EGFRTraffickingPredictionNetwork.cpp Source File

00001 // EGFRTraffickingPredictionNetwork.cpp: implementation of the CEGFRTraffickingPredictionNetwork class.
00002 //
00004 
00005 #include "EGFRTraffickingPredictionNetwork.h"
00006 
00008 // Construction/Destruction
00010 
00011 CEGFRTraffickingPredictionNetwork::CEGFRTraffickingPredictionNetwork()
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 *FreePMEGFR = new Chemical(chemicals.size(),0.0,"FreePMEGFR");
00028         chemicals.push_back(FreePMEGFR);
00029 
00030         Chemical *BoundPMEGFR = new Chemical(chemicals.size(),0.0,"BoundPMEGFR");
00031         chemicals.push_back(BoundPMEGFR);
00032         
00033         Chemical *DegradedEGFR = new Chemical(chemicals.size(),0.0,"DegradedEGFR");
00034         chemicals.push_back(DegradedEGFR);
00035 
00036         Chemical *BoundPMEGFRCoolCbl = new Chemical(chemicals.size(),0.0,"BoundPMEGFRCoolCbl");
00037         chemicals.push_back(BoundPMEGFRCoolCbl);
00038 
00039         Chemical *BoundPMEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"BoundPMEGFRCoolCblActive");
00040         chemicals.push_back(BoundPMEGFRCoolCblActive);
00041 
00042         Chemical *UbiBoundPMEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"UbiBoundPMEGFRCoolCblActive");
00043         chemicals.push_back(UbiBoundPMEGFRCoolCblActive);
00044 
00045         Chemical *CCVEGFR = new Chemical(chemicals.size(),0.0,"CCVEGFR");
00046         chemicals.push_back(CCVEGFR);
00047 
00048         Chemical *CCVEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"CCVEGFRCoolCblActive");
00049         chemicals.push_back(CCVEGFRCoolCblActive);
00050 
00051         // 10
00052         Chemical *CCVUbiEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"CCVUbiEGFRCoolCblActive");
00053         chemicals.push_back(CCVUbiEGFRCoolCblActive);
00054 
00055         Chemical *CCVEGFRACK2 = new Chemical(chemicals.size(),0.0,"CCVEGFRACK2");
00056         chemicals.push_back(CCVEGFRACK2);
00057 
00058         Chemical *CCVEGFRCoolCblActiveACK2 = new Chemical(chemicals.size(),0.0,"CCVEGFRCoolCblActiveACK2");
00059         chemicals.push_back(CCVEGFRCoolCblActiveACK2);
00060 
00061         Chemical *CCVUbiEGFRCoolCblActiveACK2 = new Chemical(chemicals.size(),0.0,"CCVUbiEGFRCoolCblActiveACK2");
00062         chemicals.push_back(CCVUbiEGFRCoolCblActiveACK2);
00063 
00064         Chemical *SortedEGFRACK2 = new Chemical(chemicals.size(),0.0,"SortedEGFRACK2");
00065         chemicals.push_back(SortedEGFRACK2);
00066 
00067         Chemical *SortedEGFRCoolCblActiveACK2 = new Chemical(chemicals.size(),0.0,"SortedEGFRCoolCblActiveACK2");
00068         chemicals.push_back(SortedEGFRCoolCblActiveACK2);
00069 
00070         Chemical *SortedUbiEGFRCoolCblActiveACK2 = new Chemical(chemicals.size(),0.0,"SortedUbiEGFRCoolCblActiveACK2");
00071         chemicals.push_back(SortedUbiEGFRCoolCblActiveACK2);
00072 
00073         Chemical *BoundEndoEGFR = new Chemical(chemicals.size(),0.0,"BoundEndoEGFR");
00074         chemicals.push_back(BoundEndoEGFR);
00075 
00076         Chemical *BoundEndoEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"BoundEndoEGFRCoolCblActive");
00077         chemicals.push_back(BoundEndoEGFRCoolCblActive);
00078 
00079         Chemical *UbiBoundEndoEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"UbiBoundEndoEGFRCoolCblActive");
