EGFRTraffickingNetwork.cpp Source File

00001 // EGFRTraffickingNetwork.cpp: implementation of the CEGFRTraffickingNetwork class.
00002 //
00004 
00005 #include "EGFRTraffickingNetwork.h"
00006 
00008 // Construction/Destruction
00010 
00011 CEGFRTraffickingNetwork::CEGFRTraffickingNetwork()
00012 {
00013         // CFactor = #molecules/1 uM
00014         double CFactor = 600000;
00015         double SecPerMin = 60.0;
00016 
00017         // chemical species
00018 
00019         // EGF/EGFR
00020         // 0
00021         Chemical *EGF = new Chemical(chemicals.size(),0.0,"EGF");
00022         chemicals.push_back(EGF);
00023 
00024         Chemical *DegradedEGF = new Chemical(chemicals.size(),0.0,"DegradedEGF");
00025         chemicals.push_back(DegradedEGF);
00026 
00027         Chemical *EndosomalEGF = new Chemical(chemicals.size(),0.0,"EndosomalEGF");
00028         chemicals.push_back(EndosomalEGF);
00029 
00030         // two species of EGFR - coated pit and non coated pit
00031         Chemical *CPFreePMEGFR = new Chemical(chemicals.size(),0.0,"CPFreePMEGFR");
00032         chemicals.push_back(CPFreePMEGFR);
00033 
00034         Chemical *NonCPFreePMEGFR = new Chemical(chemicals.size(),0.0,"NonCPFreePMEGFR");
00035         chemicals.push_back(NonCPFreePMEGFR);
00036 
00037         Chemical *CPBoundPMEGFR = new Chemical(chemicals.size(),0.0,"CPBoundPMEGFR");
00038         chemicals.push_back(CPBoundPMEGFR);
00039 
00040         Chemical *NonCPBoundPMEGFR = new Chemical(chemicals.size(),0.0,"NonCPBoundPMEGFR");
00041         chemicals.push_back(NonCPBoundPMEGFR);
00042         
00043         Chemical *DegradedEGFR = new Chemical(chemicals.size(),0.0,"DegradedEGFR");
00044         chemicals.push_back(DegradedEGFR);
00045 
00046         Chemical *CPBoundPMEGFRCoolCbl = new Chemical(chemicals.size(),0.0,"CPBoundPMEGFRCoolCbl");
00047         chemicals.push_back(CPBoundPMEGFRCoolCbl);
00048 
00049         Chemical *NonCPBoundPMEGFRCoolCbl = new Chemical(chemicals.size(),0.0,"NonCPBoundPMEGFRCoolCbl");
00050         chemicals.push_back(NonCPBoundPMEGFRCoolCbl);
00051 
00052         // 10
00053         Chemical *CPBoundPMEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"CPBoundPMEGFRCoolCblActive");
00054         chemicals.push_back(CPBoundPMEGFRCoolCblActive);
00055 
00056         Chemical *NonCPBoundPMEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"NonCPBoundPMEGFRCoolCblActive");
00057         chemicals.push_back(NonCPBoundPMEGFRCoolCblActive);
00058 
00059         Chemical *UbiCPBoundPMEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"UbiCPBoundPMEGFRCoolCblActive");
00060         chemicals.push_back(UbiCPBoundPMEGFRCoolCblActive);
00061 
00062         Chemical *UbiNonCPBoundPMEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"UbiNonCPBoundPMEGFRCoolCblActive");
00063         chemicals.push_back(UbiNonCPBoundPMEGFRCoolCblActive);
00064 
00065         Chemical *NonCoatedBoundEGFR = new Chemical(chemicals.size(),0.0,"NonCoatedBoundEGFR");
00066         chemicals.push_back(NonCoatedBoundEGFR);
00067 
00068         Chemical *NonCoatedBoundEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"NonCoatedBoundEGFRCoolCblActive");
00069         chemicals.push_back(NonCoatedBoundEGFRCoolCblActive);
00070 
00071         Chemical *NonCoatedUbiBoundEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"NonCoatedUbiBoundEGFRCoolCblActive");
00072         chemicals.push_back(NonCoatedUbiBoundEGFRCoolCblActive);
00073 
00074         Chemical *ProtoCCVEGFR = new Chemical(chemicals.size(),0.0,"ProtoCCVEGFR");
00075         chemicals.push_back(ProtoCCVEGFR);
00076 
00077         Chemical *ProtoCCVEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"ProtoCCVEGFRCoolCblActive");
00078         chemicals.push_back(ProtoCCVEGFRCoolCblActive);
00079 
00080         Chemical *ProtoCCVUbiEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"ProtoCCVUbiEGFRCoolCblActive");
00081         chemicals.push_back(ProtoCCVUbiEGFRCoolCblActive);
00082 
00083         // 20
00084         Chemical *CCVEGFR = new Chemical(chemicals.size(),0.0,"CCVEGFR");
00085         chemicals.push_back(CCVEGFR);
00086 
00087         Chemical *CCVEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"CCVEGFRCoolCblActive");
00088         chemicals.push_back(CCVEGFRCoolCblActive);
00089 
00090         Chemical *CCVUbiEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"CCVUbiEGFRCoolCblActive");
00091         chemicals.push_back(CCVUbiEGFRCoolCblActive);
00092 
00093         Chemical *CCVEGFRACK2 = new Chemical(chemicals.size(),0.0,"CCVEGFRACK2");
00094         chemicals.push_back(CCVEGFRACK2);
00095 
00096         Chemical *CCVEGFRCoolCblActiveACK2 = new Chemical(chemicals.size(),0.0,"CCVEGFRCoolCblActiveACK2");
00097         chemicals.push_back(CCVEGFRCoolCblActiveACK2);
00098 
00099         Chemical *CCVUbiEGFRCoolCblActiveACK2 = new Chemical(chemicals.size(),0.0,"CCVUbiEGFRCoolCblActiveACK2");
00100         chemicals.push_back(CCVUbiEGFRCoolCblActiveACK2);
00101 
00102         Chemical *DeliveredEGFRACK2 = new Chemical(chemicals.size(),0.0,"DeliveredEGFRACK2");
00103         chemicals.push_back(DeliveredEGFRACK2);
00104 
00105         Chemical *DeliveredEGFRCoolCblActiveACK2 = new Chemical(chemicals.size(),0.0,"DeliveredEGFRCoolCblActiveACK2");
00106         chemicals.push_back(DeliveredEGFRCoolCblActiveACK2);
00107 
00108         Chemical *DeliveredUbiEGFRCoolCblActiveACK2 = new Chemical(chemicals.size(),0.0,"DeliveredUbiEGFRCoolCblActiveACK2");
00109         chemicals.push_back(DeliveredUbiEGFRCoolCblActiveACK2);
00110 
00111         Chemical *DeliveredEGFR = new Chemical(chemicals.size(),0.0,"DeliveredEGFR");
00112         chemicals.push_back(DeliveredEGFR);
00113 
00114         // 30
00115         Chemical *DeliveredEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"DeliveredEGFRCoolCblActive");
00116         chemicals.push_back(DeliveredEGFRCoolCblActive);
00117 
00118         Chemical *DeliveredUbiEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"DeliveredUbiEGFRCoolCblActive");
00119         chemicals.push_back(DeliveredUbiEGFRCoolCblActive);
00120 
00121         Chemical *BoundEndoEGFR = new Chemical(chemicals.size(),0.0,"BoundEndoEGFR");
00122         chemicals.push_back(BoundEndoEGFR);
00123 
00124         Chemical *UbiBoundEndoEGFR = new Chemical(chemicals.size(),0.0,"UbiBoundEndoEGFR");
00125         chemicals.push_back(UbiBoundEndoEGFR);
00126 
00127         Chemical *FreeEndoEGFR = new Chemical(chemicals.size(),0.0,"FreeEndoEGFR");
00128         chemicals.push_back(FreeEndoEGFR);
00129 
00130         Chemical *UbiFreeEndoEGFR = new Chemical(chemicals.size(),0.0,"UbiFreeEndoEGFR");
00131         chemicals.push_back(UbiFreeEndoEGFR);
00132 
00133         Chemical *BoundEndoEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"BoundEndoEGFRCoolCblActive");
00134         chemicals.push_back(BoundEndoEGFRCoolCblActive);
00135 
00136         Chemical *FreeEndoEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"FreeEndoEGFRCoolCblActive");
00137         chemicals.push_back(FreeEndoEGFRCoolCblActive);
00138 
00139         Chemical *UbiBoundEndoEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"UbiBoundEndoEGFRCoolCblActive");
00140         chemicals.push_back(UbiBoundEndoEGFRCoolCblActive);
00141 
00142         Chemical *UbiFreeEndoEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"UbiFreeEndoEGFRCoolCblActive");
00143         chemicals.push_back(UbiFreeEndoEGFRCoolCblActive);
00144 
00145         // 40
