ErkSubnetwork.cpp Source File

00001 // ErkSubnetwork.cpp: implementation of the ErkSubnetwork class.
00002 //
00004 
00005 #ifdef _WINDOWS
00006 #include "stdafx.h"
00007 #endif
00008 
00009 #include "ErkSubnetwork.h"
00010 
00012 // Construction/Destruction
00014 
00015 ErkSubnetwork::ErkSubnetwork()
00016 {
00017 
00018         double CFactor = 600000.0, SecToMin = 60.0;
00019 
00020         // 1
00021         Chemical *EGF = new Chemical(chemicals.size(), 1000.0, "EGF");
00022         chemicals.push_back(EGF);
00023 
00024         // 2
00025         Chemical *NGF = new Chemical(chemicals.size(), 0.0, "NGF");
00026         chemicals.push_back(NGF);
00027 
00028         // 3
00029         Chemical *freeEGFReceptor = new Chemical(chemicals.size(), CFactor*0.00001667, "freeEGFReceptor");
00030         chemicals.push_back(freeEGFReceptor);
00031 
00032         // 4
00033         Chemical *boundEGFReceptor = new Chemical(chemicals.size(), 0.0, "boundEGFReceptor");
00034         chemicals.push_back(boundEGFReceptor);
00035 
00036         // 5
00037         Chemical *freeNGFReceptor = new Chemical(chemicals.size(), CFactor*0.00001667, "freeNGFReceptor");
00038         chemicals.push_back(freeNGFReceptor);
00039 
00040         // 6
00041         Chemical *boundNGFReceptor = new Chemical(chemicals.size(), 0.0, "boundNGFReceptor");
00042         chemicals.push_back(boundNGFReceptor);
00043 
00044         // 7
00045         Chemical *SosInactive = new Chemical(chemicals.size(), 0.1*CFactor, "SosInactive");
00046         chemicals.push_back(SosInactive);
00047                 
00048         // 8
00049         Chemical *SosActive = new Chemical(chemicals.size(), 0.0, "SosActive");
00050         chemicals.push_back(SosActive);
00051 
00052         // 9
00053         Chemical *P90RskInactive = new Chemical(chemicals.size(), 10000.0, "P90RskInactive");
00054         chemicals.push_back(P90RskInactive);
00055 
00056         // 10
00057         Chemical *P90RskActive = new Chemical(chemicals.size(), 0.0, "P90RskActive");
00058         chemicals.push_back(P90RskActive);
00059 
00060         // 11
00061         Chemical *RasInactive = new Chemical(chemicals.size(), 0.2*CFactor, "RasInactive");
00062         chemicals.push_back(RasInactive);
00063                 
00064         // 12
00065         Chemical *RasActive = new Chemical(chemicals.size(), 0.0, "RasActive");
00066         chemicals.push_back(RasActive);
00067 
00068         // 13
00069         Chemical *RasGapInactive = new Chemical(chemicals.size(), CFactor*0.002, "RasGapInactive");
00070         chemicals.push_back(RasGapInactive);
00071 
00072         // 14
00073         Chemical *RasGapActive = new Chemical(chemicals.size(), CFactor*0.002, "RasGapActive");
00074         chemicals.push_back(RasGapActive);
00075 
00076         // 15
00077         Chemical *Raf1Inactive = new Chemical(chemicals.size(), CFactor*0.2, "Raf1Inactive");
00078         chemicals.push_back(Raf1Inactive);
00079                 
00080         // 16
00081         Chemical *Raf1Active = new Chemical(chemicals.size(), 0.0, "Raf1Active");
00082         chemicals.push_back(Raf1Active);
00083 
00084         // 17
00085         Chemical *BRafInactive = new Chemical(chemicals.size(), CFactor*0.2, "BRafInactive");
00086         chemicals.push_back(BRafInactive);
00087                 
00088         // 18
00089         Chemical *BRafActive = new Chemical(chemicals.size(), 0.0, "BRafActive");
00090         chemicals.push_back(BRafActive);
00091 
00092         // 19
00093         Chemical *MekInactive = new Chemical(chemicals.size(), 0.18*CFactor, "MekInactive");
00094         chemicals.push_back(MekInactive);
00095 
00096         // 20
00097         Chemical *MekActive = new Chemical(chemicals.size(), 0.0, "MekActive");
00098         chemicals.push_back(MekActive);
00099 
00100         // 21
00101         Chemical *ErkInactiveCytoplasmic = new Chemical(chemicals.size(),0.36*CFactor, "ErkInactiveCytoplasmic");
00102         chemicals.push_back(ErkInactiveCytoplasmic);
00103                 
00104         // 22
00105         Chemical *ErkActiveCytoplasmic = new Chemical(chemicals.size(), 0.0, "ErkActiveCytoplasmic");
00106         chemicals.push_back(ErkActiveCytoplasmic);
00107 
00108 //      Chemical *ErkPhosphataseCytoplasmic2 = new Chemical(chemicals.size(), 0.1*CFactor, "ErkPhosphataseCytoplasmic2");
00109 //      chemicals.push_back(ErkPhosphataseCytoplasmic2);
00110 
00111         // 23
00112         Chemical *ErkInactiveNuclear = new Chemical(chemicals.size(), 0.0, "ErkInactiveNuclear");
00113         chemicals.push_back(ErkInactiveNuclear);
00114                 
00115         // 24
00116         Chemical *ErkActiveNuclear = new Chemical(chemicals.size(), 0.0, "ErkActiveNuclear");
00117         chemicals.push_back(ErkActiveNuclear);
00118 
00119         // 25
00120         Chemical *ErkPhosphataseNuclear = new Chemical(chemicals.size(), 0.1*CFactor, "ErkPhosphataseNuclear");
00121         chemicals.push_back(ErkPhosphataseNuclear);
00122 
00123         // 26