00080         chemicals.push_back(UbiBoundEndoEGFRCoolCblActive);
00081 
00082         // 20
00083         Chemical *UbiBoundLysoEGFR = new Chemical(chemicals.size(),0.0,"UbiBoundLysoEGFR");
00084         chemicals.push_back(UbiBoundLysoEGFR);
00085 
00086         Chemical *UbiFreeLysoEGFR = new Chemical(chemicals.size(),0.0,"UbiFreeLysoEGFR");
00087         chemicals.push_back(UbiFreeLysoEGFR);
00088 
00089         Chemical *UbiBoundLysoEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"UbiBoundLysoEGFRCoolCblActive");
00090         chemicals.push_back(UbiBoundLysoEGFRCoolCblActive);
00091 
00092         Chemical *UbiFreeLysoEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"UbiFreeLysoEGFRCoolCblActive");
00093         chemicals.push_back(UbiFreeLysoEGFRCoolCblActive);
00094 
00095         Chemical *COPIEndoBoundEGFR = new Chemical(chemicals.size(),0.0,"COPIEndoBoundEGFR");
00096         chemicals.push_back(COPIEndoBoundEGFR);
00097 
00098         Chemical *COPIEndoBoundEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"COPIEndoBoundEGFRCoolCblActive");
00099         chemicals.push_back(COPIEndoBoundEGFRCoolCblActive);
00100 
00101         Chemical *RecyclingVesicle1 = new Chemical(chemicals.size(),0.0,"RecyclingVesicle1");
00102         chemicals.push_back(RecyclingVesicle1);
00103 
00104         Chemical *RecyclingVesicle2 = new Chemical(chemicals.size(),0.0,"RecyclingVesicle2");
00105         chemicals.push_back(RecyclingVesicle2);
00106 
00107         Chemical *RecycledVesicle1 = new Chemical(chemicals.size(),0.0,"RecycledVesicle1");
00108         chemicals.push_back(RecycledVesicle1);
00109 
00110         Chemical *RecycledVesicle2 = new Chemical(chemicals.size(),0.0,"RecycledVesicle2");
00111         chemicals.push_back(RecycledVesicle2);
00112 
00113         // 30
00114         Chemical *Vesicle1Cdc42GDP = new Chemical(chemicals.size(),0.0,"Vesicle1Cdc42GDP");
00115         chemicals.push_back(Vesicle1Cdc42GDP);
00116 
00117         Chemical *Vesicle2Cdc42GDP = new Chemical(chemicals.size(),0.0,"Vesicle2Cdc42GDP");
00118         chemicals.push_back(Vesicle2Cdc42GDP);
00119 
00120         Chemical *COPIPMBoundEGFR = new Chemical(chemicals.size(),0.0,"COPIPMBoundEGFR");
00121         chemicals.push_back(COPIPMBoundEGFR);
00122 
00123         Chemical *COPIPMBoundEGFRCoolCblActive = new Chemical(chemicals.size(),0.0,"COPIPMBoundEGFRCoolCblActive");
00124         chemicals.push_back(COPIPMBoundEGFRCoolCblActive);
00125 
00126         Chemical *Cdc42GAP = new Chemical(chemicals.size(),CFactor,"Cdc42GAP");
00127         chemicals.push_back(Cdc42GAP);
00128 
00129         // Cdc42 alone
00130         Chemical *Cdc42GDP = new Chemical(chemicals.size(),CFactor,"Cdc42GDP");
00131         chemicals.push_back(Cdc42GDP);
00132 
00133         Chemical *Cdc42GTP = new Chemical(chemicals.size(),0.0,"Cdc42GTP");
00134         chemicals.push_back(Cdc42GTP);
00135 
00136         // ACK and 42
00137         Chemical *ACK2 = new Chemical(chemicals.size(),CFactor,"ACK2");
00138         chemicals.push_back(ACK2);
00139 
00140         Chemical *ACK242GTP = new Chemical(chemicals.size(),0.0,"ACK242GTP");
00141         chemicals.push_back(ACK242GTP);
00142 
00143         Chemical *ACK2Active42GTP = new Chemical(chemicals.size(),0.0,"ACK2Active42GTP");
00144         chemicals.push_back(ACK2Active42GTP);
00145 
00146         // 40