00146         Chemical *UbiFreeLysoEGFR = new Chemical(chemicals.size(),0.0,"UbiFreeLysoEGFR");
00147         chemicals.push_back(UbiFreeLysoEGFR);
00148 
00149         Chemical *EndosomalVesicle = new Chemical(chemicals.size(),0.0,"EndosomalVesicle");
00150         chemicals.push_back(EndosomalVesicle);
00151 
00152         Chemical *LysosomalVesicle = new Chemical(chemicals.size(),0.0,"LysosomalVesicle");
00153         chemicals.push_back(LysosomalVesicle);
00154 
00155         Chemical *ProtoRecyclingVesicle = new Chemical(chemicals.size(),0.0,"ProtoRecyclingVesicle");
00156         chemicals.push_back(ProtoRecyclingVesicle);
00157 
00158         Chemical *RecyclingVesicle = new Chemical(chemicals.size(),0.0,"RecyclingVesicle");
00159         chemicals.push_back(RecyclingVesicle);
00160 
00161         Chemical *Cdc42GAP = new Chemical(chemicals.size(),0.1*CFactor,"Cdc42GAP");
00162         chemicals.push_back(Cdc42GAP);
00163 
00164         // Cdc42 alone
00165         Chemical *Cdc42GDP = new Chemical(chemicals.size(),0.1*CFactor,"Cdc42GDP");
00166         chemicals.push_back(Cdc42GDP);
00167 
00168         Chemical *Cdc42GTP = new Chemical(chemicals.size(),0.0,"Cdc42GTP");
00169         chemicals.push_back(Cdc42GTP);
00170 
00171         Chemical *GolgiCdc42GDP = new Chemical(chemicals.size(),0.1*CFactor,"GolgiCdc42GDP");
00172         chemicals.push_back(GolgiCdc42GDP);
00173 
00174         Chemical *GolgiCdc42GTP = new Chemical(chemicals.size(),0.1*CFactor,"GolgiCdc42GTP");
00175         chemicals.push_back(GolgiCdc42GTP);
00176 
00177         // 50
00178         Chemical *EndoCdc42GDP = new Chemical(chemicals.size(),0.1*CFactor,"EndoCdc42GDP");
00179         chemicals.push_back(EndoCdc42GDP);
00180 
00181         // ACK and 42
00182         Chemical *ACK2 = new Chemical(chemicals.size(),1200,"ACK2");
00183         chemicals.push_back(ACK2);
00184 
00185         Chemical *ACK242GTP = new Chemical(chemicals.size(),0.0,"ACK242GTP");
00186         chemicals.push_back(ACK242GTP);
00187 
00188         Chemical *ACK2Active42GTP = new Chemical(chemicals.size(),0.0,"ACK2Active42GTP");
00189         chemicals.push_back(ACK2Active42GTP);
00190 
00191         Chemical *ACK2Active = new Chemical(chemicals.size(),0.0,"ACK2Active");
00192         chemicals.push_back(ACK2Active);
00193 
00194         Chemical *EndoACK2Active = new Chemical(chemicals.size(),0.0,"EndoACK2Active");
00195         chemicals.push_back(EndoACK2Active);
00196 
00197         Chemical *LysoACK2Active = new Chemical(chemicals.size(),0.0,"LysoACK2Active");
00198         chemicals.push_back(LysoACK2Active);
00199 
00200         Chemical *YPPTase1 = new Chemical(chemicals.size(),0.1*CFactor,"YPPTase1");
00201         chemicals.push_back(YPPTase1);
00202 
00203         // COP complex
00204         Chemical *COPI = new Chemical(chemicals.size(),0.1*CFactor,"COPI");
00205         chemicals.push_back(COPI);
00206 
00207         Chemical *EndoCOPI = new Chemical(chemicals.size(),0.0,"EndoCOPI");
00208         chemicals.push_back(EndoCOPI);
00209 
00210         // 60
00211         Chemical *GolgiCOPI42GTP = new Chemical(chemicals.size(),0.0,"GolgiCOPI42GTP");
00212         chemicals.push_back(GolgiCOPI42GTP);
00213 
00214         Chemical *EndoCOPI42GTP = new Chemical(chemicals.size(),0.0,"EndoCOPI42GTP");
00215         chemicals.push_back(EndoCOPI42GTP);
00216 
00217         Chemical *EndoCOPI42GDP = new Chemical(chemicals.size(),0.0,"EndoCOPI42GDP");
00218         chemicals.push_back(EndoCOPI42GDP);
00219 
00220         // Cool,Cbl,42
00221         Chemical *Cool1Cbl = new Chemical(chemicals.size(),0.1*CFactor,"Cool1Cbl");
00222         chemicals.push_back(Cool1Cbl);
00223 
00224         Chemical *Cool1CblActive = new Chemical(chemicals.size(),0.0,"Cool1CblActive");
00225         chemicals.push_back(Cool1CblActive);
00226 
00227         Chemical *Cool1Cbl42GTP = new Chemical(chemicals.size(),0.0,"Cool1Cbl42GTP");
00228         chemicals.push_back(Cool1Cbl42GTP);
00229 
00230         Chemical *Cool1CblActive42GTP = new Chemical(chemicals.size(),0.0,"Cool1CblActive42GTP");
00231         chemicals.push_back(Cool1CblActive42GTP);
00232                 
00233         // 67
00234         std::vector<Chemical *> vec1;
00235         vec1.push_back(CPFreePMEGFR);
00236         vec1.push_back(NonCPFreePMEGFR);
00237         vec1.push_back(CPBoundPMEGFR);
00238         vec1.push_back(NonCPBoundPMEGFR);
00239         vec1.push_back(CPBoundPMEGFRCoolCbl);
00240         vec1.push_back(NonCPBoundPMEGFRCoolCbl);
00241         vec1.push_back(CPBoundPMEGFRCoolCblActive);
00242         vec1.push_back(NonCPBoundPMEGFRCoolCblActive);
00243         vec1.push_back(UbiCPBoundPMEGFRCoolCblActive);
00244         vec1.push_back(UbiNonCPBoundPMEGFRCoolCblActive);
00245         vec1.push_back(ProtoCCVEGFR);
00246         vec1.push_back(ProtoCCVEGFRCoolCblActive);
00247         vec1.push_back(ProtoCCVUbiEGFRCoolCblActive);
00248         CAlgebraicChemical *TotalPMEGFR = new CSumChemical(chemicals.size(),"TotalPMEGFR",vec1);
00249         TotalPMEGFR->SetAll();
00250         chemicals.push_back(TotalPMEGFR);
00251         this->AddAlgebraicIndex(TotalPMEGFR);
00252 
00253         // 68
00254         std::vector<Chemical *> vec1a;
00255         vec1a.push_back(CPBoundPMEGFR);
00256         vec1a.push_back(NonCPBoundPMEGFR);
00257         vec1a.push_back(CPBoundPMEGFRCoolCbl);
00258         vec1a.push_back(NonCPBoundPMEGFRCoolCbl);
00259         vec1a.push_back(CPBoundPMEGFRCoolCblActive);
00260         vec1a.push_back(NonCPBoundPMEGFRCoolCblActive);
00261         vec1a.push_back(UbiCPBoundPMEGFRCoolCblActive);
00262         vec1a.push_back(UbiNonCPBoundPMEGFRCoolCblActive);
00263         vec1a.push_back(ProtoCCVEGFR);
00264         vec1a.push_back(ProtoCCVEGFRCoolCblActive);
00265         vec1a.push_back(ProtoCCVUbiEGFRCoolCblActive);
00266         CAlgebraicChemical *TotalBoundPMEGFR = new CSumChemical(chemicals.size(),"TotalBoundPMEGFR",vec1a);
00267         TotalBoundPMEGFR->SetAll();
00268         chemicals.push_back(TotalBoundPMEGFR);
00269         this->AddAlgebraicIndex(TotalBoundPMEGFR);
00270         
00271         // 69
00272         std::vector<Chemical *> vec2;
00273         vec2.push_back(CCVEGFR);
00274         vec2.push_back(CCVEGFRCoolCblActive);
00275         vec2.push_back(CCVUbiEGFRCoolCblActive);
00276         vec2.push_back(CCVEGFRACK2);
00277         vec2.push_back(CCVEGFRCoolCblActiveACK2);
00278         vec2.push_back(CCVUbiEGFRCoolCblActiveACK2);
00279         vec2.push_back(NonCoatedBoundEGFR);
00280         vec2.push_back(NonCoatedBoundEGFRCoolCblActive);
00281         vec2.push_back(NonCoatedUbiBoundEGFRCoolCblActive);
00282         vec2.push_back(DeliveredEGFRACK2);
00283         vec2.push_back(DeliveredEGFRCoolCblActiveACK2);
00284         vec2.push_back(DeliveredUbiEGFRCoolCblActiveACK2);
00285         vec2.push_back(DeliveredEGFR);
00286         vec2.push_back(DeliveredEGFRCoolCblActive);
00287         vec2.push_back(DeliveredUbiEGFRCoolCblActive);
00288         vec2.push_back(BoundEndoEGFR);
00289         vec2.push_back(BoundEndoEGFRCoolCblActive);
00290         vec2.push_back(UbiBoundEndoEGFR);
00291         vec2.push_back(UbiBoundEndoEGFRCoolCblActive);
00292         vec2.push_back(EndosomalEGF);
00293         CAlgebraicChemical *TotalInternalEGF = new CSumChemical(chemicals.size(),"TotalInternalEGF",vec2);
00294         TotalInternalEGF->SetAll();
00295         chemicals.push_back(TotalInternalEGF);
00296         this->AddAlgebraicIndex(TotalInternalEGF);
00297 
00298         // 70
