_Action_1_222(kdirent_162, x[31]); rate_DissocofCLBSIC_239 = Mass_Action_1_222(kdib5_158, x[4]); rate_DissocofCLBSICcomplex_237 = Mass_Action_1_222(kdib2_157, x[2]); rate_DissofromPE_307 = Mass_Action_1_222(kdiesp_159, x[28]); rate_FastDegradationofSICP_235 = Mass_Action_1_222(kd3c1_147, x[32]); rate_Inactivation_274_CDC20 = Mass_Action_1_222(_cell_0_MAD2_36_, x[8]); rate_Inactivation_274_CDH1 = MichaelisMenten_220(Vicdh_67, Jicdh_113, 1.0, x[12]); rate_Inactivation_274_IEP = MichaelisMenten_220(1.0, Jiiep_114, kiiep_176, x[22]); rate_InactivationofSWI_272 = Mass_Action_1_222(kiswi_180*x[14], x[36]); rate_NETphosphorylation_292 = Mass_Action_1_222(Vkpnet_71, x[25]); rate_PhosphorylationofC_240 = Mass_Action_1_222(Vkpc1_69, x[2]); rate_PhosphorylationofSIC_233 = Mass_Action_1_222(Vkpc1_69, x[33]); } public void __internalRateVarInitFunc_1(double time, double[] x) { rate_RENTphosphorylation_294 = Mass_Action_1_222(Vkpnet_71, x[31]); rate_TEMactivation_299 = MichaelisMenten_220(_cell_0_LTE1_35_, Jatem_110, 1.0, x[37]); rate__242 = Mass_Action_1_222(Vkpc1_69, x[4]); rate__243 = Mass_Action_1_222(Vppc1_72, x[3]); rate__245 = Mass_Action_1_222(Vdb5_64, x[4]); rate__247 = Mass_Action_1_222(kd3c1_147, x[3]); rate__249 = Mass_Action_1_222(Vdb5_64, x[3]); rate__251 = Mass_Action_1_222(Vkpf6_70, x[11]); rate__252 = Mass_Action_1_222(Vppf6_73, x[10]); rate__253 = Mass_Action_1_222(kd3f6_148, x[10]); rate__254 = Mass_Action_2_221(kasf2_134, x[14], x[11]); rate__255 = Mass_Action_1_222(kdif2_160, x[19]); rate__256 = Mass_Action_2_221(kasf5_135, x[15], x[11]); rate__257 = Mass_Action_1_222(kdif5_161, x[21]); rate__258 = Mass_Action_1_222(Vkpf6_70, x[19]); rate__259 = Mass_Action_1_222(Vppf6_73, x[18]); rate__260 = Mass_Action_1_222(Vkpf6_70, x[21]); rate__261 = Mass_Action_1_222(Vppf6_73, x[20]); rate__262 = Mass_Action_1_222(Vdb2_63, x[19]); rate__263 = Mass_Action_1_222(Vdb5_64, x[21]); rate__264 = Mass_Action_1_222(kd3f6_148, x[18]); rate__265 = Mass_Action_1_222(kd3f6_148, x[20]); rate__266 = Mass_Action_1_222(Vdb2_63, x[18]); rate__267 = Mass_Action_1_222(Vdb5_64, x[20]); rate__280 = Mass_Action_1_222(kdcdh_156, x[12]); rate__281 = Mass_Action_1_222(kdcdh_156, x[13]); rate__284 = Mass_Action_1_222(kd14_139, x[5]); rate__290 = Mass_Action_1_222(kdnet_165, x[25]); rate__291 = Mass_Action_1_222(kdnet_165, x[24]); rate__309 = Mass_Action_1_222(kdori_166, x[26]); rate__311 = Mass_Action_1_222(kdbud_155, x[0]); rate__313 = Mass_Action_1_222(kdspn_169, x[34]); rate_degradation_303_PDS1 = Mass_Action_1_222(Vdpds_65, x[27]); rate_degradation_303_PPX = Mass_Action_1_222(Vdppx_66, x[29]); rate_dephosphorylation_293_NET1P = Mass_Action_1_222(Vppnet_74, x[24]); rate_dephosphorylation_293_RENTP = Mass_Action_1_222(Vppnet_74, x[30]); rate_inactivation_300_CDC15 = Mass_Action_1_222(ki15_173, x[6]); rate_inactivation_300_TEM1GTP = MichaelisMenten_220(_cell_0_BUB2_2_, Jitem_117, 1.0, x[38]); } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _cell_0_BUB2_2_ = 0.2; // initial value of $"cell_0.BUB2_2" _cell_0_CDC14T_9_ = 2.0; // initial value of $"cell_0.CDC14T_9" _cell_0_CLB2T_21_ = 0.17; // initial value of $"cell_0.CLB2T_21" _cell_0_CLB5T_23_ = 0.12; // initial value of $"cell_0.CLB5T_23" _cell_0_LTE1_35_ = 0.1; // initial value of $"cell_0.LTE1_35" _cell_0_MAD2_36_ = 0.01; // initial value of $"cell_0.MAD2_36" _cell_0_MASS_37_ = 1.206019; // initial value of $"cell_0.MASS_37" _cell_0_NET1T_42_ = 2.8; // initial value of $"cell_0.NET1T_42" C0_78 = 0.4; // initial value of C0_78 CDC15T_79 = 1.0; // initial value of CDC15T_79 Dn3_80 = 1.0; // initial value of Dn3_80 ESP1T_103 = 1.0; // initial value of ESP1T_103 IET_104 = 1.0; // initial value of IET_104 J20ppx_105 = 0.15; // initial value of J20ppx_105 Jacdh_106 = 0.03; // initial value of Jacdh_106 Jaiep_107 = 0.1; // initial value of Jaiep_107 Jamcm_108 = 0.1; // initial value of Jamcm_108 Jasbf_109 = 0.01; // initial value of Jasbf_109 Jatem_110 = 0.1; // initial value of Jatem_110 Jd2c1_111 = 0.05; // initial value of Jd2c1_111 Jd2f6_112 = 0.05; // initial value of Jd2f6_112 Jicdh_113 = 0.03; // initial value of Jicdh_113 Jiiep_114 = 0.1; // initial value of Jiiep_114 Jimcm_115 = 0.1; // initial value of Jimcm_115 Jisbf_116 = 0.01; // initial value of Jisbf_116 Jitem_117 = 0.1; // initial value of Jitem_117 Jn3_118 = 6.0; // initial value of Jn3_118 Jpds_119 = 0.04; // initial value of Jpds_119 KEZ2_172 = 0.2; // initial value of KEZ2_172 KEZ_171 = 0.3; // initial value of KEZ_171 TEM1T_217 = 1.0; // initial value of TEM1T_217 b0_75 = 0.054; // initial value of b0_75 bub2h_76 = 1.0; // initial value of bub2h_76 bub2l_77 = 0.2; // initial value of bub2l_77 ec1b2_84 = 0.45; // initial value of ec1b2_84 ec1b5_85 = 0.1; // initial value of ec1b5_85 ec1k2_86 = 0.03; // initial value of ec1k2_86 ec1n2_87 = 0.06; // initial value of ec1n2_87 ec1n3_88 = 0.3; // initial value of ec1n3_88 ef6b2_89 = 0.55; // initial value of ef6b2_89 ef6b5_90 = 0.1; // initial value of ef6b5_90 ef6k2_91 = 0.03; // initial value of ef6k2_91 ef6n2_92 = 0.06; // initial value of ef6n2_92 ef6n3_93 = 0.3; // initial value of ef6n3_93 eicdhb2_94 = 1.2; // initial value of eicdhb2_94 eicdhb5_95 = 8.0; // initial value of eicdhb5_95 eicdhn2_96 = 0.4; // initial value of eicdhn2_96 eicdhn3_97 = 0.25; // initial value of eicdhn3_97 esbfb5_100 = 2.0; // initial value of esbfb5_100 esbfn2_101 = 2.0; // initial value of esbfn2_101 esbfn3_102 = 10.0; // initial value of esbfn3_102 ka15p_123 = 0.0010; // initial value of ka15p_123 ka_121 = 0.0020; // initial value of ka_121 ka_122 = 1.0; // initial value of ka_122 ka_124 = 0.05; // initial value of ka_124 ka_125 = 0.2; // initial value of ka_125 kacdh_126 = 0.01; // initial value of kacdh_126 kacdh_127 = 0.8; // initial value of kacdh_127 kaiep_128 = 0.1; // initial value of kaiep_128 kamcm_129 = 1.0; // initial value of kamcm_129 kasb2_130 = 50.0; // initial value of kasb2_130 kasb5_131 = 50.0; // initial value of kasb5_131 kasbf_132 = 0.38; // initial value of kasbf_132 kasesp_133 = 50.0; // initial value of kasesp_133 kasf2_134 = 15.0; // initial value of kasf2_134 kasf5_135 = 0.01; // initial value of kasf5_135 kasrent_136 = 200.0; // initial value of kasrent_136 kasrentp_137 = 1.0; // initial value of kasrentp_137 kaswi_138 = 2.0; // initial value of kaswi_138 kd14_139 = 0.1; // initial value of kd14_139 kd1c1_140 = 0.01; // initial value of kd1c1_140 kd1f6_141 = 0.01; // initial value of kd1f6_141 kd20_143 = 0.3; // initial value of kd20_143 kd2c1_144 = 1.0; // initial value of kd2c1_144 kd2f6_145 = 1.0; // initial value of kd2f6_145 kd3c1_147 = 1.0; // initial value of kd3c1_147 kd3f6_148 = 1.0; // initial value of kd3f6_148 