00147         Chemical *ACK2Active = new Chemical(chemicals.size(),0.0,"ACK2Active");
00148         chemicals.push_back(ACK2Active);
00149 
00150         Chemical *YPPTase1 = new Chemical(chemicals.size(),CFactor,"YPPTase1");
00151         chemicals.push_back(YPPTase1);
00152 
00153         // Free COP complex
00154         Chemical *COPI = new Chemical(chemicals.size(),10*CFactor,"COPI");
00155         chemicals.push_back(COPI);
00156 
00157         // Cool,Cbl,42
00158         Chemical *Cool1Cbl = new Chemical(chemicals.size(),CFactor,"Cool1Cbl");
00159         chemicals.push_back(Cool1Cbl);
00160 
00161         Chemical *Cool1CblActive = new Chemical(chemicals.size(),0.0,"Cool1CblActive");
00162         chemicals.push_back(Cool1CblActive);
00163 
00164         Chemical *Cool1Cbl42GTP = new Chemical(chemicals.size(),0.0,"Cool1Cbl42GTP");
00165         chemicals.push_back(Cool1Cbl42GTP);
00166 
00167         Chemical *Cool1CblActive42GTP = new Chemical(chemicals.size(),0.0,"Cool1CblActive42GTP");
00168         chemicals.push_back(Cool1CblActive42GTP);
00169                 
00170         // 47
00171         std::vector<Chemical *> vec1;
00172         vec1.push_back(FreePMEGFR);
00173         vec1.push_back(BoundPMEGFR);
00174         vec1.push_back(BoundPMEGFRCoolCbl);
00175         vec1.push_back(BoundPMEGFRCoolCblActive);
00176         vec1.push_back(UbiBoundPMEGFRCoolCblActive);
00177         CAlgebraicChemical *TotalPMEGFR = new CSumChemical(chemicals.size(),"TotalPMEGFR",vec1);
00178         TotalPMEGFR->SetAll();
00179         chemicals.push_back(TotalPMEGFR);
00180         this->AddAlgebraicIndex(TotalPMEGFR);
00181 
00182         std::vector<Chemical *> vec1a;
00183         vec1a.push_back(BoundPMEGFR);
00184         vec1a.push_back(BoundPMEGFRCoolCbl);
00185         vec1a.push_back(BoundPMEGFRCoolCblActive);
00186         vec1a.push_back(UbiBoundPMEGFRCoolCblActive);
00187         CAlgebraicChemical *TotalBoundPMEGFR = new CSumChemical(chemicals.size(),"TotalBoundPMEGFR",vec1a);
00188         TotalBoundPMEGFR->SetAll();
00189         chemicals.push_back(TotalBoundPMEGFR);
00190         this->AddAlgebraicIndex(TotalBoundPMEGFR);
00191         
00192         std::vector<Chemical *> vec2;
00193         vec2.push_back(CCVEGFR);
00194         vec2.push_back(CCVEGFRCoolCblActive);
00195         vec2.push_back(CCVUbiEGFRCoolCblActive);
00196         vec2.push_back(CCVEGFRACK2);
00197         vec2.push_back(CCVEGFRCoolCblActiveACK2);
00198         vec2.push_back(CCVUbiEGFRCoolCblActiveACK2);
00199         vec2.push_back(SortedEGFRACK2);
00200         vec2.push_back(SortedEGFRCoolCblActiveACK2);
00201         vec2.push_back(SortedUbiEGFRCoolCblActiveACK2);
00202         vec2.push_back(BoundEndoEGFR);
00203         vec2.push_back(BoundEndoEGFRCoolCblActive);
00204         vec2.push_back(UbiBoundEndoEGFRCoolCblActive);
00205         vec2.push_back(UbiBoundLysoEGFR);
00206         vec2.push_back(UbiBoundLysoEGFRCoolCblActive);
00207         vec2.push_back(COPIEndoBoundEGFR);
00208         vec2.push_back(COPIEndoBoundEGFRCoolCblActive);
00209         vec2.push_back(RecyclingVesicle1);
00210         vec2.push_back(RecyclingVesicle2);
00211         vec2.push_back(RecycledVesicle1);
00212         vec2.push_back(RecycledVesicle2);
00213         vec2.push_back(Vesicle1Cdc42GDP);
00214         vec2.push_back(Vesicle2Cdc42GDP);