00299         std::vector<Chemical *> vec3;
00300         vec3.push_back(CCVEGFR);
00301         vec3.push_back(CCVEGFRCoolCblActive);
00302         vec3.push_back(CCVUbiEGFRCoolCblActive);
00303         vec3.push_back(CCVEGFRACK2);
00304         vec3.push_back(CCVEGFRCoolCblActiveACK2);
00305         vec3.push_back(CCVUbiEGFRCoolCblActiveACK2);
00306         vec3.push_back(NonCoatedBoundEGFR);
00307         vec3.push_back(NonCoatedBoundEGFRCoolCblActive);
00308         vec3.push_back(NonCoatedUbiBoundEGFRCoolCblActive);
00309         vec3.push_back(DeliveredEGFRACK2);
00310         vec3.push_back(DeliveredEGFRCoolCblActiveACK2);
00311         vec3.push_back(DeliveredUbiEGFRCoolCblActiveACK2);
00312         vec3.push_back(DeliveredEGFR);
00313         vec3.push_back(DeliveredEGFRCoolCblActive);
00314         vec3.push_back(DeliveredUbiEGFRCoolCblActive);
00315         vec3.push_back(BoundEndoEGFR);
00316         vec3.push_back(UbiBoundEndoEGFR);
00317         vec3.push_back(BoundEndoEGFRCoolCblActive);
00318         vec3.push_back(UbiBoundEndoEGFRCoolCblActive);
00319         vec3.push_back(FreeEndoEGFR);
00320         vec3.push_back(UbiFreeEndoEGFR);
00321         vec3.push_back(FreeEndoEGFRCoolCblActive);
00322         vec3.push_back(UbiFreeEndoEGFRCoolCblActive);
00323         vec3.push_back(UbiFreeLysoEGFR);
00324         vec3.push_back(ProtoRecyclingVesicle);
00325         vec3.push_back(RecyclingVesicle);
00326         vec3.push_back(EndosomalVesicle);
00327         vec3.push_back(LysosomalVesicle);
00328         CAlgebraicChemical *TotalInternalEGFR = new CSumChemical(chemicals.size(),"TotalInternalEGFR",vec3);
00329         TotalInternalEGFR->SetAll();
00330         chemicals.push_back(TotalInternalEGFR);
00331         this->AddAlgebraicIndex(TotalInternalEGFR);
00332         
00333         std::vector<Chemical *> vec4;
00334         vec4.push_back(CCVEGFR);
00335         vec4.push_back(CCVEGFRCoolCblActive);
00336         vec4.push_back(CCVUbiEGFRCoolCblActive);
00337         vec4.push_back(CCVEGFRACK2);
00338         vec4.push_back(CCVEGFRCoolCblActiveACK2);
00339         vec4.push_back(CCVUbiEGFRCoolCblActiveACK2);
00340         CAlgebraicChemical *TotalCCVEGFR = new CSumChemical(chemicals.size(),"TotalCCVEGFR",vec4);
00341         TotalCCVEGFR->SetAll();
00342         chemicals.push_back(TotalCCVEGFR);
00343         this->AddAlgebraicIndex(TotalCCVEGFR);
00344 
00345         std::vector<Chemical *> vec5;
00346         vec5.push_back(FreeEndoEGFR);
00347         vec5.push_back(UbiFreeEndoEGFR);
00348         vec5.push_back(FreeEndoEGFRCoolCblActive);
00349         vec5.push_back(UbiFreeEndoEGFRCoolCblActive);
00350         vec5.push_back(BoundEndoEGFR);
00351         vec5.push_back(UbiBoundEndoEGFR);
00352         vec5.push_back(BoundEndoEGFRCoolCblActive);
00353         vec5.push_back(UbiBoundEndoEGFRCoolCblActive);
00354         vec5.push_back(EndosomalVesicle);
00355         vec5.push_back(ProtoRecyclingVesicle);
00356         vec5.push_back(RecyclingVesicle);
00357         CAlgebraicChemical *TotalEndoEGFR = new CSumChemical(chemicals.size(),"TotalEndoEGFR",vec5);
00358         TotalEndoEGFR->SetAll();
00359         chemicals.push_back(TotalEndoEGFR);
00360         this->AddAlgebraicIndex(TotalEndoEGFR);
00361 
00362 
00363         Chemical *ACK242GDP= new Chemical(chemicals.size(),0.0,"ACK242GDP");
00364         chemicals.push_back(ACK242GDP);
00365 
00366         Chemical *ACK2Active42GDP = new Chemical(chemicals.size(),0.0,"ACK2Active42GDP");
00367         chemicals.push_back(ACK2Active42GDP);
00368 
00369         Chemical *Cool1Cbl42GDP = new Chemical(chemicals.size(),0.0,"Cool1Cbl42GDP");
00370         chemicals.push_back(Cool1Cbl42GDP);
00371 
00372         Chemical *Cool1CblActive42GDP = new Chemical(chemicals.size(),0.0,"Cool1CblActive42GDP");
00373         chemicals.push_back(Cool1CblActive42GDP);
00374 
00375         // 77
00376         std::vector<Chemical *> vec7;
00377         vec7.push_back(CPFreePMEGFR);
00378         vec7.push_back(NonCPFreePMEGFR);
00379         vec7.push_back(CPBoundPMEGFR);
00380         vec7.push_back(NonCPBoundPMEGFR);
00381         vec7.push_back(CPBoundPMEGFRCoolCbl);
00382         vec7.push_back(NonCPBoundPMEGFRCoolCbl);
00383         vec7.push_back(CPBoundPMEGFRCoolCblActive);
00384         vec7.push_back(NonCPBoundPMEGFRCoolCblActive);
00385         vec7.push_back(UbiCPBoundPMEGFRCoolCblActive);
00386         vec7.push_back(UbiNonCPBoundPMEGFRCoolCblActive);
00387         vec7.push_back(ProtoCCVEGFR);
00388         vec7.push_back(ProtoCCVEGFRCoolCblActive);
00389         vec7.push_back(ProtoCCVUbiEGFRCoolCblActive);
00390         vec7.push_back(CCVEGFR);
00391         vec7.push_back(CCVEGFRCoolCblActive);
00392         vec7.push_back(CCVUbiEGFRCoolCblActive);
00393         vec7.push_back(CCVEGFRACK2);
00394         vec7.push_back(CCVEGFRCoolCblActiveACK2);
00395         vec7.push_back(CCVUbiEGFRCoolCblActiveACK2);
00396         vec7.push_back(NonCoatedBoundEGFR);
00397         vec7.push_back(NonCoatedBoundEGFRCoolCblActive);
00398         vec7.push_back(NonCoatedUbiBoundEGFRCoolCblActive);
00399         vec7.push_back(DeliveredEGFRACK2);
00400         vec7.push_back(DeliveredEGFRCoolCblActiveACK2);
00401         vec7.push_back(DeliveredUbiEGFRCoolCblActiveACK2);
00402         vec7.push_back(DeliveredEGFR);
00403         vec7.push_back(DeliveredEGFRCoolCblActive);
00404         vec7.push_back(DeliveredUbiEGFRCoolCblActive);
00405         vec7.push_back(BoundEndoEGFR);
00406         vec7.push_back(UbiBoundEndoEGFR);
00407         vec7.push_back(BoundEndoEGFRCoolCblActive);
00408         vec7.push_back(UbiBoundEndoEGFRCoolCblActive);
00409         vec7.push_back(FreeEndoEGFR);
00410         vec7.push_back(UbiFreeEndoEGFR);
00411         vec7.push_back(FreeEndoEGFRCoolCblActive);
00412         vec7.push_back(UbiFreeEndoEGFRCoolCblActive);
00413         vec7.push_back(UbiFreeLysoEGFR);
00414         vec7.push_back(ProtoRecyclingVesicle);
00415         vec7.push_back(RecyclingVesicle);
00416         vec7.push_back(EndosomalVesicle);
00417         vec7.push_back(LysosomalVesicle);
00418         CAlgebraicChemical *TotalEGFR = new CSumChemical(chemicals.size(),"TotalEGFR",vec7);
00419         TotalEGFR->SetAll();
00420         chemicals.push_back(TotalEGFR);
00421         this->AddAlgebraicIndex(TotalEGFR);
00422 
00423         std::vector<Chemical *> vec8;
00424         vec8.push_back(UbiCPBoundPMEGFRCoolCblActive);
00425         vec8.push_back(UbiNonCPBoundPMEGFRCoolCblActive);
00426         vec8.push_back(ProtoCCVUbiEGFRCoolCblActive);
00427         vec8.push_back(CCVUbiEGFRCoolCblActive);
00428         vec8.push_back(CCVUbiEGFRCoolCblActiveACK2);
00429         vec8.push_back(DeliveredUbiEGFRCoolCblActiveACK2);
00430         vec8.push_back(DeliveredUbiEGFRCoolCblActive);
00431         vec8.push_back(UbiBoundEndoEGFRCoolCblActive);
00432         vec8.push_back(UbiFreeEndoEGFRCoolCblActive);
00433         vec8.push_back(UbiBoundEndoEGFR);
00434         vec8.push_back(UbiFreeEndoEGFR);
00435         vec8.push_back(EndosomalVesicle);
00436         vec8.push_back(LysosomalVesicle);
00437         vec8.push_back(UbiFreeLysoEGFR);
00438         CAlgebraicChemical *TotalUbiEGFR = new CSumChemical(chemicals.size(),"TotalUbiEGFR",vec8);
00439         TotalUbiEGFR->SetAll();
00440         chemicals.push_back(TotalUbiEGFR);
00441         this->AddAlgebraicIndex(TotalUbiEGFR);
00442 
00443         Chemical *AP2 = new Chemical(chemicals.size(),1200,"AP2");