00124         Chemical *PI3KInactive = new Chemical(chemicals.size(), 0.1*CFactor, "PI3KInactive");
00125         chemicals.push_back(PI3KInactive);
00126 
00127         // 27
00128         Chemical *PI3KActive = new Chemical(chemicals.size(), 0.0, "PI3KActive");
00129         chemicals.push_back(PI3KActive);
00130 
00131         // 28
00132         Chemical *AktInactive = new Chemical(chemicals.size(), 0.1*CFactor, "AktInactive");
00133         chemicals.push_back(AktInactive);
00134 
00135         // 29
00136         Chemical *AktActive = new Chemical(chemicals.size(), 0.0, "AktActive");
00137         chemicals.push_back(AktActive);
00138 
00139         // 30 
00140         Chemical *RapGEFInactive = new Chemical(chemicals.size(), 0.1*CFactor, "RapGEFInactive");
00141         chemicals.push_back(RapGEFInactive);
00142                 
00143         // 31
00144         Chemical *RapGEFActive = new Chemical(chemicals.size(), 0.0, "RapGEFActive");
00145         chemicals.push_back(RapGEFActive);
00146 
00147         // 32
00148         Chemical *RapInactive = new Chemical(chemicals.size(), 0.1*CFactor, "RapInactive");
00149         chemicals.push_back(RapInactive);
00150 
00151         // 33
00152         Chemical *RapActive = new Chemical(chemicals.size(), 0.0, "RapActive");
00153         chemicals.push_back(RapActive);
00154 
00155         // 34
00156         Chemical *RapGapInactive = new Chemical(chemicals.size(), 0.0, "RapGapInactive");
00157         chemicals.push_back(RapGapInactive);
00158                 
00159         // 35
00160         Chemical *RapGapActive = new Chemical(chemicals.size(), 0.1*CFactor, "RapGapActive");
00161         chemicals.push_back(RapGapActive);
00162         
00163         // 36
00164         Chemical *Sp1Inactive = new Chemical(chemicals.size(), 0.1*CFactor, "Sp1Inactive");
00165         chemicals.push_back(Sp1Inactive);
00166 
00167         // 37
00168         Chemical *Sp1Active = new Chemical(chemicals.size(), 0.0, "Sp1Active");
00169         chemicals.push_back(Sp1Active);
00170 
00171         // 38
00172         Chemical *CyclinDfreePromoter = new Chemical(chemicals.size(), 1.0, "CyclinDfreePromoter");
00173         chemicals.push_back(CyclinDfreePromoter);
00174 
00175         // 39
00176         Chemical *CyclinDboundPromoter = new Chemical(chemicals.size(), 0.0, "CyclinDboundPromoter");
00177         chemicals.push_back(CyclinDboundPromoter);
00178 
00179         // 40
00180         Chemical *CyclinDmRNA = new Chemical(chemicals.size(), 0.0, "CyclinDmRNA");
00181         chemicals.push_back(CyclinDmRNA);
00182 
00183         // 41
00184         Chemical *CyclinD = new Chemical(chemicals.size(), 0.0, "CyclinD");
00185         chemicals.push_back(CyclinD);
00186 
00187         // 42
00188         Chemical *P21freePromoter = new Chemical(chemicals.size(), 1.0, "P21freePromoter");
00189         chemicals.push_back(P21freePromoter);
00190 
00191         // 43
00192         Chemical *P21boundPromoter = new Chemical(chemicals.size(), 0.0, "P21boundPromoter");
00193         chemicals.push_back(P21boundPromoter);
00194 
00195         // 44
00196         Chemical *P21mRNA = new Chemical(chemicals.size(), 0.0, "P21mRNA");
00197         chemicals.push_back(P21mRNA);
00198 
00199         // 45
00200         Chemical *P21 = new Chemical(chemicals.size(), 0.0, "P21");
00201         chemicals.push_back(P21);
00202 
00203         // 46
00204         Chemical *CFosfreePromoter = new Chemical(chemicals.size(), 1.0, "CFosfreePromoter");
00205         chemicals.push_back(CFosfreePromoter);
00206 
00207         // 47
00208         Chemical *CFosboundPromoter = new Chemical(chemicals.size(), 0.0, "CFosboundPromoter");
00209         chemicals.push_back(CFosboundPromoter);
00210 
00211         // 48
00212         Chemical *CFosmRNA = new Chemical(chemicals.size(), 0.0, "CFosmRNA");
00213         chemicals.push_back(CFosmRNA);
00214 
00215         // 49
00216         Chemical *CFos = new Chemical(chemicals.size(), 0.0, "CFos");
00217         chemicals.push_back(CFos);
00218 
00219         // 50
00220         Chemical *ErkPhosphataseCytoplasmicfreePromoter = new Chemical(chemicals.size(), 1.0, "ErkPhosphataseCytoplasmicfreePromoter");
00221         chemicals.push_back(ErkPhosphataseCytoplasmicfreePromoter);
00222 
00223         // 51
00224         Chemical *ErkPhosphataseCytoplasmicboundPromoter = new Chemical(chemicals.size(), 0.0, "ErkPhosphataseCytoplasmicboundPromoter");
00225         chemicals.push_back(ErkPhosphataseCytoplasmicboundPromoter);
00226 
00227         // 52
00228         Chemical *ErkPhosphataseCytoplasmicmRNA = new Chemical(chemicals.size(), 0.0, "ErkPhosphataseCytoplasmicmRNA");
00229         chemicals.push_back(ErkPhosphataseCytoplasmicmRNA);
00230 
00231         // 53
00232         Chemical *ErkPhosphataseCytoplasmic = new Chemical(chemicals.size(), 0.0, "ErkPhosphataseCytoplasmic");
00233         chemicals.push_back(ErkPhosphataseCytoplasmic);
00234 
00235         // 54
00236         Chemical *freePromoter = new Chemical(chemicals.size(), 1.0, "freePromoter");