00215         vec2.push_back(COPIPMBoundEGFR);
00216         vec2.push_back(COPIPMBoundEGFRCoolCblActive);
00217         CAlgebraicChemical *TotalInternalEGF = new CSumChemical(chemicals.size(),"TotalInternalEGF",vec2);
00218         TotalInternalEGF->SetAll();
00219         chemicals.push_back(TotalInternalEGF);
00220         this->AddAlgebraicIndex(TotalInternalEGF);
00221 
00222         // 50
00223         std::vector<Chemical *> vec3;
00224         vec3.push_back(CCVEGFR);
00225         vec3.push_back(CCVEGFRCoolCblActive);
00226         vec3.push_back(CCVUbiEGFRCoolCblActive);
00227         vec3.push_back(CCVEGFRACK2);
00228         vec3.push_back(CCVEGFRCoolCblActiveACK2);
00229         vec3.push_back(CCVUbiEGFRCoolCblActiveACK2);
00230         vec3.push_back(SortedEGFRACK2);
00231         vec3.push_back(SortedEGFRCoolCblActiveACK2);
00232         vec3.push_back(SortedUbiEGFRCoolCblActiveACK2);
00233         vec3.push_back(BoundEndoEGFR);
00234         vec3.push_back(BoundEndoEGFRCoolCblActive);
00235         vec3.push_back(UbiBoundEndoEGFRCoolCblActive);
00236         vec3.push_back(UbiBoundLysoEGFR);
00237         vec3.push_back(UbiBoundLysoEGFRCoolCblActive);
00238         vec3.push_back(UbiFreeLysoEGFR);
00239         vec3.push_back(UbiFreeLysoEGFRCoolCblActive);
00240         vec3.push_back(COPIEndoBoundEGFR);
00241         vec3.push_back(COPIEndoBoundEGFRCoolCblActive);
00242         vec3.push_back(RecyclingVesicle1);
00243         vec3.push_back(RecyclingVesicle2);
00244         vec3.push_back(RecycledVesicle1);
00245         vec3.push_back(RecycledVesicle2);
00246         vec3.push_back(Vesicle1Cdc42GDP);
00247         vec3.push_back(Vesicle2Cdc42GDP);
00248         vec3.push_back(COPIPMBoundEGFR);
00249         vec3.push_back(COPIPMBoundEGFRCoolCblActive);
00250         CAlgebraicChemical *TotalInternalEGFR = new CSumChemical(chemicals.size(),"TotalInternalEGFR",vec3);
00251         TotalInternalEGFR->SetAll();
00252         chemicals.push_back(TotalInternalEGFR);
00253         this->AddAlgebraicIndex(TotalInternalEGFR);
00254         
00255         std::vector<Chemical *> vec4;
00256         vec4.push_back(CCVEGFR);
00257         vec4.push_back(CCVEGFRCoolCblActive);
00258         vec4.push_back(CCVUbiEGFRCoolCblActive);
00259         vec4.push_back(CCVEGFRACK2);
00260         vec4.push_back(CCVEGFRCoolCblActiveACK2);
00261         vec4.push_back(CCVUbiEGFRCoolCblActiveACK2);
00262         CAlgebraicChemical *TotalCCVEGFR = new CSumChemical(chemicals.size(),"TotalCCVEGFR",vec4);
00263         TotalCCVEGFR->SetAll();
00264         chemicals.push_back(TotalCCVEGFR);
00265         this->AddAlgebraicIndex(TotalCCVEGFR);
00266 
00267         std::vector<Chemical *> vec5;
00268         vec5.push_back(SortedEGFRACK2);
00269         vec5.push_back(SortedEGFRCoolCblActiveACK2);
00270         vec5.push_back(SortedUbiEGFRCoolCblActiveACK2);
00271         vec5.push_back(BoundEndoEGFR);
00272         vec5.push_back(BoundEndoEGFRCoolCblActive);
00273         vec5.push_back(UbiBoundEndoEGFRCoolCblActive);
00274         CAlgebraicChemical *TotalEndoEGFR = new CSumChemical(chemicals.size(),"TotalEndoEGFR",vec5);
00275         TotalEndoEGFR->SetAll();
00276         chemicals.push_back(TotalEndoEGFR);
00277         this->AddAlgebraicIndex(TotalEndoEGFR);
00278 
00279         std::vector<Chemical *> vec6;