00444         chemicals.push_back(AP2);
00445 
00446         // 80
00447         Chemical *RasGDP = new Chemical(chemicals.size(),30000,"RasGDP");
00448         chemicals.push_back(RasGDP);
00449 
00450         Chemical *RasGTP = new Chemical(chemicals.size(),0.0,"RasGTP");
00451         chemicals.push_back(RasGTP);
00452 
00453         Chemical *Erk = new Chemical(chemicals.size(),30000,"Erk");
00454         chemicals.push_back(Erk);
00455 
00456         Chemical *ErkP = new Chemical(chemicals.size(),0.0,"ErkP");
00457         chemicals.push_back(ErkP);
00458 
00459         Chemical *RasGAP = new Chemical(chemicals.size(),30000,"RasGAP");
00460         chemicals.push_back(RasGAP);
00461 
00462         // 85
00463         Chemical *PP2A = new Chemical(chemicals.size(),30000,"PP2A");
00464         chemicals.push_back(PP2A);
00465 
00466         // rate constants
00467         // EGF binding/unbinding
00468         // 0
00469         RateConstant *kbEGF = new RateConstant(1.0e-07,"kbEGF");
00470         rateConstants.push_back(kbEGF);
00471 
00472         RateConstant *kuEGF = new RateConstant(0.02,0.02*0.2,"kuEGF");
00473         rateConstants.push_back(kuEGF);
00474 
00475         // EGF dissociation in endosomes
00476         RateConstant *kuEndoEGF = new RateConstant(0.1,0.1*0.2,"kuEndoEGF");
00477         rateConstants.push_back(kuEndoEGF);
00478 
00479         // 42 activation
00480         RateConstant *kEGFR42 = new RateConstant(0.2,"kEGFR42");
00481         rateConstants.push_back(kEGFR42);
00482 
00483         RateConstant *KmEGFR42 = new RateConstant(CFactor,"KmEGFR42");
00484         rateConstants.push_back(KmEGFR42);
00485 
00486         // Gapping of 42
00487         RateConstant *kGAP = new RateConstant(0.1,"kGAP");
00488         rateConstants.push_back(kGAP);
00489 
00490         RateConstant *KmGAP = new RateConstant(2.9*CFactor,"KmGAP");
00491         rateConstants.push_back(KmGAP);
00492 
00493         // binding/unbinding of AP-2
00494         RateConstant *kbAP2 = new RateConstant(1.0e-07,"kbAP2");
00495         rateConstants.push_back(kbAP2);
00496 
00497         RateConstant *kuAP2 = new RateConstant(0.02,"kuAP2");
00498         rateConstants.push_back(kuAP2);
00499 
00500         // allow possibility of different endocytic rates depending upon 
00501         // whether receptor is ubiquitinated or not 
00502 
00503         RateConstant *kEndo1 = new RateConstant(3.0,"kEndo1");
00504         rateConstants.push_back(kEndo1);
00505         
00506         // 10
00507         RateConstant *kEndo2 = new RateConstant(3.0,"kEndo2");
00508         rateConstants.push_back(kEndo2);
00509 
00510         RateConstant *kSlowEndo = new RateConstant(0.02,0.02*0.2,"kSlowEndo");
00511         rateConstants.push_back(kSlowEndo);
00512 
00513         // ACK2 binding/unbinding to 42
00514 
00515         RateConstant *kbACKActive = new RateConstant(1.0e-07,"kbACKActive");
00516         rateConstants.push_back(kbACKActive);
00517 
00518         RateConstant *kuACKActive = new RateConstant(0.02,"kuACKActive");
00519         rateConstants.push_back(kuACKActive);
00520 
00521         RateConstant *kbACK2 = new RateConstant(1.0e-07,"kbACK2");
00522         rateConstants.push_back(kbACK2);
00523 
00524         RateConstant *kuACK2 = new RateConstant(0.02,"kuACK2");
00525         rateConstants.push_back(kuACK2);
00526 
00527         RateConstant *kuACK242GDP = new RateConstant(0.1,"kuACK242GDP");
00528         rateConstants.push_back(kuACK242GDP);
00529 
00530         RateConstant *kuACK2Active42GDP = new RateConstant(0.1,"kuACK2Active42GDP");
00531         rateConstants.push_back(kuACK2Active42GDP);
00532         
00533         // ACK2 activation
00534         
00535         RateConstant *kACK2 = new RateConstant(5.0,"kACK2");
00536         rateConstants.push_back(kACK2);
00537 
00538         // ACK2 dephosphorylation by PPtase
00539 
00540         RateConstant *kdACK2 = new RateConstant(0.1,"kdACK2");
00541         rateConstants.push_back(kdACK2);
00542 
00543         // 20
00544         RateConstant *KmdACK2 = new RateConstant(CFactor,"KmdACK2");
00545         rateConstants.push_back(KmdACK2);
00546 
00547         // ACK2 binding/unbinding to the CCV
00548 
00549         RateConstant *kbACK2CCV = new RateConstant(1.0e-07,"kbACK2CCV");
00550         rateConstants.push_back(kbACK2CCV);
00551 
00552         RateConstant *kuACK2CCV = new RateConstant(0.02,"kuACK2CCV");
00553         rateConstants.push_back(kuACK2CCV);
00554 
00555         // Delivery of ACK-bound CCVs
00556 
00557         RateConstant *kTrans = new RateConstant(1.5,"kTrans");
00558         rateConstants.push_back(kTrans);
00559 
00560         // Delivery of non clathrin-coated vesicles
00561         RateConstant *kSlowTrans = new RateConstant(0.05,0.05*0.2,"kSlowTrans");
00562         rateConstants.push_back(kSlowTrans);
00563 
00564         // Endosomal to lysosomal transfer
00565 
00566         RateConstant *kEndoLyso = new RateConstant(1.5,"kEndoLyso");
00567         rateConstants.push_back(kEndoLyso);
00568 
00569         // Degradation of EGF
00570 
00571         RateConstant *kdegEGF = new RateConstant(0.25,"kdegEGF");
00572         rateConstants.push_back(kdegEGF);
00573 
00574         // Proteolysis of EGFR
00575 
00576         RateConstant *kProt = new RateConstant(2.5,"kProt");
00577         rateConstants.push_back(kProt);
00578 
00579         // Cbl binding to the receptor
00580         
00581         RateConstant *kbCbl = new RateConstant(1.0e-07,"kbCbl");
00582         rateConstants.push_back(kbCbl);
00583 
00584         // Cbl unbinding from a ubiquitinated receptor
00585         
00586         RateConstant *kuCblUbi = new RateConstant(1.0e-02,"kuCblUbi");
00587         rateConstants.push_back(kuCblUbi);
00588 
00589         // Cbl when bound to EGF receptor - activation and ubiquitination
00590         // 30
00591         RateConstant *kCbl = new RateConstant(5.0,"kCbl");
00592         rateConstants.push_back(kCbl);
00593 
00594         RateConstant *kUbi = new RateConstant(5.0,"kUbi");
00595         rateConstants.push_back(kUbi);
00596 
00597         // Cool/Cbl and 42 binding/unbinding
00598 
00599         RateConstant *kbCbl42 = new RateConstant(1.0e-07,"kbCbl42");
00600         rateConstants.push_back(kbCbl42);
00601 
00602         RateConstant *kuCbl42 = new RateConstant(0.02,"kuCbl42");
00603         rateConstants.push_back(kuCbl42);
00604 
00605         RateConstant *kbCblActive42 = new RateConstant(1.0e-07,"kbCblActive42");
00606         rateConstants.push_back(kbCblActive42);
00607 
00608         RateConstant *kuCblActive42 = new RateConstant(0.02,"kuCblActive42");
00609         rateConstants.push_back(kuCblActive42);
00610 
00611         RateConstant *kuCool1Cbl42GDP = new RateConstant(0.1,"kuCool1Cbl42GDP");
00612         rateConstants.push_back(kuCool1Cbl42GDP);
00613 
00614         RateConstant *kuCool1CblActive42GDP = new RateConstant(0.1,"kuCool1CblActive42GDP");
00615         rateConstants.push_back(kuCool1CblActive42GDP);
00616 
00617         RateConstant *kbCOPI = new RateConstant(1.0e-07,"kbCOPI");
00618         rateConstants.push_back(kbCOPI);
00619 
00620         RateConstant *kuCOPI = new RateConstant(0.02,"kuCOPI");
00621         rateConstants.push_back(kuCOPI);
00622 
00623         RateConstant *kRec = new RateConstant(0.5,"kRec");
00624         rateConstants.push_back(kRec);
00625 
00626         // rapid recyling from non-clathrin coated pathway
00627 
00628         RateConstant *kFastRec = new RateConstant(2.0,"kFastRec");