00237         chemicals.push_back(freePromoter);
00238 
00239         // 55
00240         Chemical *boundPromoter = new Chemical(chemicals.size(), 0.0, "boundPromoter");
00241         chemicals.push_back(boundPromoter);
00242 
00243         // 56
00244         Chemical *mRNA = new Chemical(chemicals.size(), 0.0, "mRNA");
00245         chemicals.push_back(mRNA);
00246 
00247         // 57
00248         Chemical *protein = new Chemical(chemicals.size(), 0.0, "protein");
00249         chemicals.push_back(protein);
00250 
00251         // 58
00252         Chemical *filler = new Chemical(chemicals.size(), 1.0, "filler");
00253         chemicals.push_back(filler);
00254 
00255 
00256         RateConstant *k_rb_EGF = new RateConstant(SecToMin*0.000007, "k_rb_EGF");
00257         RateConstant *k_ru_EGF = new RateConstant(SecToMin*0.25, "k_ru_EGF");
00258         RateConstant *k_rb_NGF = new RateConstant(SecToMin*0.000007, "k_rb_NGF");
00259         RateConstant *k_ru_NGF = new RateConstant(SecToMin*0.25, "k_ru_NGF");
00260 
00261         RateConstant *k_EGF = new RateConstant(SecToMin*5976, "k_EGF");
00262         RateConstant *Km_EGF = new RateConstant(CFactor*0.8333, "Km_EGF");
00263         RateConstant *k_NGF = new RateConstant(SecToMin*0.25, "k_NGF");
00264         RateConstant *Km_NGF = new RateConstant(CFactor*0.8333, "Km_NGF");
00265 
00266         RateConstant *k_dSos = new RateConstant(0.00167*SecToMin, "k_dSos");
00267         RateConstant *Km_dSos = new RateConstant(100000.0, "Km_dSos");
00268         RateConstant *k_Sos = new RateConstant(SecToMin*0.02, "k_Sos");
00269         RateConstant *Km_Sos = new RateConstant(0.505*CFactor, "Km_Sos");
00270 
00271         RateConstant *k_RasGap = new RateConstant(10.0*SecToMin, "k_RasGap");
00272         RateConstant *Km_RasGap = new RateConstant(CFactor*1.0104, "Km_RasGap");
00273         RateConstant *k_RasToRaf1 = new RateConstant(0.01, "k_RasToRaf1");
00274         RateConstant *Km_RasToRaf1 = new RateConstant(300000.0, "Km_RasToRaf1");
00275 
00276         RateConstant *k_pRaf1 = new RateConstant(0.1*SecToMin, "k_pRaf1");
00277         RateConstant *Km_pRaf1 = new RateConstant(300000.0, "Km_pRaf1");
00278         RateConstant *k_pBRaf = new RateConstant(0.01*SecToMin, "k_pBRaf");
00279         RateConstant *Km_pBRaf = new RateConstant(300000.0, "Km_pBRaf");
00280         RateConstant *k_dMek = new RateConstant(0.01*SecToMin*1000000, "k_dMek");
00281         RateConstant *Km_dMek = new RateConstant(300000.0, "Km_dMek");
00282 
00283         RateConstant *k_pMek_Cytoplasmic = new RateConstant(0.01*SecToMin, "k_pMek_Cytoplasmic");
00284         RateConstant *Km_pMek_Cytoplasmic = new RateConstant(300000.0, "Km_pMek_Cytoplasmic");
00285         RateConstant *k_dErk_Cytoplasmic = new RateConstant(0.01*SecToMin, "k_dErk_Cytoplasmic");
00286         RateConstant *Km_dErk_Cytoplasmic = new RateConstant(300000.0, "Km_dErk_Cytoplasmic");
00287 //      RateConstant *k_dErk_Cytoplasmic2 = new RateConstant(0.001*SecToMin, "k_dErk_Cytoplasmic2");
00288 //      RateConstant *Km_dErk_Cytoplasmic2 = new RateConstant(300000.0, "Km_dErk_Cytoplasmic2");
00289         RateConstant *k_pP90Rsk = new RateConstant(0.01*SecToMin, "k_pP90Rsk");
00290         RateConstant *Km_pP90Rsk = new RateConstant(300000.0, "Km_pP90Rsk");
00291 
00292         RateConstant *k_PI3K = new RateConstant(0.01*SecToMin, "k_PI3K");
00293         RateConstant *Km_PI3K = new RateConstant(300000.0, "Km_PI3K");
00294         RateConstant *k_PI3K_Ras = new RateConstant(0.01*SecToMin, "k_PI3K_Ras");
00295         RateConstant *Km_PI3K_Ras = new RateConstant(300000.0, "Km_PI3K_Ras");
00296         RateConstant *k_dPI3K = new RateConstant(0.01*SecToMin, "k_dPI3K");
00297         RateConstant *Km_dPI3K = new RateConstant(300000.0, "Km_dPI3K");
00298         RateConstant *k_Akt = new RateConstant(0.01, "k_Akt");
00299         RateConstant *Km_Akt = new RateConstant(300000.0, "Km_Akt");
00300         RateConstant *k_dAkt = new RateConstant(0.01*SecToMin, "k_dAkt");
00301         RateConstant *Km_dAkt = new RateConstant(300000.0, "Km_dAkt");
00302         RateConstant *k_dRaf1ByAkt = new RateConstant(0.01*SecToMin, "k_dRaf1ByAkt");
00303         RateConstant *Km_Raf1ByAkt = new RateConstant(300000.0, "Km_Raf1ByAkt"); 
00304 
00305         RateConstant *k_Rap_GEF_NGF = new RateConstant(0.01*SecToMin, "k_Rap_GEF_NGF");
00306         RateConstant *Km_RapGef_NGF = new RateConstant(300000.0, "Km_RapGef_NGF");
00307         RateConstant *k_dRapGEF = new RateConstant(0.01*SecToMin, "k_dRapGEF");
00308         RateConstant *Km_dRapGEF = new RateConstant(300000.0, "Km_dRapGEF");
00309         RateConstant *k_RapGEF = new RateConstant(0.01*SecToMin, "k_RapGEF"); 
00310         RateConstant *Km_RapGEF = new RateConstant(300000.0, "Km_RapGEF");
00311         RateConstant *k_RapGap = new RateConstant(0.01*SecToMin, "k_RapGap");
00312         RateConstant *Km_RapGap = new RateConstant(300000.0, "Km_RapGap");
00313         RateConstant *k_RapToBRaf = new RateConstant(0.01*SecToMin, "k_RapToBRaf");