kdb2p_152 = 0.15; // initial value of kdb2p_152 kdb_150 = 0.0030; // initial value of kdb_150 kdb_151 = 0.4; // initial value of kdb_151 kdb_153 = 0.01; // initial value of kdb_153 kdb_154 = 0.16; // initial value of kdb_154 kdbud_155 = 0.06; // initial value of kdbud_155 kdcdh_156 = 0.01; // initial value of kdcdh_156 kdib2_157 = 0.05; // initial value of kdib2_157 kdib5_158 = 0.06; // initial value of kdib5_158 kdiesp_159 = 0.5; // initial value of kdiesp_159 kdif2_160 = 0.5; // initial value of kdif2_160 kdif5_161 = 0.01; // initial value of kdif5_161 kdirent_162 = 1.0; // initial value of kdirent_162 kdirentp_163 = 2.0; // initial value of kdirentp_163 kdn2_164 = 0.12; // initial value of kdn2_164 kdnet_165 = 0.03; // initial value of kdnet_165 kdori_166 = 0.06; // initial value of kdori_166 kdpds_142 = 0.01; // initial value of kdpds_142 kdpds_146 = 0.2; // initial value of kdpds_146 kdpds_149 = 0.04; // initial value of kdpds_149 kdppx_167 = 0.17; // initial value of kdppx_167 kdppx_168 = 2.0; // initial value of kdppx_168 kdspn_169 = 0.06; // initial value of kdspn_169 kdswi_170 = 0.08; // initial value of kdswi_170 ki15_173 = 0.5; // initial value of ki15_173 kicdh_174 = 0.0010; // initial value of kicdh_174 kicdh_175 = 0.08; // initial value of kicdh_175 kiiep_176 = 0.15; // initial value of kiiep_176 kimcm_177 = 0.15; // initial value of kimcm_177 kisbf_178 = 0.6; // initial value of kisbf_178 kisbf_179 = 8.0; // initial value of kisbf_179 kiswi_180 = 0.05; // initial value of kiswi_180 kkpnet_181 = 0.01; // initial value of kkpnet_181 kkpnet_182 = 0.6; // initial value of kkpnet_182 kppc1_183 = 4.0; // initial value of kppc1_183 kppf6_184 = 4.0; // initial value of kppf6_184 kppnet_185 = 0.05; // initial value of kppnet_185 kppnet_186 = 3.0; // initial value of kppnet_186 lte1h_212 = 1.0; // initial value of lte1h_212 lte1l_213 = 0.1; // initial value of lte1l_213 mad2h_214 = 8.0; // initial value of mad2h_214 mad2l_215 = 0.01; // initial value of mad2l_215 mdt_216 = 90.0; // initial value of mdt_216 } /* * Model variables initial values */ protected double _cell_0_BCK2_1_; protected double _cell_0_BUB2_2_; protected double _cell_0_CDC14T_9_; protected double _cell_0_CDC6T_16_; protected double _cell_0_CKIT_19_; protected double _cell_0_CLB2T_21_; protected double _cell_0_CLB5T_23_; protected double _cell_0_CLN3_25_; protected double _cell_0_LTE1_35_; protected double _cell_0_MAD2_36_; protected double _cell_0_MASS_37_; protected double _cell_0_MCM1_38_; protected double _cell_0_NET1T_42_; protected double _cell_0_SBF_49_; protected double _cell_0_SIC1T_52_; protected double rate_Activation_282; protected double rate_ActivationofCDC_278; protected double rate_ActivationofIEP_273; protected double rate_ActivationofSWI_271; protected double rate_AssocofCLBandSIC_236; protected double rate_AssocofCLBandSIC_238; protected double rate_AssocwithESPtoformPE_306; protected double rate_AssocwithNETPtoformRENTP_287; protected double rate_AssocwithNETtoformRENT_285; protected double rate_CDCactivation_301; protected double rate_CDCanotherCKIlikeSIC_250; protected double rate_DegradationofCDCinRENTP_298; protected double rate_DegradationofCDCinRENT_297; protected double rate_DegradationofCLB_229; protected double rate_DegradationofCLB_231; protected double rate_DegradationofCLBinCP_248; protected