00629         rateConstants.push_back(kFastRec);
00630 
00631         // autoactivation of F28
00632 
00633         RateConstant *kF28 = new RateConstant(10.0,"kF28");
00634         rateConstants.push_back(kF28);
00635 
00636         // transition parameters between the two pools
00637         RateConstant *k12 = new RateConstant(0.1,"k12");
00638         rateConstants.push_back(k12);
00639 
00640         RateConstant *k21 = new RateConstant(0.01,"k21");
00641         rateConstants.push_back(k21);
00642 
00643         RateConstant *K = new RateConstant(10000,"K");
00644         rateConstants.push_back(K);
00645 
00646         RateConstant *kbEV = new RateConstant(1.0e-07,"kbEV");
00647         rateConstants.push_back(kbEV);
00648 
00649         RateConstant *kuEV = new RateConstant(0.2,"kuEV");
00650         rateConstants.push_back(kuEV);
00651 
00652         RateConstant *ktACK2 = new RateConstant(2.0,"ktACK2");
00653         rateConstants.push_back(ktACK2);
00654 
00655         RateConstant *kt42 = new RateConstant(2.0,"kt42");
00656         rateConstants.push_back(kt42);
00657 
00658         RateConstant *ktCOPI = new RateConstant(2.0,"ktCOPI");
00659         rateConstants.push_back(ktCOPI);
00660 
00661         RateConstant *ktg42 = new RateConstant(2.0,"ktg42");
00662         rateConstants.push_back(ktg42);
00663 
00664         RateConstant *kbRV = new RateConstant(1.0e-07,"kbRV");
00665         rateConstants.push_back(kbRV);
00666 
00667         RateConstant *kuRV = new RateConstant(0.2,"kuRV");
00668         rateConstants.push_back(kuRV);
00669 
00670         // MAPK cascade
00671 
00672         RateConstant *kRas = new RateConstant(1.1,"kRas");
00673         rateConstants.push_back(kRas);
00674 
00675         RateConstant *KmRas = new RateConstant(60000,"KmRas");
00676         rateConstants.push_back(KmRas);
00677 
00678         RateConstant *kRasGAP = new RateConstant(0.5,"kRasGAP");
00679         rateConstants.push_back(kRasGAP);
00680 
00681         RateConstant *KmRasGAP = new RateConstant(60000,"KmRasGAP");
00682         rateConstants.push_back(KmRasGAP);
00683 
00684         RateConstant *kErk = new RateConstant(1.1,"kErk");
00685         rateConstants.push_back(kErk);
00686 
00687         RateConstant *KmErk = new RateConstant(60000,"KmErk");
00688         rateConstants.push_back(KmErk);
00689 
00690         RateConstant *kdErk = new RateConstant(0.5,"kdErk");
00691         rateConstants.push_back(kdErk);
00692 
00693         RateConstant *KmdErk = new RateConstant(60000,"KmdErk");
00694         rateConstants.push_back(KmdErk);
00695 
00696         RateConstant *kErkRas = new RateConstant(1.1,"kErkRas");
00697         rateConstants.push_back(kErkRas);
00698 
00699         RateConstant *KmErkRas = new RateConstant(60000,"KmErkRas");
00700         rateConstants.push_back(KmErkRas);
00701 
00702 
00703         // reactions
00704         // 0
00705         // EGF binding/unbinding
00706         Reaction *EGFBinding1 = new ReceptorBindingReaction(EGF,CPFreePMEGFR,CPBoundPMEGFR,kbEGF,"EGFBinding1");
00707         reactions.push_back(EGFBinding1);
00708 
00709         Reaction *EGFBinding2 = new ReceptorBindingReaction(EGF,NonCPFreePMEGFR,NonCPBoundPMEGFR,kbEGF,"EGFBinding2");
00710         reactions.push_back(EGFBinding2);
00711 
00712         Reaction *EGFUnbinding1 = new ReceptorUnbindingReaction(CPBoundPMEGFR,CPFreePMEGFR,EGF,kuEGF,"EGFUnbinding1");
00713         reactions.push_back(EGFUnbinding1);
00714 
00715         Reaction *EGFUnbinding2 = new ReceptorUnbindingReaction(NonCPBoundPMEGFR,NonCPFreePMEGFR,EGF,kuEGF,"EGFUnbinding2");
00716         reactions.push_back(EGFUnbinding2);
00717 
00718         // transitions between the two pools
00719         Reaction *CPToNonCP1 = new TransformationReaction(CPFreePMEGFR,NonCPFreePMEGFR,k21,"CPToNonCP1");
00720         reactions.push_back(CPToNonCP1);
00721 
00722         Reaction *CPToNonCP2 = new TransformationReaction(CPBoundPMEGFR,NonCPBoundPMEGFR,k21,"CPToNonCP2");
00723         reactions.push_back(CPToNonCP2);
00724         
00725         Reaction *CPToNonCP3 = new TransformationReaction(CPBoundPMEGFRCoolCbl,NonCPBoundPMEGFRCoolCbl,k21,"CPToNonCP3");
00726         reactions.push_back(CPToNonCP3);
00727         
00728         Reaction *CPToNonCP4 = new TransformationReaction(CPBoundPMEGFRCoolCblActive,NonCPBoundPMEGFRCoolCblActive,k21,"CPToNonCP4");
00729         reactions.push_back(CPToNonCP4);
00730 
00731         Reaction *CPToNonCP5 = new TransformationReaction(UbiCPBoundPMEGFRCoolCblActive,UbiNonCPBoundPMEGFRCoolCblActive,k21,"CPToNonCP5");
00732         reactions.push_back(CPToNonCP5);
00733         
00734         // transitions between the two pools
00735         Reaction *NonCPToCP1 = new CPoolTransitionReaction(NonCPFreePMEGFR,CPFreePMEGFR,k12,K,"NonCPToCP1");
00736         reactions.push_back(NonCPToCP1);
00737 
00738         // 10
00739         Reaction *NonCPToCP2 = new CPoolTransitionReaction(NonCPBoundPMEGFR,CPBoundPMEGFR,k12,K,"NonCPToCP2");
00740         reactions.push_back(NonCPToCP2);
00741         
00742         Reaction *NonCPToCP3 = new CPoolTransitionReaction(NonCPBoundPMEGFRCoolCbl,CPBoundPMEGFRCoolCbl,k12,K,"NonCPToCP3");
00743         reactions.push_back(NonCPToCP3);
00744         
00745         Reaction *NonCPToCP4 = new CPoolTransitionReaction(NonCPBoundPMEGFRCoolCblActive,CPBoundPMEGFRCoolCblActive,k12,K,"NonCPToCP4");
00746         reactions.push_back(NonCPToCP4);
00747 
00748         Reaction *NonCPToCP5 = new CPoolTransitionReaction(UbiNonCPBoundPMEGFRCoolCblActive,UbiCPBoundPMEGFRCoolCblActive,k12,K,"NonCPToCP5");
00749         reactions.push_back(NonCPToCP5);
00750 
00751 
00752         // 42 activation - PM
00753 
00754         Reaction *Cdc42PMActivation1 = new MichaelisMentenGProteinActivationReaction(CPBoundPMEGFR,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation1");
00755         reactions.push_back(Cdc42PMActivation1);
00756 
00757         Reaction *Cdc42PMActivation2 = new MichaelisMentenGProteinActivationReaction(CPBoundPMEGFRCoolCbl,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation2");
00758         reactions.push_back(Cdc42PMActivation2);
00759 
00760         Reaction *Cdc42PMActivation3 = new MichaelisMentenGProteinActivationReaction(CPBoundPMEGFRCoolCblActive,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation3");
00761         reactions.push_back(Cdc42PMActivation3);
00762 
00763         Reaction *Cdc42PMActivation4 = new MichaelisMentenGProteinActivationReaction(UbiCPBoundPMEGFRCoolCblActive,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation4");
00764         reactions.push_back(Cdc42PMActivation4);
00765 
00766         Reaction *Cdc42PMActivation5 = new MichaelisMentenGProteinActivationReaction(NonCPBoundPMEGFR,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation5");
00767         reactions.push_back(Cdc42PMActivation5);
00768 
00769         Reaction *Cdc42PMActivation6 = new MichaelisMentenGProteinActivationReaction(NonCPBoundPMEGFRCoolCbl,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation6");
00770         reactions.push_back(Cdc42PMActivation6);
00771 
00772         // 20
00773         Reaction *Cdc42PMActivation7 = new MichaelisMentenGProteinActivationReaction(NonCPBoundPMEGFRCoolCblActive,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation7");
00774         reactions.push_back(Cdc42PMActivation7);
00775 
00776         Reaction *Cdc42PMActivation8 = new MichaelisMentenGProteinActivationReaction(UbiNonCPBoundPMEGFRCoolCblActive,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation8");