00280         vec6.push_back(UbiBoundLysoEGFR);
00281         vec6.push_back(UbiBoundLysoEGFRCoolCblActive);
00282         vec6.push_back(UbiFreeLysoEGFR);
00283         vec6.push_back(UbiFreeLysoEGFRCoolCblActive);
00284         CAlgebraicChemical *TotalLysoEGFR = new CSumChemical(chemicals.size(),"TotalLysoEGFR",vec6);
00285         TotalLysoEGFR->SetAll();
00286         chemicals.push_back(TotalLysoEGFR);
00287         this->AddAlgebraicIndex(TotalLysoEGFR);
00288 
00289         Chemical *ACK242GDP= new Chemical(chemicals.size(),0.0,"ACK242GDP");
00290         chemicals.push_back(ACK242GDP);
00291 
00292         Chemical *ACK2Active42GDP = new Chemical(chemicals.size(),0.0,"ACK2Active42GDP");
00293         chemicals.push_back(ACK2Active42GDP);
00294 
00295         Chemical *Cool1Cbl42GDP = new Chemical(chemicals.size(),0.0,"Cool1Cbl42GDP");
00296         chemicals.push_back(Cool1Cbl42GDP);
00297 
00298         Chemical *Cool1CblActive42GDP = new Chemical(chemicals.size(),0.0,"Cool1CblActive42GDP");
00299         chemicals.push_back(Cool1CblActive42GDP);
00300 
00301 
00302         // mutant Cdc42
00303         Chemical *MutRecyclingVesicle1 = new Chemical(chemicals.size(),0.0,"MutRecyclingVesicle1");
00304         chemicals.push_back(MutRecyclingVesicle1);
00305 
00306         Chemical *MutRecyclingVesicle2 = new Chemical(chemicals.size(),0.0,"MutRecyclingVesicle2");
00307         chemicals.push_back(MutRecyclingVesicle2);
00308 
00309         // 60
00310         Chemical *MutRecycledVesicle1 = new Chemical(chemicals.size(),0.0,"MutRecycledVesicle1");
00311         chemicals.push_back(MutRecycledVesicle1);
00312 
00313         Chemical *MutRecycledVesicle2 = new Chemical(chemicals.size(),0.0,"MutRecycledVesicle2");
00314         chemicals.push_back(MutRecycledVesicle2);
00315 
00316         Chemical *MutVesicle1Cdc42GDP = new Chemical(chemicals.size(),0.0,"MutVesicle1Cdc42GDP");
00317         chemicals.push_back(MutVesicle1Cdc42GDP);
00318 
00319         Chemical *MutVesicle2Cdc42GDP = new Chemical(chemicals.size(),0.0,"MutVesicle2Cdc42GDP");
00320         chemicals.push_back(MutVesicle2Cdc42GDP);
00321 
00322         Chemical *MutCdc42GDP = new Chemical(chemicals.size(),0.0,"MutCdc42GDP");
00323         chemicals.push_back(MutCdc42GDP);
00324 
00325         Chemical *MutCdc42GTP = new Chemical(chemicals.size(),0.0,"MutCdc42GTP");
00326         chemicals.push_back(MutCdc42GTP);
00327 
00328         Chemical *MutACK242GTP = new Chemical(chemicals.size(),0.0,"ACK242GTP");
00329         chemicals.push_back(MutACK242GTP);
00330 
00331         Chemical *MutACK2Active42GTP = new Chemical(chemicals.size(),0.0,"MutACK2Active42GTP");
00332         chemicals.push_back(MutACK2Active42GTP);
00333 
00334         Chemical *MutCool1Cbl42GTP = new Chemical(chemicals.size(),0.0,"MutCool1Cbl42GTP");
00335         chemicals.push_back(MutCool1Cbl42GTP);
00336 
00337         Chemical *MutCool1CblActive42GTP = new Chemical(chemicals.size(),0.0,"MutCool1CblActive42GTP");
00338         chemicals.push_back(MutCool1CblActive42GTP);
00339 
00340         // 70
00341         Chemical *MutACK242GDP= new Chemical(chemicals.size(),0.0,"MutACK242GDP");
00342         chemicals.push_back(MutACK242GDP);
00343 
00344         Chemical *MutACK2Active42GDP = new Chemical(chemicals.size(),0.0,"MutACK2Active42GDP");
00345         chemicals.push_back(MutACK2Active42GDP);