double rate_DegradationofCLBinC_244; protected double rate_DegradationofCLN_227; protected double rate_DegradationofNETPinRENTP_296; protected double rate_DegradationofNETinRENT_295; protected double rate_DegradationofPDSinPE_305; protected double rate_DegradationofSICinCP_246; protected double rate_DegradationofSWIP_270; protected double rate_DegradationofSWI_269; protected double rate_DegradationofactiveCDC_277; protected double rate_DegradationofinactiveCDC_276; protected double rate_DephosphorylationofCP_241; protected double rate_DephosphorylationofSIC_234; protected double rate_DissocfromRENP_288; protected double rate_DissocfromRENT_286; protected double rate_DissocofCLBSIC_239; protected double rate_DissocofCLBSICcomplex_237; protected double rate_DissofromPE_307; protected double rate_FastDegradationofSICP_235; protected double rate_Growth_225; protected double rate_Inactivation_274_CDC20; protected double rate_Inactivation_274_CDH1; protected double rate_Inactivation_274_IEP; protected double rate_InactivationofSWI_272; protected double rate_NETphosphorylation_292; protected double rate_PDSsynthesis_304; protected double rate_PPXsynthesis_302; protected double rate_PhosphorylationofC_240; protected double rate_PhosphorylationofSIC_233; protected double rate_RENTphosphorylation_294; protected double rate_SynthesisofCLB_228; protected double rate_SynthesisofCLB_230; protected double rate_SynthesisofCLN_226; protected double rate_SynthesisofSIC_232; protected double rate_SynthesisofSWI_268; protected double rate_SynthesisofinactiveCDC_275; protected double rate_TEMactivation_299; protected double rate__242; protected double rate__243; protected double rate__245; protected double rate__247; protected double rate__249; protected double rate__251; protected double rate__252; protected double rate__253; protected double rate__254; protected double rate__255; protected double rate__256; protected double rate__257; protected double rate__258; protected double rate__259; protected double rate__260; protected double rate__261; protected double rate__262; protected double rate__263; protected double rate__264; protected double rate__265; protected double rate__266; protected double rate__267; protected double rate__279; protected double rate__280; protected double rate__281; protected double rate__283; protected double rate__284; protected double rate__289; protected double rate__290; protected double rate__291; protected double rate__308; protected double rate__309; protected double rate__310; protected double rate__311; protected double rate__312; protected double rate__313; protected double rate_degradation_303_PDS1; protected double rate_degradation_303_PPX; protected double rate_dephosphorylation_293_NET1P; protected double rate_dephosphorylation_293_RENTP; protected double rate_inactivation_300_CDC15; protected double rate_inactivation_300_TEM1GTP; protected double C0_78; protected double CDC15T_79; protected double D_26; protected double Dn3_80; protected double ESP1T_103; protected double F_28; protected double IET_104; protected double J20ppx_105; protected double Jacdh_106; protected double Jaiep_107; protected double Jamcm_108; protected double Jasbf_109; protected double Jatem_110; protected double Jd2c1_111; protected double Jd2f6_112; protected double