00777         reactions.push_back(Cdc42PMActivation8);
00778 
00779         // 42 activation - Golgi
00780 
00781         Reaction *Cdc42GolgiActivation1 = new MichaelisMentenGProteinActivationReaction(CPBoundPMEGFR,GolgiCdc42GDP,GolgiCdc42GTP,kEGFR42,KmEGFR42,"Cdc42GolgiActivation1");
00782         reactions.push_back(Cdc42GolgiActivation1);
00783 
00784         Reaction *Cdc42GolgiActivation2 = new MichaelisMentenGProteinActivationReaction(CPBoundPMEGFRCoolCbl,GolgiCdc42GDP,GolgiCdc42GTP,kEGFR42,KmEGFR42,"Cdc42GolgiActivation2");
00785         reactions.push_back(Cdc42GolgiActivation2);
00786 
00787         Reaction *Cdc42GolgiActivation3 = new MichaelisMentenGProteinActivationReaction(CPBoundPMEGFRCoolCblActive,GolgiCdc42GDP,GolgiCdc42GTP,kEGFR42,KmEGFR42,"Cdc42GolgiActivation3");
00788         reactions.push_back(Cdc42GolgiActivation3);
00789 
00790         Reaction *Cdc42GolgiActivation4 = new MichaelisMentenGProteinActivationReaction(UbiCPBoundPMEGFRCoolCblActive,GolgiCdc42GDP,GolgiCdc42GTP,kEGFR42,KmEGFR42,"Cdc42GolgiActivation4");
00791         reactions.push_back(Cdc42GolgiActivation4);
00792 
00793         Reaction *Cdc42GolgiActivation5 = new MichaelisMentenGProteinActivationReaction(NonCPBoundPMEGFR,GolgiCdc42GDP,GolgiCdc42GTP,kEGFR42,KmEGFR42,"Cdc42GolgiActivation5");
00794         reactions.push_back(Cdc42GolgiActivation5);
00795 
00796         Reaction *Cdc42GolgiActivation6 = new MichaelisMentenGProteinActivationReaction(NonCPBoundPMEGFRCoolCbl,GolgiCdc42GDP,GolgiCdc42GTP,kEGFR42,KmEGFR42,"Cdc42GolgiActivation6");
00797         reactions.push_back(Cdc42GolgiActivation6);
00798 
00799         Reaction *Cdc42GolgiActivation7 = new MichaelisMentenGProteinActivationReaction(NonCPBoundPMEGFRCoolCblActive,GolgiCdc42GDP,GolgiCdc42GTP,kEGFR42,KmEGFR42,"Cdc42GolgiActivation7");
00800         reactions.push_back(Cdc42GolgiActivation7);
00801 
00802         Reaction *Cdc42GolgiActivation8 = new MichaelisMentenGProteinActivationReaction(UbiNonCPBoundPMEGFRCoolCblActive,GolgiCdc42GDP,GolgiCdc42GTP,kEGFR42,KmEGFR42,"Cdc42GolgiActivation8");
00803         reactions.push_back(Cdc42GolgiActivation8);
00804 
00805 
00806         // gapping of free 42
00807         // 30
00808         Reaction *Cdc42GAPHydrolysis1 = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,Cdc42GTP,Cdc42GDP,kGAP,KmGAP,"Cdc42GAPHydrolysis1");
00809         reactions.push_back(Cdc42GAPHydrolysis1);
00810 
00811         Reaction *Cdc42GAPHydrolysis2 = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,GolgiCdc42GTP,GolgiCdc42GDP,kGAP,KmGAP,"Cdc42GAPHydrolysis2"); 
00812         reactions.push_back(Cdc42GAPHydrolysis2);
00813 
00814         // assembly of proto CCV
00815         Reaction *Proto1 = new HeterodimerizationReaction(CPBoundPMEGFR,AP2,ProtoCCVEGFR,kbAP2,"Proto1");
00816         reactions.push_back(Proto1);
00817 
00818         Reaction *Proto2 = new HeterodimerizationReaction(CPBoundPMEGFRCoolCblActive,AP2,ProtoCCVEGFRCoolCblActive,kbAP2,"Proto2");
00819         reactions.push_back(Proto2);
00820 
00821         Reaction *Proto3 = new HeterodimerizationReaction(UbiCPBoundPMEGFRCoolCblActive,AP2,ProtoCCVUbiEGFRCoolCblActive,kbAP2,"Proto3");
00822         reactions.push_back(Proto3);
00823 
00824         // endocytosis
00825         Reaction *Endocytosis1 = new TransformationReaction(ProtoCCVEGFR,CCVEGFR,kEndo1,"Endocytosis1");
00826         reactions.push_back(Endocytosis1);
00827 
00828         Reaction *Endocytosis2 = new TransformationReaction(ProtoCCVEGFRCoolCblActive,CCVEGFRCoolCblActive,kEndo1,"Endocytosis2");
00829         reactions.push_back(Endocytosis2);
00830 
00831         Reaction *Endocytosis3 = new TransformationReaction(ProtoCCVUbiEGFRCoolCblActive,CCVUbiEGFRCoolCblActive,kEndo2,"Endocytosis3");
00832         reactions.push_back(Endocytosis3);
00833 
00834         Reaction *SlowEndo1 = new TransformationReaction(NonCPBoundPMEGFR,NonCoatedBoundEGFR,kSlowEndo,"SlowEndo1");
00835         reactions.push_back(SlowEndo1);
00836 
00837         Reaction *SlowEndo2 = new TransformationReaction(NonCPBoundPMEGFRCoolCblActive,NonCoatedBoundEGFRCoolCblActive,kSlowEndo,"SlowEndo1");
00838         reactions.push_back(SlowEndo2);
00839 
00840         // 40
00841         Reaction *SlowEndo3 = new TransformationReaction(UbiNonCPBoundPMEGFRCoolCblActive,NonCoatedUbiBoundEGFRCoolCblActive,kSlowEndo,"SlowEndo3");
00842         reactions.push_back(SlowEndo3);
00843 
00844         // ACK2 and 42 cycle
00845         Reaction *ACK42Binding = new HeterodimerizationReaction(ACK2,Cdc42GTP,ACK242GTP,kbACK2,"ACK42Binding");
00846         reactions.push_back(ACK42Binding);
00847 
00848         Reaction *ACK42Unbinding = new HeterodimerDissociationReaction(ACK242GTP,ACK2,Cdc42GTP,kuACK2,"ACK42Unbinding");
00849         reactions.push_back(ACK42Unbinding);
00850 
00851         Reaction *ACK2Active42Binding = new HeterodimerizationReaction(ACK2Active,Cdc42GTP,ACK2Active42GTP,kbACKActive,"ACK2Active42Binding");
00852         reactions.push_back(ACK2Active42Binding);
00853 
00854         Reaction *ACK2Active42Unbinding = new HeterodimerDissociationReaction(ACK2Active42GTP,ACK2Active,Cdc42GTP,kuACKActive,"ACK2Active42Unbinding");
00855         reactions.push_back(ACK2Active42Unbinding);
00856 
00857         Reaction *ACK2Activation = new TransformationReaction(ACK242GTP,ACK2Active42GTP,kACK2,"ACK2Activation");
00858         reactions.push_back(ACK2Activation);
00859 
00860         Reaction *ACK2Deactivation = new MichaelisMentenDephosphorylationReaction(YPPTase1,ACK2Active,ACK2,kdACK2,KmdACK2,"ACK2Deactivation");
00861         reactions.push_back(ACK2Deactivation);
00862 
00863         Reaction *ACK242GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,ACK242GTP,ACK242GDP,kGAP,KmGAP,"ACK242GAPing");
00864         reactions.push_back(ACK242GAPing);
00865 
00866         Reaction *ACK2Active42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,ACK2Active42GTP,ACK2Active42GDP,kGAP,KmGAP,"ACK2Active42GAPing");
00867         reactions.push_back(ACK2Active42GAPing);
00868 
00869         Reaction *ACK242GDPRelease = new HeterodimerDissociationReaction(ACK242GDP,ACK2,Cdc42GDP,kuACK242GDP,"ACK242GDPRelease");
00870         reactions.push_back(ACK242GDPRelease);
00871 
00872         // 50
00873         Reaction *ACK2Active42GDPRelease = new HeterodimerDissociationReaction(ACK2Active42GDP,ACK2Active,Cdc42GDP,kuACK2Active42GDP,"ACK2Active42GDPRelease");
00874         reactions.push_back(ACK2Active42GDPRelease);
00875 
00876         // Cool/Cbl and 42 cycle
00877         Reaction *CoolCbl42Binding = new HeterodimerizationReaction(Cool1Cbl,Cdc42GTP,Cool1Cbl42GTP,kbCbl42,"CoolCbl42Binding");
00878         reactions.push_back(CoolCbl42Binding);
00879 
00880         Reaction *CoolCbl42Unbinding = new HeterodimerDissociationReaction(Cool1Cbl42GTP,Cool1Cbl,Cdc42GTP,kuCbl42,"CoolCbl42Unbinding");
00881         reactions.push_back(CoolCbl42Unbinding);
00882 
00883         Reaction *CoolCblActive42Binding = new HeterodimerizationReaction(Cool1CblActive,Cdc42GTP,Cool1CblActive42GTP,kbCblActive42,"CoolCblActive42Binding");
00884         reactions.push_back(CoolCblActive42Binding);
00885 
00886         Reaction *CoolCblActive42Unbinding = new HeterodimerDissociationReaction(Cool1CblActive42GTP,Cool1CblActive,Cdc42GTP,kuCblActive42,"CoolCblActive42Unbinding");
00887         reactions.push_back(CoolCblActive42Unbinding);
00888 
00889         Reaction *CoolCbl42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,Cool1Cbl42GTP,Cool1Cbl42GDP,kGAP,KmGAP,"CoolCbl42GAPing");