00314         RateConstant *Km_RapToBRaf = new RateConstant(300000.0, "Km_RapToBRaf");
00315         RateConstant *k_dRapToRaf1 = new RateConstant(0.01*SecToMin, "k_dRapToRaf1");
00316         RateConstant *Km_dRapToRaf1 = new RateConstant(300000.0, "Km_dRapToRaf1");
00317 
00318         RateConstant *ktrans_Erk = new RateConstant(0.01*SecToMin, "ktrans_Erk");
00319         RateConstant *k_dErkActiveNuclear = new RateConstant(0.1*SecToMin, "k_dErkActiveNuclear");
00320         RateConstant *Km_dErkActiveNuclear = new RateConstant(300000.0, "Km_dErkActiveNuclear");
00321 
00322         RateConstant *k_pSp1 = new RateConstant(0.01*SecToMin, "k_pSp1");
00323         RateConstant *Km_pSp1 = new RateConstant(300000.0, "Km_pSp1");
00324         RateConstant *k_dSp1 = new RateConstant(0.01*SecToMin, "k_dSp1");
00325         RateConstant *Km_dSp1 = new RateConstant(300000.0, "Km_dSp1");
00326 
00327     RateConstant *kb_CyclinD = new RateConstant(0.006, "kb_CyclinD");
00328     RateConstant *ku_CyclinD = new RateConstant(0.0006, "ku_CyclinD");
00329     RateConstant *ktm_CyclinD = new RateConstant(1.0, "ktm_CyclinD");
00330     RateConstant *kdm_CyclinD = new RateConstant(1.0/30.0, "kdm_CyclinD");
00331     RateConstant *kt_CyclinD = new RateConstant(1.0/6.0, "kt_CyclinD");
00332     RateConstant *kd_CyclinD = new RateConstant(1.0/100.0, "kd_CyclinD");  
00333 
00334     RateConstant *kb_P21 = new RateConstant(0.006, "kb_P21");
00335     RateConstant *ku_P21 = new RateConstant(0.0006, "ku_P21");
00336     RateConstant *ktm_P21 = new RateConstant(1.0, "ktm_P21");
00337     RateConstant *kdm_P21 = new RateConstant(1.0/30.0, "kdm_P21");
00338     RateConstant *kt_P21 = new RateConstant(1.0/6.0, "kt_P21");
00339     RateConstant *kd_P21 = new RateConstant(1.0/100.0, "kd_P21");
00340 
00341     RateConstant *kb_CFos = new RateConstant(0.006, "kb_CFos");
00342     RateConstant *ku_CFos = new RateConstant(0.0006, "ku_CFos");
00343     RateConstant *ktm_CFos = new RateConstant(1.0, "ktm_CFos");
00344     RateConstant *kdm_CFos = new RateConstant(1.0/30.0, "kdm_CFos");
00345     RateConstant *kt_CFos = new RateConstant(1.0/6.0, "kt_CFos");
00346     RateConstant *kd_CFos = new RateConstant(1.0/100.0, "kd_CFos");     
00347 
00348     RateConstant *kb_ErkPhosphataseCytoplasmic = new RateConstant(0.006, "kb_ErkPhosphataseCytoplasmic");
00349     RateConstant *ku_ErkPhosphataseCytoplasmic = new RateConstant(0.0006, "ku_ErkPhosphataseCytoplasmic");
00350     RateConstant *ktm_ErkPhosphataseCytoplasmic = new RateConstant(1.0, "ktm_ErkPhosphataseCytoplasmic");
00351     RateConstant *kdm_ErkPhosphataseCytoplasmic = new RateConstant(1.0/30.0,"kdm_ErkPhosphataseCytoplasmic");
00352     RateConstant *kt_ErkPhosphataseCytoplasmic = new RateConstant(1.0/6.0, "kt_ErkPhosphataseCytoplasmic");
00353     RateConstant *kd_ErkPhosphataseCytoplasmic = new RateConstant(1.0/100.0,"kd_ErkPhosphataseCytoplasmic");
00354 
00355     RateConstant *kb = new RateConstant(0.006, "kb");
00356     RateConstant *ku = new RateConstant(0.0006, "ku");
00357     RateConstant *ktm = new RateConstant(1.0, "ktm");
00358     RateConstant *kdm = new RateConstant(1.0/30.0, "kdm");
00359     RateConstant *kt = new RateConstant(1.0/6.0, "kt");
00360     RateConstant *kd = new RateConstant(1.0/100.0, "kd");                  
00361 
00362 
00363         rateConstants.push_back(k_rb_EGF);
00364         rateConstants.push_back(k_ru_EGF);
00365         rateConstants.push_back(k_rb_NGF);
00366         rateConstants.push_back(k_ru_NGF);
00367 
00368         rateConstants.push_back(k_EGF);
00369         rateConstants.push_back(Km_EGF);
00370         rateConstants.push_back(k_NGF);
00371         rateConstants.push_back(Km_NGF);
00372 
00373         rateConstants.push_back(k_dSos);
00374         rateConstants.push_back(Km_dSos);
00375         rateConstants.push_back(k_Sos);
00376         rateConstants.push_back(Km_Sos);
00377         rateConstants.push_back(k_RasGap);
00378         rateConstants.push_back(Km_RasGap);
00379         rateConstants.push_back(k_RasToRaf1);
00380         rateConstants.push_back(Km_RasToRaf1);
00381         rateConstants.push_back(k_pRaf1);
00382         rateConstants.push_back(Km_pRaf1);
00383         rateConstants.push_back(k_pBRaf);
00384         rateConstants.push_back(Km_pBRaf);
00385         rateConstants.push_back(k_dMek);
00386         rateConstants.push_back(Km_dMek);
00387 
00388         rateConstants.push_back(k_pMek_Cytoplasmic);
00389         rateConstants.push_back(Km_pMek_Cytoplasmic);
00390         rateConstants.push_back(k_dErk_Cytoplasmic);
00391         rateConstants.push_back(Km_dErk_Cytoplasmic);
00392 //      rateConstants.push_back(k_dErk_Cytoplasmic2);
00393 //      rateConstants.push_back(Km_dErk_Cytoplasmic2);
00394         rateConstants.push_back(k_pP90Rsk);
00395         rateConstants.push_back(Km_pP90Rsk);
00396 
00397         rateConstants.push_back(k_PI3K);
00398         rateConstants.push_back(Km_PI3K);
00399         rateConstants.push_back(k_PI3K_Ras);