00346 
00347         Chemical *MutCool1Cbl42GDP = new Chemical(chemicals.size(),0.0,"MutCool1Cbl42GDP");
00348         chemicals.push_back(MutCool1Cbl42GDP);
00349 
00350         Chemical *MutCool1CblActive42GDP = new Chemical(chemicals.size(),0.0,"MutCool1CblActive42GDP");
00351         chemicals.push_back(MutCool1CblActive42GDP);
00352 
00353         std::vector<Chemical *> vec7;
00354         vec7.push_back(CCVEGFR);
00355         vec7.push_back(CCVEGFRCoolCblActive);
00356         vec7.push_back(CCVUbiEGFRCoolCblActive);
00357         vec7.push_back(CCVEGFRACK2);
00358         vec7.push_back(CCVEGFRCoolCblActiveACK2);
00359         vec7.push_back(CCVUbiEGFRCoolCblActiveACK2);
00360         vec7.push_back(SortedEGFRACK2);
00361         vec7.push_back(SortedEGFRCoolCblActiveACK2);
00362         vec7.push_back(SortedUbiEGFRCoolCblActiveACK2);
00363         vec7.push_back(BoundEndoEGFR);
00364         vec7.push_back(BoundEndoEGFRCoolCblActive);
00365         vec7.push_back(UbiBoundEndoEGFRCoolCblActive);
00366         vec7.push_back(UbiBoundLysoEGFR);
00367         vec7.push_back(UbiBoundLysoEGFRCoolCblActive);
00368         vec7.push_back(COPIEndoBoundEGFR);
00369         vec7.push_back(COPIEndoBoundEGFRCoolCblActive);
00370         vec7.push_back(RecyclingVesicle1);
00371         vec7.push_back(MutRecyclingVesicle1);
00372         vec7.push_back(RecyclingVesicle2);
00373         vec7.push_back(MutRecyclingVesicle2);
00374         vec7.push_back(RecycledVesicle1);
00375         vec7.push_back(MutRecycledVesicle1);
00376         vec7.push_back(RecycledVesicle2);
00377         vec7.push_back(MutRecycledVesicle2);
00378         vec7.push_back(Vesicle1Cdc42GDP);
00379         vec7.push_back(MutVesicle1Cdc42GDP);
00380         vec7.push_back(Vesicle2Cdc42GDP);
00381         vec7.push_back(MutVesicle2Cdc42GDP);
00382         vec7.push_back(COPIPMBoundEGFR);
00383         vec7.push_back(COPIPMBoundEGFRCoolCblActive);
00384         CAlgebraicChemical *MutTotalInternalEGF = new CSumChemical(chemicals.size(),"MutTotalInternalEGF",vec7);
00385         MutTotalInternalEGF->SetAll();
00386         chemicals.push_back(MutTotalInternalEGF);
00387         this->AddAlgebraicIndex(MutTotalInternalEGF);
00388 
00389         std::vector<Chemical *> vec8;
00390         vec8.push_back(CCVEGFR);
00391         vec8.push_back(CCVEGFRCoolCblActive);
00392         vec8.push_back(CCVUbiEGFRCoolCblActive);
00393         vec8.push_back(CCVEGFRACK2);
00394         vec8.push_back(CCVEGFRCoolCblActiveACK2);
00395         vec8.push_back(CCVUbiEGFRCoolCblActiveACK2);
00396         vec8.push_back(SortedEGFRACK2);
00397         vec8.push_back(SortedEGFRCoolCblActiveACK2);
00398         vec8.push_back(SortedUbiEGFRCoolCblActiveACK2);
00399         vec8.push_back(BoundEndoEGFR);
00400         vec8.push_back(BoundEndoEGFRCoolCblActive);
00401         vec8.push_back(UbiBoundEndoEGFRCoolCblActive);
00402         vec8.push_back(UbiBoundLysoEGFR);
00403         vec8.push_back(UbiBoundLysoEGFRCoolCblActive);
00404         vec8.push_back(UbiFreeLysoEGFR);
00405         vec8.push_back(UbiFreeLysoEGFRCoolCblActive);
00406         vec8.push_back(COPIEndoBoundEGFR);
00407         vec8.push_back(COPIEndoBoundEGFRCoolCblActive);
00408         vec8.push_back(RecyclingVesicle1);
00409         vec8.push_back(MutRecyclingVesicle1);
00410         vec8.push_back(RecyclingVesicle2);