00890         reactions.push_back(CoolCbl42GAPing);
00891 
00892         Reaction *CoolCblActive42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,Cool1CblActive42GTP,Cool1CblActive42GDP,kGAP,KmGAP,"CoolCblActive42GAPing");
00893         reactions.push_back(CoolCblActive42GAPing);
00894 
00895         Reaction *CoolCbl42GDPRelease = new HeterodimerDissociationReaction(Cool1Cbl42GDP,Cool1Cbl,Cdc42GDP,kuCool1Cbl42GDP,"CoolCbl42GDPRelease");
00896         reactions.push_back(CoolCbl42GDPRelease);
00897         
00898         Reaction *CoolCblActive42GDPRelease = new HeterodimerDissociationReaction(Cool1CblActive42GDP,Cool1CblActive,Cdc42GDP,kuCool1CblActive42GDP,"CoolCblActive42GDPRelease");
00899         reactions.push_back(CoolCblActive42GDPRelease);
00900 
00901         // transfer to endosomes
00902 
00903         Reaction *ACKBinding1 = new HeterodimerizationReaction(ACK2Active,CCVEGFR,CCVEGFRACK2,kbACK2CCV,"ACKBinding1");
00904         reactions.push_back(ACKBinding1);
00905 
00906         // 60
00907         Reaction *ACKBinding2 = new HeterodimerizationReaction(ACK2Active,CCVEGFRCoolCblActive,CCVEGFRCoolCblActiveACK2,kbACK2CCV,"ACKBinding2");
00908         reactions.push_back(ACKBinding2);
00909         
00910         Reaction *ACKBinding3 = new HeterodimerizationReaction(ACK2Active,CCVUbiEGFRCoolCblActive,CCVUbiEGFRCoolCblActiveACK2,kbACK2CCV,"ACKBinding3");
00911         reactions.push_back(ACKBinding3);
00912 
00913         Reaction *Delivery1 = new TransformationReaction(CCVEGFRACK2,DeliveredEGFRACK2,kTrans,"Delivery1");
00914         reactions.push_back(Delivery1);
00915 
00916         Reaction *Delivery2 = new TransformationReaction(CCVEGFRCoolCblActiveACK2,DeliveredEGFRCoolCblActiveACK2,kTrans,"Delivery2");
00917         reactions.push_back(Delivery2);
00918 
00919         Reaction *Delivery3 = new TransformationReaction(CCVUbiEGFRCoolCblActiveACK2,DeliveredUbiEGFRCoolCblActiveACK2,kTrans,"Delivery3");
00920         reactions.push_back(Delivery3);
00921 
00922         Reaction *Delivery4 = new TransformationReaction(CCVEGFR,DeliveredEGFR,kTrans,"Delivery4");
00923         reactions.push_back(Delivery4);
00924 
00925         Reaction *Delivery5 = new TransformationReaction(CCVEGFRCoolCblActive,DeliveredEGFRCoolCblActive,kTrans,"Delivery5");
00926         reactions.push_back(Delivery5);
00927 
00928         Reaction *Delivery6 = new TransformationReaction(CCVUbiEGFRCoolCblActive,DeliveredUbiEGFRCoolCblActive,kTrans,"Delivery6");
00929         reactions.push_back(Delivery6);
00930 
00931         Reaction *ACKRelease1 = new HeterodimerDissociationReaction(DeliveredEGFRACK2,DeliveredEGFR,EndoACK2Active,kuACK2CCV,"ACKRelease1");
00932         reactions.push_back(ACKRelease1);
00933 
00934         Reaction *ACKRelease2 = new HeterodimerDissociationReaction(DeliveredEGFRCoolCblActiveACK2,DeliveredEGFRCoolCblActive,EndoACK2Active,kuACK2CCV,"ACKRelease2");
00935         reactions.push_back(ACKRelease2);
00936 
00937         // 70
00938         Reaction *ACKRelease3 = new HeterodimerDissociationReaction(DeliveredUbiEGFRCoolCblActiveACK2,DeliveredUbiEGFRCoolCblActive,EndoACK2Active,kuACK2CCV,"ACKRelease3");
00939         reactions.push_back(ACKRelease3);
00940 
00941         Reaction *SlowSort1 = new TransformationReaction(NonCoatedBoundEGFR,BoundEndoEGFR,kSlowTrans,"SlowSort1");
00942         reactions.push_back(SlowSort1);
00943 
00944         Reaction *SlowSort2 = new TransformationReaction(NonCoatedBoundEGFRCoolCblActive,BoundEndoEGFRCoolCblActive,kSlowTrans,"SlowSort2");
00945         reactions.push_back(SlowSort2);
00946 
00947         Reaction *SlowSort3 = new TransformationReaction(NonCoatedUbiBoundEGFRCoolCblActive,UbiBoundEndoEGFRCoolCblActive,kSlowTrans,"SlowSort3");
00948         reactions.push_back(SlowSort3);
00949 
00950         // fusion with endosome, AP2 release
00951         Reaction *EndoFusion1 = new HeterodimerDissociationReaction(DeliveredEGFR,BoundEndoEGFR,AP2,kuAP2,"EndoFusion1");
00952         reactions.push_back(EndoFusion1);
00953 
00954         Reaction *EndoFusion2 = new HeterodimerDissociationReaction(DeliveredEGFRCoolCblActive,BoundEndoEGFRCoolCblActive,AP2,kuAP2,"EndoFusion2");
00955         reactions.push_back(EndoFusion2);
00956 
00957         Reaction *EndoFusion3 = new HeterodimerDissociationReaction(DeliveredUbiEGFRCoolCblActive,UbiBoundEndoEGFRCoolCblActive,AP2,kuAP2,"EndoFusion3");
00958         reactions.push_back(EndoFusion3);
00959 
00960         // Formation of sorting vesicles and lysosomal transfer
00961 
00962         Reaction *SortingVesicleFormation = new HeterodimerizationReaction(UbiFreeEndoEGFR,EndoACK2Active,EndosomalVesicle,kbEV,"SortingVesicleFormation");
00963         reactions.push_back(SortingVesicleFormation);
00964 
00965         Reaction *LysosomalTransfer = new TransformationReaction(EndosomalVesicle,LysosomalVesicle,kEndoLyso,"LysosomalTransfer");
00966         reactions.push_back(LysosomalTransfer);
00967 
00968         Reaction *LysosomalFusion = new HeterodimerDissociationReaction(LysosomalVesicle,LysoACK2Active,UbiFreeLysoEGFR,kuEV,"LysosomalFusion");
00969         reactions.push_back(LysosomalFusion);
00970 
00971         // 80
00972         Reaction *ACK2Recycling = new TransformationReaction(LysoACK2Active,EndoACK2Active,ktACK2,"ACK2Recycling");
00973         reactions.push_back(ACK2Recycling);
00974 
00975 
00976         // EGF dissociation/degradation in endosomes
00977         Reaction *EGFDissociation1 = new ReceptorUnbindingReaction(BoundEndoEGFR,FreeEndoEGFR,EndosomalEGF,kuEndoEGF,"EGFDissociation1");
00978         reactions.push_back(EGFDissociation1);
00979 
00980         Reaction *EGFDissociation2 = new ReceptorUnbindingReaction(UbiBoundEndoEGFR,UbiFreeEndoEGFR,EndosomalEGF,kuEndoEGF,"EGFDissociation2");
00981         reactions.push_back(EGFDissociation2);
00982 
00983         Reaction *EGFDissociation3 = new ReceptorUnbindingReaction(BoundEndoEGFRCoolCblActive,FreeEndoEGFRCoolCblActive,EndosomalEGF,kuEndoEGF,"EGFDissociation3");
00984         reactions.push_back(EGFDissociation3);
00985 
00986         Reaction *EGFDissociation4 = new ReceptorUnbindingReaction(UbiBoundEndoEGFRCoolCblActive,UbiFreeEndoEGFRCoolCblActive,EndosomalEGF,kuEndoEGF,"EGFDissociation4");
00987         reactions.push_back(EGFDissociation4);
00988 
00989         Reaction *LigandDegradation = new TransformationReaction(EndosomalEGF,DegradedEGF,kdegEGF,"EGFDegradation");
00990         reactions.push_back(LigandDegradation);
00991 
00992         // CoolCbl binding to receptor
00993         Reaction *EGFRCoolCblBinding1 = new HeterodimerizationReaction(CPBoundPMEGFR,Cool1Cbl,CPBoundPMEGFRCoolCbl,kbCbl,"InactiveCblBinding1");
00994         reactions.push_back(EGFRCoolCblBinding1);
00995 
00996         Reaction *EGFRCoolCblBinding2 = new HeterodimerizationReaction(NonCPBoundPMEGFR,Cool1Cbl,NonCPBoundPMEGFRCoolCbl,kbCbl,"InactiveCblBinding2");
00997         reactions.push_back(EGFRCoolCblBinding2);
00998 
00999         Reaction *EGFRCoolCblActiveBinding1 = new HeterodimerizationReaction(CPBoundPMEGFR,Cool1CblActive,CPBoundPMEGFRCoolCblActive,kbCbl,"ActiveCblBinding1");
01000         reactions.push_back(EGFRCoolCblActiveBinding1);
01001 
01002         Reaction *EGFRCoolCblActiveBinding2 = new HeterodimerizationReaction(NonCPBoundPMEGFR,Cool1CblActive,NonCPBoundPMEGFRCoolCblActive,kbCbl,"ActiveCblBinding2");
01003         reactions.push_back(EGFRCoolCblActiveBinding2);
01004 
01005         // 90