00400         rateConstants.push_back(Km_PI3K_Ras);
00401         rateConstants.push_back(k_dPI3K);
00402         rateConstants.push_back(Km_dPI3K);
00403 
00404         rateConstants.push_back(k_Akt);
00405         rateConstants.push_back(Km_Akt);
00406         rateConstants.push_back(k_dAkt);
00407         rateConstants.push_back(Km_dAkt);
00408         rateConstants.push_back(k_dRaf1ByAkt);
00409         rateConstants.push_back(Km_Raf1ByAkt);
00410 
00411         rateConstants.push_back(k_Rap_GEF_NGF);
00412         rateConstants.push_back(Km_RapGef_NGF);
00413         rateConstants.push_back(k_dRapGEF);
00414         rateConstants.push_back(Km_dRapGEF);
00415         rateConstants.push_back(k_RapGEF);
00416         rateConstants.push_back(Km_RapGEF);
00417         rateConstants.push_back(k_RapGap);
00418         rateConstants.push_back(Km_RapGap);
00419         rateConstants.push_back(k_RapToBRaf);
00420         rateConstants.push_back(Km_RapToBRaf);
00421         rateConstants.push_back(k_dRapToRaf1);
00422         rateConstants.push_back(Km_dRapToRaf1);
00423 
00424         rateConstants.push_back(ktrans_Erk);
00425         rateConstants.push_back(k_dErkActiveNuclear);
00426         rateConstants.push_back(Km_dErkActiveNuclear);
00427 
00428         rateConstants.push_back(k_pSp1);
00429         rateConstants.push_back(Km_pSp1);
00430         rateConstants.push_back(k_dSp1);
00431         rateConstants.push_back(Km_dSp1);
00432 
00433         rateConstants.push_back(kb_CyclinD);
00434         rateConstants.push_back(ku_CyclinD);
00435         rateConstants.push_back(ktm_CyclinD);
00436         rateConstants.push_back(kdm_CyclinD);
00437         rateConstants.push_back(kt_CyclinD);
00438         rateConstants.push_back(kd_CyclinD);
00439 
00440         rateConstants.push_back(kb_P21);
00441         rateConstants.push_back(ku_P21);
00442         rateConstants.push_back(ktm_P21);
00443         rateConstants.push_back(kdm_P21);
00444         rateConstants.push_back(kt_P21);
00445         rateConstants.push_back(kd_P21);
00446 
00447         rateConstants.push_back(kb_CFos);
00448         rateConstants.push_back(ku_CFos);
00449         rateConstants.push_back(ktm_CFos);
00450         rateConstants.push_back(kdm_CFos);
00451         rateConstants.push_back(kt_CFos);
00452         rateConstants.push_back(kd_CFos);
00453 
00454         rateConstants.push_back(kb_ErkPhosphataseCytoplasmic);
00455         rateConstants.push_back(ku_ErkPhosphataseCytoplasmic);
00456         rateConstants.push_back(ktm_ErkPhosphataseCytoplasmic);
00457         rateConstants.push_back(kdm_ErkPhosphataseCytoplasmic);
00458         rateConstants.push_back(kt_ErkPhosphataseCytoplasmic);
00459         rateConstants.push_back(kd_ErkPhosphataseCytoplasmic);
00460 
00461         rateConstants.push_back(kb);
00462         rateConstants.push_back(ku);
00463         rateConstants.push_back(ktm);
00464         rateConstants.push_back(kdm);
00465         rateConstants.push_back(kt);
00466         rateConstants.push_back(kd);
00467 
00468 
00469         ReceptorBindingReaction *EGFBindingReaction = new ReceptorBindingReaction(EGF, freeEGFReceptor, boundEGFReceptor, k_rb_EGF, "EGFBindingReaction");
00470         ReceptorUnbindingReaction *EGFUnbindingReaction = new ReceptorUnbindingReaction(boundEGFReceptor, freeEGFReceptor, EGF, k_ru_EGF, "EGFUnbindingReaction");
00471         ReceptorBindingReaction *NGFBindingReaction = new ReceptorBindingReaction(NGF, freeNGFReceptor, boundNGFReceptor, k_rb_NGF, "NGFBindingReaction");
00472         ReceptorUnbindingReaction *NGFUnbindingReaction = new ReceptorUnbindingReaction(boundNGFReceptor, freeNGFReceptor, NGF, k_ru_NGF, "NGFUnbindingReaction");
00473 
00474         MichaelisMentenPhosphorylationReaction *SosActivationByEGFReaction = new MichaelisMentenPhosphorylationReaction(boundEGFReceptor, SosInactive, SosActive, k_EGF, Km_EGF, "SosActivationbyEGFReaction");
00475         MichaelisMentenPhosphorylationReaction *SosActivationByNGFReaction = new MichaelisMentenPhosphorylationReaction(boundNGFReceptor, SosInactive, SosActive, k_NGF, Km_NGF, "SosActivationbyNGFReaction");
00476         MichaelisMentenDephosphorylationReaction *SosDeactivationReaction = new MichaelisMentenDephosphorylationReaction(P90RskActive, SosActive, SosInactive, k_dSos, Km_dSos, "SosDeactivationReaction");
00477         MichaelisMentenGProteinActivationReaction *RasActivationReaction = new MichaelisMentenGProteinActivationReaction(SosActive, RasInactive, RasActive, k_Sos, Km_Sos, "RasActivationReaction");
00478         MichaelisMentenGProteinDeactivationReaction *RasDeactivationReaction = new MichaelisMentenGProteinDeactivationReaction(RasGapActive, RasActive, RasInactive, k_RasGap, Km_RasGap, "RasDeactivationReaction");
00479         MichaelisMentenProteinProteinActivationReaction *Raf1ByRasActivationReaction = new MichaelisMentenProteinProteinActivationReaction(RasActive, Raf1Inactive, Raf1Active, k_RasToRaf1, Km_RasToRaf1, "Raf1ByRasActivationReaction");
00480 