Jicdh_113; protected double Jiiep_114; protected double Jimcm_115; protected double Jisbf_116; protected double Jitem_117; protected double Jn3_118; protected double Jpds_119; protected double KEZ2_172; protected double KEZ_171; protected double TEM1T_217; protected double Vacdh_58; protected double Vaiep_59; protected double Vasbf_60; protected double Vd2c1_61; protected double Vd2f6_62; protected double Vdb2_63; protected double Vdb5_64; protected double Vdpds_65; protected double Vdppx_66; protected double Vicdh_67; protected double Visbf_68; protected double Vkpc1_69; protected double Vkpf6_70; protected double Vkpnet_71; protected double Vppc1_72; protected double Vppf6_73; protected double Vppnet_74; protected double b0_75; protected double bub2h_76; protected double bub2l_77; protected double ec1b2_84; protected double ec1b5_85; protected double ec1k2_86; protected double ec1n2_87; protected double ec1n3_88; protected double ef6b2_89; protected double ef6b5_90; protected double ef6k2_91; protected double ef6n2_92; protected double ef6n3_93; protected double eicdhb2_94; protected double eicdhb5_95; protected double eicdhn2_96; protected double eicdhn3_97; protected double esbfb5_100; protected double esbfn2_101; protected double esbfn3_102; protected double ka15p_123; protected double ka_121; protected double ka_122; protected double ka_124; protected double ka_125; protected double kacdh_126; protected double kacdh_127; protected double kaiep_128; protected double kamcm_129; protected double kasb2_130; protected double kasb5_131; protected double kasbf_132; protected double kasesp_133; protected double kasf2_134; protected double kasf5_135; protected double kasrent_136; protected double kasrentp_137; protected double kaswi_138; protected double kd14_139; protected double kd1c1_140; protected double kd1f6_141; protected double kd20_143; protected double kd2c1_144; protected double kd2f6_145; protected double kd3c1_147; protected double kd3f6_148; protected double kdb2p_152; protected double kdb_150; protected double kdb_151; protected double kdb_153; protected double kdb_154; protected double kdbud_155; protected double kdcdh_156; protected double kdib2_157; protected double kdib5_158; protected double kdiesp_159; protected double kdif2_160; protected double kdif5_161; protected double kdirent_162; protected double kdirentp_163; protected double kdn2_164; protected double kdnet_165; protected double kdori_166; protected double kdpds_142; protected double kdpds_146; protected double kdpds_149; protected double kdppx_167; protected double kdppx_168; protected double kdspn_169; protected double kdswi_170; protected double ki15_173; protected double kicdh_174; protected double kicdh_175; protected double kiiep_176; protected double kimcm_177; protected double kisbf_178; protected double kisbf_179; protected double kiswi_180; protected double kkpnet_181; protected double kkpnet_182; protected double kppc1_183; protected double kppf6_184; protected double kppnet_185; protected double kppnet_186; protected double lte1h_212; protected double lte1l_213; protected double mad2h_214; protected double mad2l_215; protected double mdt_216; protected double mu_39; public double[] extendResult(double time,double [] x) { this.time = time; double [] algebraicResult = new double [4]; AlgFuncBegin_0(algebraicResult); this.x = x; try { NewtonSolver.solve(algebraicResult, this); } catch (Throwable t) { t.printStackTrace(); } AlgFuncEnd_0(algebraicResult); __internalVarInitFunc_0(time, x); double[] y = new double[78]; y[0] = _cell_0_BCK2_1_; y[1] = _cell_0_BUB2_2_; y[2] = x[0]; y[3] = x[1]; y[4] = x[2]; y[5] = x[3]; y[6] = x[4]; y[7] = _cell_0_CDC14T_9_; y[8] = x[5]; y[9] = x[6]; y[10] = x[7]; y[11] = x[8]; y[12] = x[9]; y[13] = x[10]; y[14] = _cell_0_CDC6T_16_; y[15] = x[11]; y[16] = x[12]; y[17] = x[13]; y[18] = _cell_0_CKIT_19_; y[19] = _cell_0_CLB2T_21_; y[20] = x[14]; y[21] = _cell_0_CLB5T_23_; y[22] = x[15]; y[23] = x[16]; y[24] = _cell_0_CLN3_25_; y[25] = x[17]; y[26] = x[18]; y[27] = x[19]; y[28] = x[20]; y[29] = x[21]; y[30] = x[22]; y[31] = x[23]; y[32] = _cell_0_LTE1_35_; y[33] = _cell_0_MAD2_36_; y[34] = _cell_0_MASS_37_; y[35] = _cell_0_MCM1_38_; y[36] = x[24]; y[37] = _cell_0_NET1T_42_; y[38] = x[25]; y[39] = x[26]; y[40] = x[27]; y[41] = x[28]; y[42] = x[29]; y[43] = x[30]; y[44] = x[31]; y[45] = _cell_0_SBF_49_; y[46] = x[32]; y[47] = _cell_0_SIC1T_52_; y[48] = x[33]; y[49] = x[34]; y[50] = x[35]; y[51] = x[36]; y[52] = x[37]; y[53] = x[38]; y[54] = CDC15T_79; y[55] = D_26; y[56] = ESP1T_103; y[57] = F_28; y[58] = IET_104; y[59] = TEM1T_217; y[60] = Vacdh_58; y[61] = Vaiep_59; y[62] = Vasbf_60; y[63] = Vd2c1_61; y[64] = Vd2f6_62; y[65] = Vdb2_63; y[66] = Vdb5_64; y[67] = Vdpds_65; y[68] = Vdppx_66; y[69] = Vicdh_67; y[70] = Visbf_68; y[71] = Vkpc1_69; y[72] = Vkpf6_70; y[73] = Vkpnet_71; y[74] = Vppc1_72; y[75] = Vppf6_73; y[76] = Vppnet_74; y[77] = mu_39; return y; } public double[] getInitialValues() { double [] x = new double[39]; this.time = 0.0; x[0] = 0.008473; // - $"cell_0.BUD_3" x[1] = 0.024034; // - $"cell_0.C2P_5" x[2] = 0.238404; // - $"cell_0.C2_4" x[3] = 0.006878; // - $"cell_0.C5P_7" x[4] = 0.070081; // - $"cell_0.C5_6" x[5] = 0.468344; // - $"cell_0.CDC14_8" x[6] = 0.656533; // - $"cell_0.CDC15_10" x[7] = 0.343466; // - $"cell_0.CDC15i_11" x[8] = 0.444296; // - $"cell_0.CDC20_12" x[9] = 1.472044; // - $"cell_0.CDC20i_13" x[10] = 0.015486; // - $"cell_0.CDC6P_15" x[11] = 0.10758; // - $"cell_0.CDC6_14" x[12] = 0.930499; // - $"cell_0.CDH1_17" x[13] = 0.0695; // - $"cell_0.CDH1i_18" x[14] = 0.1469227; // - $"cell_0.CLB2_20" x[15] = 0.0518014; // - $"cell_0.CLB5_22" x[16] = 0.0652511; // - $"cell_0.CLN2_24" x[17] = 0.301313; // - $"cell_0.ESP1_27" x[18] = 0.0273938; // - $"cell_0.F2P_30" x[19] = 0.236058; // - $"cell_0.F2_29" x[20] = 7.91E-5; // - $"cell_0.F5P_32" x[21] = 7.24E-5; // - $"cell_0.F5_31" x[22] = 0.1015; // - $"cell_0.IEP_34" x[23] = 0.8985; // - $"cell_0.IE_33" x[24] = 0.970271; // - $"cell_0.NET1P_41" x[25] = 0.018645; // - $"cell_0.NET1_40" x[26] = 9.09E-4; // - $"cell_0.ORI_43" x[27] = 0.025612; // - $"cell_0.PDS1_44" x[28] = 0.7; // - $"cell_0.PE_45" x[29] = 0.123179; // - $"cell_0.PPX_46" x[30] = 0.6; // - $"cell_0.RENTP_48" x[31] = 1.04954; // - $"cell_0.RENT_47" x[32] = 0.00641; // - $"cell_0.SIC1P_51" x[33] = 0.0228776; // - $"cell_0.SIC1_50" x[34] = 0.03; // - $"cell_0.SPN_53" x[35] = 0.02; // - $"cell_0.SWI5P_55" x[36] = 0.95; // - $"cell_0.SWI5_54" x[37] = 0.1; // - $"cell_0.TEM1GDP_56" x[38] = 0.9; // - $"cell_0.TEM1GTP_57" __internalVarInitFunc_0(time, x); __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); return x; } protected