00411         vec8.push_back(MutRecyclingVesicle2);
00412         vec8.push_back(RecycledVesicle1);
00413         vec8.push_back(MutRecycledVesicle1);
00414         vec8.push_back(RecycledVesicle2);
00415         vec8.push_back(MutRecycledVesicle2);
00416         vec8.push_back(Vesicle1Cdc42GDP);
00417         vec8.push_back(MutVesicle1Cdc42GDP);
00418         vec8.push_back(Vesicle2Cdc42GDP);
00419         vec8.push_back(MutVesicle2Cdc42GDP);
00420         vec8.push_back(COPIPMBoundEGFR);
00421         vec8.push_back(COPIPMBoundEGFRCoolCblActive);
00422         CAlgebraicChemical *MutTotalInternalEGFR = new CSumChemical(chemicals.size(),"MutTotalInternalEGFR",vec8);
00423         MutTotalInternalEGFR->SetAll();
00424         chemicals.push_back(MutTotalInternalEGFR);
00425         this->AddAlgebraicIndex(MutTotalInternalEGFR);
00426         
00427 
00428         std::vector<Chemical *> vec9;
00429         vec9.push_back(FreePMEGFR);
00430         vec9.push_back(BoundPMEGFR);
00431         vec9.push_back(BoundPMEGFRCoolCbl);
00432         vec9.push_back(BoundPMEGFRCoolCblActive);
00433         vec9.push_back(UbiBoundPMEGFRCoolCblActive);
00434         vec9.push_back(CCVEGFR);
00435         vec9.push_back(CCVEGFRCoolCblActive);
00436         vec9.push_back(CCVUbiEGFRCoolCblActive);
00437         vec9.push_back(CCVEGFRACK2);
00438         vec9.push_back(CCVEGFRCoolCblActiveACK2);
00439         vec9.push_back(CCVUbiEGFRCoolCblActiveACK2);
00440         vec9.push_back(SortedEGFRACK2);
00441         vec9.push_back(SortedEGFRCoolCblActiveACK2);
00442         vec9.push_back(SortedUbiEGFRCoolCblActiveACK2);
00443         vec9.push_back(BoundEndoEGFR);
00444         vec9.push_back(BoundEndoEGFRCoolCblActive);
00445         vec9.push_back(UbiBoundEndoEGFRCoolCblActive);
00446         vec9.push_back(UbiBoundLysoEGFR);
00447         vec9.push_back(UbiBoundLysoEGFRCoolCblActive);
00448         vec9.push_back(UbiFreeLysoEGFR);
00449         vec9.push_back(UbiFreeLysoEGFRCoolCblActive);
00450         vec9.push_back(COPIEndoBoundEGFR);
00451         vec9.push_back(COPIEndoBoundEGFRCoolCblActive);
00452         vec9.push_back(RecyclingVesicle1);
00453         vec9.push_back(MutRecyclingVesicle1);
00454         vec9.push_back(RecyclingVesicle2);
00455         vec9.push_back(MutRecyclingVesicle2);
00456         vec9.push_back(RecycledVesicle1);
00457         vec9.push_back(MutRecycledVesicle1);
00458         vec9.push_back(RecycledVesicle2);
00459         vec9.push_back(MutRecycledVesicle2);
00460         vec9.push_back(Vesicle1Cdc42GDP);
00461         vec9.push_back(MutVesicle1Cdc42GDP);
00462         vec9.push_back(Vesicle2Cdc42GDP);
00463         vec9.push_back(MutVesicle2Cdc42GDP);
00464         vec9.push_back(COPIPMBoundEGFR);
00465         vec9.push_back(COPIPMBoundEGFRCoolCblActive);
00466         CAlgebraicChemical *MutTotalEGFR = new CSumChemical(chemicals.size(),"MutTotalIEGFR",vec9);
00467         MutTotalEGFR->SetAll();
00468         chemicals.push_back(MutTotalEGFR);
00469         this->AddAlgebraicIndex(MutTotalEGFR);
00470 
00471         // rate constants
00472         // EGF binding/unbinding
00473         RateConstant *kbEGF = new RateConstant(1.0e-07,"kbEGF");
00474         rateConstants.push_back(kbEGF);
00475 
00476         RateConstant *kuEGF = new RateConstant(0.02,"kuEGF");