01006         Reaction *EndoCoolCblActiveBinding = new HeterodimerizationReaction(BoundEndoEGFR,Cool1CblActive,BoundEndoEGFRCoolCblActive,kbCbl,"EndoActiveCblBinding");
01007         reactions.push_back(EndoCoolCblActiveBinding);
01008 
01009         // CoolCbl phosphorylation
01010         Reaction *EGFRCoolCblActivation1 = new TransformationReaction(CPBoundPMEGFRCoolCbl,CPBoundPMEGFRCoolCblActive,kCbl,"EGFRCoolCblActivation1");
01011         reactions.push_back(EGFRCoolCblActivation1);
01012 
01013         Reaction *EGFRCoolCblActivation2 = new TransformationReaction(NonCPBoundPMEGFRCoolCbl,NonCPBoundPMEGFRCoolCblActive,kCbl,"EGFRCoolCblActivation2");
01014         reactions.push_back(EGFRCoolCblActivation2);
01015 
01016         // ubiquitination 
01017         Reaction *MembraneUbi1 = new TransformationReaction(CPBoundPMEGFRCoolCblActive,UbiCPBoundPMEGFRCoolCblActive,kUbi,"MembraneUbi1");
01018         reactions.push_back(MembraneUbi1);
01019 
01020         Reaction *MembraneUbi2 = new TransformationReaction(NonCPBoundPMEGFRCoolCblActive,UbiNonCPBoundPMEGFRCoolCblActive,kUbi,"MembraneUbi2");
01021         reactions.push_back(MembraneUbi2);
01022 
01023         Reaction *ProtoUbi = new TransformationReaction(ProtoCCVEGFRCoolCblActive,ProtoCCVUbiEGFRCoolCblActive,kUbi,"ProtoUbi");
01024         reactions.push_back(ProtoUbi);
01025 
01026         Reaction *VesicleUbi = new TransformationReaction(CCVEGFRCoolCblActive,CCVUbiEGFRCoolCblActive,kUbi,"VesicleUbi");
01027         reactions.push_back(VesicleUbi);
01028 
01029         Reaction *VesicleUbi2 = new TransformationReaction(CCVEGFRCoolCblActiveACK2,CCVUbiEGFRCoolCblActiveACK2,kUbi,"VesicleUbi2");
01030         reactions.push_back(VesicleUbi2);
01031 
01032         Reaction *DeliveredUbi1 = new TransformationReaction(DeliveredEGFRCoolCblActiveACK2,DeliveredUbiEGFRCoolCblActiveACK2,kUbi,"DeliveredUbi1");
01033         reactions.push_back(DeliveredUbi1);
01034 
01035         Reaction *DeliveredUbi2 = new TransformationReaction(DeliveredEGFRCoolCblActive,DeliveredUbiEGFRCoolCblActive,kUbi,"DeliveredUbi2");
01036         reactions.push_back(DeliveredUbi2);
01037 
01038         // 100
01039         Reaction *NonCoatedUbi = new TransformationReaction(NonCoatedBoundEGFRCoolCblActive,NonCoatedUbiBoundEGFRCoolCblActive,kUbi,"NonCoatedUbi");
01040         reactions.push_back(NonCoatedUbi);
01041 
01042         Reaction *EndoUbi1 = new TransformationReaction(BoundEndoEGFRCoolCblActive,UbiBoundEndoEGFRCoolCblActive,kUbi,"EndoUbi1");
01043         reactions.push_back(EndoUbi1);
01044 
01045         Reaction *EndoUbi2 = new TransformationReaction(FreeEndoEGFRCoolCblActive,UbiFreeEndoEGFRCoolCblActive,kUbi,"EndoUbi2");
01046         reactions.push_back(EndoUbi2);
01047 
01048         // CoolCbl release
01049 
01050         Reaction *CoolCblDissociation1 = new HeterodimerDissociationReaction(UbiBoundEndoEGFRCoolCblActive,UbiBoundEndoEGFR,Cool1CblActive,kuCblUbi,"CoolCblDissociation1");
01051         reactions.push_back(CoolCblDissociation1);
01052 
01053         Reaction *CoolCblDissociation2 = new HeterodimerDissociationReaction(UbiFreeEndoEGFRCoolCblActive,UbiFreeEndoEGFR,Cool1CblActive,kuCblUbi,"CoolCblDissociation2");
01054         reactions.push_back(CoolCblDissociation2);
01055 
01056         // EGFR proteolysis 
01057         Reaction *FreeEGFRProteolysis = new TransformationReaction(UbiFreeLysoEGFR,DegradedEGFR,kProt,"FreeEGFRProteolysis");
01058         reactions.push_back(FreeEGFRProteolysis);
01059 
01060         // 42 movement between Golgi and Endosomes
01061         Reaction *Cdc42COPIBinding = new HeterodimerizationReaction(GolgiCdc42GTP,COPI,GolgiCOPI42GTP,kbCOPI,"Cdc42COPIBinding");
01062         reactions.push_back(Cdc42COPIBinding);
01063 
01064         Reaction *Endosomal42Transfer = new TransformationReaction(GolgiCOPI42GTP,EndoCOPI42GTP,kt42,"Endosomal42Transfer");
01065         reactions.push_back(Endosomal42Transfer);
01066 
01067         Reaction *Endosomal42COPIGAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,EndoCOPI42GTP,EndoCOPI42GDP,kGAP,KmGAP,"Endosomal42COPIGAPing");
01068         reactions.push_back(Endosomal42COPIGAPing);
01069 
01070         Reaction *Endosomal42COPIFusion = new HeterodimerDissociationReaction(EndoCOPI42GDP,EndoCOPI,EndoCdc42GDP,kuCOPI,"Endosomal42COPIFusion");
01071         reactions.push_back(Endosomal42COPIFusion);
01072 
01073         // 110
01074         Reaction *COPIRecycling = new TransformationReaction(EndoCOPI,COPI,ktCOPI,"COPIRecycling");
01075         reactions.push_back(COPIRecycling);
01076 
01077         Reaction *Cdc42Recycling = new TransformationReaction(EndoCdc42GDP,GolgiCdc42GDP,ktg42,"Cdc42Recycling");
01078         reactions.push_back(Cdc42Recycling);
01079 
01080         // assembly of recycling vesicle
01081         Reaction *ProtoRVFormation = new HeterodimerizationReaction(EndoCdc42GDP,FreeEndoEGFR,ProtoRecyclingVesicle,kbRV,"ProtoRVFormation");
01082         reactions.push_back(ProtoRVFormation);
01083 
01084 
01085         Reaction *RVFormation = new HeterodimerDissociationReaction(ProtoRecyclingVesicle,RecyclingVesicle,EndoCdc42GDP,kuRV,"RVFormation");
01086         reactions.push_back(RVFormation);
01087         
01088         // recycling
01089 
01090         Reaction *Recycling = new TransformationReaction(RecyclingVesicle,NonCPFreePMEGFR,kRec,"Recycling1");
01091         reactions.push_back(Recycling);
01092 
01093         // auto-activation (used w/ fast cycler, comment out otherwise)
01094         // 115
01095         Reaction *AutoActivation = new TransformationReaction(Cdc42GDP,Cdc42GTP,kF28,"AutoActivation");
01096         reactions.push_back(AutoActivation);
01097         
01098         Reaction *RapidRec1 = new TransformationReaction(NonCoatedBoundEGFR,NonCPBoundPMEGFR,kFastRec,"RapidRec1");
01099         reactions.push_back(RapidRec1);
01100 
01101         Reaction *RapidRec2 = new TransformationReaction(NonCoatedBoundEGFRCoolCblActive,NonCPBoundPMEGFRCoolCblActive,kFastRec,"RapidRec2");
01102         reactions.push_back(RapidRec2);
01103 
01104         Reaction *RapidRec3 = new TransformationReaction(NonCoatedUbiBoundEGFRCoolCblActive,UbiNonCPBoundPMEGFRCoolCblActive,kFastRec,"RapidRec3");
01105         reactions.push_back(RapidRec3);
01106 
01107         // MAPK cascade
01108         Reaction *RasActivation1 = new MichaelisMentenGProteinActivationReaction(CPBoundPMEGFR,RasGDP,RasGTP,kRas,KmRas,"RasActivation1");
01109         reactions.push_back(RasActivation1);
01110 
01111         // 120
01112         Reaction *RasActivation2 = new MichaelisMentenGProteinActivationReaction(NonCPBoundPMEGFR,RasGDP,RasGTP,kRas,KmRas,"RasActivation2");
01113         reactions.push_back(RasActivation2);
01114 
01115         Reaction *RasDeactivation = new MichaelisMentenGProteinDeactivationReaction(RasGAP,RasGTP,RasGDP,kRasGAP,KmRasGAP,"RasDeactivation");
01116         reactions.push_back(RasDeactivation);
01117 
01118         Reaction *ErkActivation = new MichaelisMentenPhosphorylationReaction(RasGTP,Erk,ErkP,kErk,KmErk,"ErkActivation");
01119         reactions.push_back(ErkActivation);
01120 
01121         Reaction *ErkDeactivation = new MichaelisMentenDephosphorylationReaction(PP2A,ErkP,Erk,kdErk,KmdErk,"ErkDeactivation");
01122         reactions.push_back(ErkDeactivation);
01123 
01124         Reaction *ErkFeedback = new MichaelisMentenProteinProteinDeactivationReaction(ErkP,RasGTP,RasGDP,kErkRas,KmErkRas,"ErkFeedback");
01125         reactions.push_back(ErkFeedback);
01126 }
01127 
01128 CEGFRTraffickingNetwork::~CEGFRTraffickingNetwork()
01129 {
01130 
01131 }