00481         MichaelisMentenPhosphorylationReaction *MekbyRaf1ActivationReaction = new MichaelisMentenPhosphorylationReaction(Raf1Active, MekInactive, MekActive, k_pRaf1, Km_pRaf1, "MekbyRaf1ActivationReaction");
00482         MichaelisMentenPhosphorylationReaction *MekbyBRafActivationReaction = new MichaelisMentenPhosphorylationReaction(BRafActive, MekInactive, MekActive, k_pBRaf, Km_pBRaf, "MekbyBRafActivationReaction");
00483         MichaelisMentenDephosphorylationReaction *MekDeactivationReaction = new MichaelisMentenDephosphorylationReaction(filler, MekActive, MekInactive, k_dMek, Km_dMek, "MekDeactivationReaction");
00484         MichaelisMentenPhosphorylationReaction *ErkActivationCytoplasmicReaction = new MichaelisMentenPhosphorylationReaction(MekActive, ErkInactiveCytoplasmic, ErkActiveCytoplasmic, k_pMek_Cytoplasmic, Km_pMek_Cytoplasmic, "ErkActivationCytoplasmicReaction");
00485         MichaelisMentenDephosphorylationReaction *ErkDeactivationCytoplasmicReaction = new MichaelisMentenDephosphorylationReaction(ErkPhosphataseCytoplasmic, ErkActiveCytoplasmic, ErkInactiveCytoplasmic, k_dErk_Cytoplasmic, Km_dErk_Cytoplasmic, "ErkDeactivationCytoplasmicReaction");
00486 //      MichaelisMentenDephosphorylationReaction *ErkDeactivationCytoplasmicReaction2 = new MichaelisMentenDephosphorylationReaction(ErkPhosphataseCytoplasmic2, ErkActiveCytoplasmic, ErkInactiveCytoplasmic, k_dErk_Cytoplasmic2, Km_dErk_Cytoplasmic2, "ErkDeactivationCytoplasmicReaction2");
00487         MichaelisMentenPhosphorylationReaction *P90RskActivationReaction = new MichaelisMentenPhosphorylationReaction(ErkActiveCytoplasmic, P90RskInactive, P90RskActive, k_pP90Rsk, Km_pP90Rsk, "P90RskActivationReaction");
00488 
00489         MichaelisMentenPhosphorylationReaction *PI3KEGFActivationReaction = new MichaelisMentenPhosphorylationReaction(boundEGFReceptor, PI3KInactive, PI3KActive, k_PI3K, Km_PI3K, "PI3KEGFActivationReaction");
00490         MichaelisMentenProteinProteinActivationReaction *PI3KRasActivationReaction = new MichaelisMentenProteinProteinActivationReaction(RasActive, PI3KInactive, PI3KActive, k_PI3K_Ras, Km_PI3K_Ras, "PI3KRasActivationReaction");
00491         MichaelisMentenDephosphorylationReaction *PI3KDeactivationReaction = new MichaelisMentenDephosphorylationReaction(filler, PI3KActive, PI3KInactive, k_dPI3K, Km_dPI3K, "PI3KDeactivationReaction");
00492         MichaelisMentenPhosphorylationReaction *AktActivationReaction = new MichaelisMentenPhosphorylationReaction(PI3KActive, AktInactive, AktActive, k_Akt, Km_Akt, "AktActivationReaction");
00493         MichaelisMentenDephosphorylationReaction *AktDeactivationReaction = new MichaelisMentenDephosphorylationReaction(filler, AktActive, AktInactive, k_dAkt, Km_dAkt, "AktDeactivationReaction");   
00494         MichaelisMentenProteinProteinDeactivationReaction *Raf1ByAktDeactivationReaction = new MichaelisMentenProteinProteinDeactivationReaction(AktActive, Raf1Active, Raf1Inactive, k_dRaf1ByAkt, Km_Akt, "RafByAktDeactivationReaction");
00495 
00496         MichaelisMentenPhosphorylationReaction *RapGEFActivationReaction = new MichaelisMentenPhosphorylationReaction(boundNGFReceptor, SosInactive, SosActive, k_Rap_GEF_NGF, Km_RapGef_NGF, "RapGEFActivationReaction");
00497         MichaelisMentenDephosphorylationReaction *RapGEFDeactivationReaction = new MichaelisMentenDephosphorylationReaction(filler, RapGEFActive, RapGEFInactive, k_dRapGEF, Km_dRapGEF, "RapGEFDeactivationReaction");
00498         MichaelisMentenGProteinActivationReaction *RapActivationReaction = new MichaelisMentenGProteinActivationReaction(RapGEFActive, RapInactive, RapActive, k_RapGEF, Km_RapGEF, "RapActivationReaction");
00499         MichaelisMentenGProteinDeactivationReaction *RapDeactivationReaction = new MichaelisMentenGProteinDeactivationReaction(RapGapActive, RapActive, RapInactive, k_RapGap, Km_RapGap, "RapDeactivationReaction");
00500         MichaelisMentenProteinProteinActivationReaction *BRafByRapActivationReaction = new MichaelisMentenProteinProteinActivationReaction(RapActive, BRafInactive, BRafActive, k_RapToBRaf, Km_RapToBRaf, "BRafByRapActivationReaction");
00501         MichaelisMentenProteinProteinDeactivationReaction *Raf1ByRapDeactivationReaction = new MichaelisMentenProteinProteinDeactivationReaction(RapActive, Raf1Active, Raf1Inactive, k_dRapToRaf1, Km_dRapToRaf1, "Raf1ByRapDeactivationReaction");
00502 
00503         ChemicalTransportReaction *ErkActiveNuclearTranslocationReaction = new ChemicalTransportReaction(ErkActiveCytoplasmic, ErkActiveNuclear, ktrans_Erk, "ErkActiveNuclearTranslocation");
00504         ChemicalTransportReaction *ErkActiveCytoplasmicTranslocationReaction = new ChemicalTransportReaction(ErkActiveNuclear, ErkActiveCytoplasmic, ktrans_Erk, "ErkActiveCytoplasmicTranslocation");  
00505         MichaelisMentenDephosphorylationReaction *ErkActiveNuclearDephosphorylationReaction = new MichaelisMentenDephosphorylationReaction(ErkPhosphataseNuclear, ErkActiveNuclear, ErkInactiveNuclear, k_dErkActiveNuclear, Km_dErkActiveNuclear, "ErkActiveNuclearDephosphorylationReaction");