double[] x = null; public double[] solveAlgebraic(double time, double[] z) { this.time = time; CDC15T_79 = z[0]; ESP1T_103 = z[1]; IET_104 = z[2]; TEM1T_217 = z[3]; double [] result = new double [4]; result[0] = x[6] + x[7] - CDC15T_79; result[1] = x[23] + x[22] - IET_104; result[2] = x[17] + x[28] - ESP1T_103; result[3] = x[37] + x[38] - TEM1T_217; return result; } /* * code for algebraic rules calculations */ public void AlgFuncBegin_0(double [] algebraicResult) { algebraicResult[0] = CDC15T_79; algebraicResult[1] = ESP1T_103; algebraicResult[2] = IET_104; algebraicResult[3] = TEM1T_217; } public void AlgFuncEnd_0(double [] algebraicResult) { CDC15T_79 = algebraicResult[0]; ESP1T_103 = algebraicResult[1]; IET_104 = algebraicResult[2]; TEM1T_217 = algebraicResult[3]; } /* * 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 'BIOMD0000000056.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = -rate__311; result[1] = -rate_DegradationofCLBinCP_248-rate_DegradationofSICinCP_246-rate_DephosphorylationofCP_241+rate_PhosphorylationofC_240; result[2] = +rate_AssocofCLBandSIC_236-rate_DegradationofCLBinC_244+rate_DephosphorylationofCP_241-rate_DissocofCLBSICcomplex_237-rate_PhosphorylationofC_240; result[3] = +rate__242-rate__243-rate__247-rate__249; result[4] = +rate_AssocofCLBandSIC_238-rate_DissocofCLBSIC_239-rate__242+rate__243-rate__245; result[5] = -rate_AssocwithNETPtoformRENTP_287-rate_AssocwithNETtoformRENT_285+rate_DegradationofNETPinRENTP_296+rate_DegradationofNETinRENT_295+rate_DissocfromRENP_288+rate_DissocfromRENT_286-rate__284; result[6] = +rate_CDCactivation_301-rate_inactivation_300_CDC15; result[7] = -rate_CDCactivation_301+rate_inactivation_300_CDC15; result[8] = +rate_ActivationofCDC_278-rate_DegradationofactiveCDC_277-rate_Inactivation_274_CDC20; result[9] = -rate_ActivationofCDC_278-rate_DegradationofinactiveCDC_276+rate_Inactivation_274_CDC20; result[10] = +rate__251-rate__252-rate__253+rate__266+rate__267; result[11] = -rate__251+rate__252-rate__254+rate__255-rate__256+rate__257+rate__262+rate__263; result[12] = +rate_Activation_282-rate_Inactivation_274_CDH1-rate__280; result[13] = -rate_Activation_282+rate_Inactivation_274_CDH1-rate__281; result[14] = -rate_AssocofCLBandSIC_236-rate_DegradationofCLB_229+rate_DegradationofSICinCP_246+rate_DissocofCLBSICcomplex_237-rate__254+rate__255+rate__264; result[15] = -rate_AssocofCLBandSIC_238-rate_DegradationofCLB_231+rate_DissocofCLBSIC_239+rate__247-rate__256+rate__257+rate__265; result[16] = -rate_DegradationofCLN_227; result[17] = -rate_AssocwithESPtoformPE_306+rate_DegradationofPDSinPE_305+rate_DissofromPE_307; result[18] = +rate__258-rate__259-rate__264-rate__266; result[19] = +rate__254-rate__255-rate__258+rate__259-rate__262; result[20] = +rate__260-rate__261-rate__265-rate__267; result[21] = +rate__256-rate__257-rate__260+rate__261-rate__263; result[22] = +rate_ActivationofIEP_273-rate_Inactivation_274_IEP; result[23] = -rate_ActivationofIEP_273+rate_Inactivation_274_IEP; result[24] = -rate_AssocwithNETPtoformRENTP_287+rate_DegradationofCDCinRENTP_298+rate_DissocfromRENP_288+rate_NETphosphorylation_292-rate__291-rate_dephosphorylation_293_NET1P; result[25] = -rate_AssocwithNETtoformRENT_285+rate_DegradationofCDCinRENT_297+rate_DissocfromRENT_286-rate_NETphosphorylation_292-rate__290+rate_dephosphorylation_293_NET1P; result[26] = -rate__309; result[27] = -rate_AssocwithESPtoformPE_306+rate_DissofromPE_307-rate_degradation_303_PDS1; result[28] = +rate_AssocwithESPtoformPE_306-rate_DegradationofPDSinPE_305-rate_DissofromPE_307; result[29] = -rate_degradation_303_PPX; result[30] = +rate_AssocwithNETPtoformRENTP_287-rate_DegradationofCDCinRENTP_298-rate_DegradationofNETPinRENTP_296-rate_DissocfromRENP_288+rate_RENTphosphorylation_294-rate_dephosphorylation_293_RENTP; result[31] = +rate_AssocwithNETtoformRENT_285-rate_DegradationofCDCinRENT_297-rate_DegradationofNETinRENT_295-rate_DissocfromRENT_286-rate_RENTphosphorylation_294+rate_dephosphorylation_293_RENTP; result[32] = +rate_DegradationofCLBinCP_248-rate_DephosphorylationofSIC_234-rate_FastDegradationofSICP_235+rate_PhosphorylationofSIC_233+rate__249; result[33] = -rate_AssocofCLBandSIC_236-rate_AssocofCLBandSIC_238+rate_DegradationofCLBinC_244+rate_DephosphorylationofSIC_234+rate_DissocofCLBSIC_239+rate_DissocofCLBSICcomplex_237-rate_PhosphorylationofSIC_233+rate__245; result[34] = -rate__313; result[35] = -rate_ActivationofSWI_271-rate_DegradationofSWIP_270+rate_InactivationofSWI_272; result[36] = +rate_ActivationofSWI_271-rate_DegradationofSWI_269-rate_InactivationofSWI_272; result[37] = -rate_TEMactivation_299+rate_inactivation_300_TEM1GTP; result[38] = +rate_TEMactivation_299-rate_inactivation_300_TEM1GTP; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[39]; __internalDyDt_0(time, x, result); return result; } public double[] dy_dt(double time, double[] x) { this.time = time; double [] algebraicResult = new double [4]; AlgFuncBegin_0(algebraicResult); this.x = x; try { NewtonSolver.solve(algebraicResult, this); } catch (Throwable t) { t.printStackTrace(); } AlgFuncEnd_0(algebraicResult); 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); double [] flags = new double[4]; flags[0] = (x[14] + x[15] - KEZ2_172 < 0.0) ? +1 : -1; //event_1 flags[1] = (x[26] - 1.0 > 0.0) ? +1 : -1; //event_2 flags[2] = (x[34] - 1.0 > 0.0) ? +1 : -1; //event_3 flags[3] = (x[14] - KEZ_171 < 0.0) ? +1 : -1; //event_4 return flags; } public void processEvent(int __internalVar12060038815150, double time, double[] x) { this.time = time; if ( __internalVar12060038815150 == 0) //event_1 { x[26] = 0.0; } else if ( __internalVar12060038815150 == 1) //event_2 { _cell_0_MAD2_36_ = mad2h_214; _cell_0_BUB2_2_ = bub2h_76; } else if ( __internalVar12060038815150 == 2) //event_3 { _cell_0_MAD2_36_ = mad2l_215; _cell_0_LTE1_35_ = lte1h_212; _cell_0_BUB2_2_ = bub2l_77; } else if ( __internalVar12060038815150 == 3) //event_4 { _cell_0_MASS_37_ = F_28*_cell_0_MASS_37_; _cell_0_LTE1_35_ = lte1l_213; x[0] = 0.0; x[34] = 0.0; } } protected double BB_218(double A1, double A2, double A3, double A4) { return A2 - A1 + A3*A2 + A4*A1; } protected double GK_219(double A1, double A2, double A3, double A4) { return 2.0*A4*A1/(BB_218(A1, A2, A3, A4) + Math.pow(Math.pow(BB_218(A1, A2, A3, A4), 2.0) - 4.0*(A2 - A1)*A4*A1, 1.0/( (double)(2.0)))); } protected double Mass_Action_0_223(double k1) { return k1; } protected double Mass_Action_1_222(double k1, double S1) { return k1*S1; } protected double Mass_Action_2_221(double k1, double S1, double S2) { return k1*S1*S2; } protected double MichaelisMenten_220(double M1, double J1, double k1, double S1) { return k1*S1*M1/(J1 + S1); } } // class ...