00506 
00507         MichaelisMentenPhosphorylationReaction *Sp1ActivationReaction = new MichaelisMentenPhosphorylationReaction(ErkActiveNuclear, Sp1Inactive, Sp1Active, k_pSp1, Km_pSp1, "Sp1ActivationReaction");
00508         MichaelisMentenDephosphorylationReaction *Sp1DeactivationReaction = new MichaelisMentenDephosphorylationReaction(filler, Sp1Active, Sp1Inactive, k_dSp1, Km_dSp1, "Sp1DeactivationReaction");
00509 
00510         PromoterBindingReaction *CyclinDbindingReaction = new PromoterBindingReaction(CyclinDfreePromoter, Sp1Active, CyclinDboundPromoter, kb, "CyclinDbindingReaction");
00511         PromoterUnbindingReaction *CyclinDunbindingReaction = new PromoterUnbindingReaction(CyclinDboundPromoter, CyclinDfreePromoter, Sp1Active, ku_CyclinD, "CyclinDunbindingReaction");
00512         TranscriptionReaction *CyclinDtranscriptionReaction = new TranscriptionReaction(CyclinDboundPromoter, CyclinDmRNA, ktm_CyclinD, "CyclinDtranscriptionReaction");
00513         RNADegradationReaction *CyclinDmRNADegradationReaction = new RNADegradationReaction(CyclinDmRNA, kdm_CyclinD, "CyclinDmRNADegradationReaction");
00514         ProteinTranslationReaction *CyclinDtranslationReaction = new ProteinTranslationReaction(CyclinDmRNA, CyclinD, kt_CyclinD, "CyclinDtranslationReaction");
00515         UnstableProteinDegradationReaction *CyclinDproteinDegradationReaction = new UnstableProteinDegradationReaction(CyclinD, kd_CyclinD, "CyclinDproteinDegradationReaction");
00516 
00517         PromoterBindingReaction *P21bindingReaction = new PromoterBindingReaction(P21freePromoter, Sp1Active, P21boundPromoter, kb_P21, "P21bindingReaction");
00518         PromoterUnbindingReaction *P21unbindingReaction = new PromoterUnbindingReaction(P21boundPromoter, P21freePromoter, Sp1Active, ku_P21, "P21unbindingReaction");
00519         TranscriptionReaction *P21transcriptionReaction = new TranscriptionReaction(P21boundPromoter, P21mRNA, ktm_P21, "P21transcriptionReaction");
00520         RNADegradationReaction *P21mRNADegradationReaction = new RNADegradationReaction(P21mRNA, kdm_P21, "P21mRNADegradationReaction");
00521         ProteinTranslationReaction *P21translationReaction = new ProteinTranslationReaction(P21mRNA, P21, kt_P21, "P21translationReaction");
00522         UnstableProteinDegradationReaction *P21proteinDegradationReaction = new UnstableProteinDegradationReaction(P21, kd_P21, "P21proteinDegradationReaction");
00523 
00524         PromoterBindingReaction *CFosbindingReaction = new PromoterBindingReaction(CFosfreePromoter, Sp1Active, CFosboundPromoter, kb_CFos, "CFosbindingReaction");
00525         PromoterUnbindingReaction *CFosunbindingReaction = new PromoterUnbindingReaction(CFosboundPromoter, CFosfreePromoter, Sp1Active, ku_CFos, "CFosunbindingReaction");
00526         TranscriptionReaction *CFostranscriptionReaction = new TranscriptionReaction(CFosboundPromoter, CFosmRNA, ktm_CFos, "CFostranscriptionReaction");
00527         RNADegradationReaction *CFosmRNADegradationReaction = new RNADegradationReaction(CFosmRNA, kdm_CFos, "CFosmRNADegradationReaction");
00528         ProteinTranslationReaction *CFostranslationReaction = new ProteinTranslationReaction(CFosmRNA, CFos, kt_CFos, "CFostranslationReaction");
00529         UnstableProteinDegradationReaction *CFosproteinDegradationReaction = new UnstableProteinDegradationReaction(CFos, kd_CFos, "CFosproteinDegradationReaction");
00530 
00531         PromoterBindingReaction *ErkPhosphataseCytoplasmicbindingReaction = new PromoterBindingReaction(ErkPhosphataseCytoplasmicfreePromoter, Sp1Active, ErkPhosphataseCytoplasmicboundPromoter, kb_ErkPhosphataseCytoplasmic, "ErkPhosphataseCytoplasmicbindingReaction");
00532         PromoterUnbindingReaction *ErkPhosphataseCytoplasmicunbindingReaction = new PromoterUnbindingReaction(ErkPhosphataseCytoplasmicboundPromoter, ErkPhosphataseCytoplasmicfreePromoter, Sp1Active, ku_ErkPhosphataseCytoplasmic, "ErkPhosphataseCytoplasmicunbindingReaction");
00533         TranscriptionReaction *ErkPhosphataseCytoplasmictranscriptionReaction = new TranscriptionReaction(ErkPhosphataseCytoplasmicboundPromoter, ErkPhosphataseCytoplasmicmRNA, ktm_ErkPhosphataseCytoplasmic, "ErkPhosphataseCytoplasmictranscriptionReaction");
00534         RNADegradationReaction *ErkPhosphataseCytoplasmicmRNADegradationReaction = new RNADegradationReaction(ErkPhosphataseCytoplasmicmRNA, kdm_ErkPhosphataseCytoplasmic, "ErkPhosphataseCytoplasmicmRNADegradationReaction");
00535         ProteinTranslationReaction *ErkPhosphataseCytoplasmictranslationReaction = new ProteinTranslationReaction(ErkPhosphataseCytoplasmicmRNA, ErkPhosphataseCytoplasmic, kt_ErkPhosphataseCytoplasmic, "ErkPhosphataseCytoplasmictranslationReaction");
00536         UnstableProteinDegradationReaction *ErkPhosphataseCytoplasmicproteinDegradationReaction = new UnstableProteinDegradationReaction(ErkPhosphataseCytoplasmic, kd_ErkPhosphataseCytoplasmic, "ErkPhosphataseCytoplasmicproteinDegradationReaction");
00537 
00538         PromoterBindingReaction *bindingReaction = new PromoterBindingReaction(freePromoter, protein, boundPromoter, kb, "PromoterBindingReaction");
00539         PromoterUnbindingReaction *unbindingReaction = new PromoterUnbindingReaction(boundPromoter, freePromoter, protein, ku, "unbindingReaction");
00540         TranscriptionReaction *transcriptionReaction = new TranscriptionReaction(boundPromoter, mRNA, ktm, "transcriptionReaction");
00541         RNADegradationReaction *mRNADegradationReaction = new RNADegradationReaction(mRNA, kdm, "mRNADegradationReaction");
00542         ProteinTranslationReaction *translationReaction = new ProteinTranslationReaction(mRNA, protein, kt, "translationReaction");
00543         UnstableProteinDegradationReaction *proteinDegradationReaction = new UnstableProteinDegradationReaction(protein, kd, "proteinDegradationReaction");
00544 
00545         reactions.push_back(EGFBindingReaction);
00546         reactions.push_back(EGFUnbindingReaction);
00547         reactions.push_back(NGFBindingReaction);
00548         reactions.push_back(NGFUnbindingReaction);
00549 
00550         reactions.push_back(SosActivationByEGFReaction);
00551         reactions.push_back(SosActivationByNGFReaction);
00552         reactions.push_back(SosDeactivationReaction);
00553         reactions.push_back(RasActivationReaction);
00554         reactions.push_back(RasDeactivationReaction);
00555         reactions.push_back(Raf1ByRasActivationReaction);
00556 
00557         reactions.push_back(MekbyRaf1ActivationReaction);
00558         reactions.push_back(MekbyBRafActivationReaction);
00559         reactions.push_back(MekDeactivationReaction);
00560         reactions.push_back(ErkActivationCytoplasmicReaction);
00561         reactions.push_back(ErkDeactivationCytoplasmicReaction);
00562 //      reactions.push_back(ErkDeactivationCytoplasmicReaction2);
00563         reactions.push_back(P90RskActivationReaction);
00564 
00565         reactions.push_back(PI3KEGFActivationReaction);
00566         reactions.push_back(PI3KRasActivationReaction);
00567         reactions.push_back(PI3KDeactivationReaction);
00568         reactions.push_back(AktActivationReaction);
00569         reactions.push_back(AktDeactivationReaction);
00570         reactions.push_back(Raf1ByAktDeactivationReaction);
00571 
00572         reactions.push_back(RapGEFActivationReaction);
00573         reactions.push_back(RapGEFDeactivationReaction);
00574         reactions.push_back(RapActivationReaction);
00575         reactions.push_back(RapDeactivationReaction);
00576         reactions.push_back(BRafByRapActivationReaction);
00577         reactions.push_back(Raf1ByRapDeactivationReaction);
00578 
00579         reactions.push_back(ErkActiveNuclearTranslocationReaction);
00580         reactions.push_back(ErkActiveCytoplasmicTranslocationReaction);
00581         reactions.push_back(ErkActiveNuclearDephosphorylationReaction);
00582 
00583         reactions.push_back(Sp1ActivationReaction);
00584         reactions.push_back(Sp1DeactivationReaction);
00585 
00586         reactions.push_back(CyclinDbindingReaction);
00587         reactions.push_back(CyclinDunbindingReaction);
00588         reactions.push_back(CyclinDtranscriptionReaction);
00589         reactions.push_back(CyclinDmRNADegradationReaction);
00590         reactions.push_back(CyclinDtranslationReaction);
00591         reactions.push_back(CyclinDproteinDegradationReaction);
00592 
00593         reactions.push_back(P21bindingReaction);
00594         reactions.push_back(P21unbindingReaction);
00595         reactions.push_back(P21transcriptionReaction);
00596         reactions.push_back(P21mRNADegradationReaction);
00597         reactions.push_back(P21translationReaction);
00598         reactions.push_back(P21proteinDegradationReaction);
00599 
00600         reactions.push_back(CFosbindingReaction);
00601         reactions.push_back(CFosunbindingReaction);
00602         reactions.push_back(CFostranscriptionReaction);
00603         reactions.push_back(CFosmRNADegradationReaction);
00604         reactions.push_back(CFostranslationReaction);
00605         reactions.push_back(CFosproteinDegradationReaction);
00606 
00607         reactions.push_back(ErkPhosphataseCytoplasmicbindingReaction);
00608         reactions.push_back(ErkPhosphataseCytoplasmicunbindingReaction);
00609         reactions.push_back(ErkPhosphataseCytoplasmictranscriptionReaction);
00610         reactions.push_back(ErkPhosphataseCytoplasmicmRNADegradationReaction);
00611         reactions.push_back(ErkPhosphataseCytoplasmictranslationReaction);
00612         reactions.push_back(ErkPhosphataseCytoplasmicproteinDegradationReaction);
00613 
00614         reactions.push_back(bindingReaction);
00615         reactions.push_back(unbindingReaction);
00616         reactions.push_back(transcriptionReaction);
00617         reactions.push_back(mRNADegradationReaction);
00618         reactions.push_back(translationReaction);
00619         reactions.push_back(proteinDegradationReaction);
00620 }
00621 
00622 ErkSubnetwork::~ErkSubnetwork()
00623 {
00624         
00625 }