00477         rateConstants.push_back(kuEGF);
00478 
00479         // 42 activation
00480         RateConstant *kEGFR42 = new RateConstant(0.02*SecPerMin,"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(0.01*SecPerMin,"kGAP");
00488         rateConstants.push_back(kGAP);
00489 
00490         RateConstant *KmGAP = new RateConstant(2.9*CFactor,"KmGAP");
00491         rateConstants.push_back(KmGAP);
00492 
00493         // allow possibility of different endocytic rates depending upon 
00494         // whether receptor is ubiquitinated or not 
00495 
00496         RateConstant *kEndo1 = new RateConstant(1.0/15.0,"kEndo1");
00497         rateConstants.push_back(kEndo1);
00498         
00499         RateConstant *kEndo2 = new RateConstant(1.0/15.0,"kEndo2");
00500         rateConstants.push_back(kEndo2);
00501 
00502         // ACK2 binding/unbinding to 42
00503 
00504         RateConstant *kbACKActive = new RateConstant(1.0e-07,"kbACKActive");
00505         rateConstants.push_back(kbACKActive);
00506 
00507         RateConstant *kuACKActive = new RateConstant(0.02,"kuACKActive");
00508         rateConstants.push_back(kuACKActive);
00509 
00510         RateConstant *kbACK2 = new RateConstant(1.0e-07,"kbACK2");
00511         rateConstants.push_back(kbACK2);
00512 
00513         RateConstant *kuACK2 = new RateConstant(0.02,"kuACK2");
00514         rateConstants.push_back(kuACK2);
00515 
00516         RateConstant *kuACK242GDP = new RateConstant(0.1,"kuACK242GDP");
00517         rateConstants.push_back(kuACK242GDP);
00518 
00519         RateConstant *kuACK2Active42GDP = new RateConstant(0.1,"kuACK2Active42GDP");
00520         rateConstants.push_back(kuACK2Active42GDP);
00521         
00522         // ACK2 activation
00523         
00524         RateConstant *kACK2 = new RateConstant(0.5*SecPerMin,"kACK2");
00525         rateConstants.push_back(kACK2);
00526 
00527         // ACK2 dephosphorylation by PPtase
00528 
00529         RateConstant *kdACK2 = new RateConstant(0.1*SecPerMin,"kdACK2");
00530         rateConstants.push_back(kdACK2);
00531 
00532         RateConstant *KmdACK2 = new RateConstant(CFactor,"KmdACK2");
00533         rateConstants.push_back(KmdACK2);
00534 
00535         // ACK2 binding/unbinding to the CCV
00536 
00537         RateConstant *kbACK2CCV = new RateConstant(1.0e-07,"kbACK2CCV");
00538         rateConstants.push_back(kbACK2CCV);
00539 
00540         RateConstant *kuACK2CCV = new RateConstant(0.02,"kuACK2CCV");
00541         rateConstants.push_back(kuACK2CCV);
00542 
00543         // Sorting of ACK-bound CCVs
00544 
00545         RateConstant *kSort = new RateConstant(0.25*SecPerMin,"kSort");
00546         rateConstants.push_back(kSort);
00547 
00548         // Endosomal to lysosomal transfer
00549 
00550         RateConstant *kEndoLyso = new RateConstant(0.25*SecPerMin,"kEndoLyso");
00551         rateConstants.push_back(kEndoLyso);
00552 
00553         // Degradation of EGF
00554 
00555         RateConstant *kdegEGF = new RateConstant(0.25*SecPerMin,"kdegEGF");
00556         rateConstants.push_back(kdegEGF);
00557 
00558         // Proteolysis of EGFR
00559 
00560         RateConstant *kProt = new RateConstant(0.25*SecPerMin,"kProt");
00561         rateConstants.push_back(kProt);
00562 
00563         // Cbl binding to the receptor
00564         
00565         RateConstant *kbCbl = new RateConstant(1.0e-07,"kbCbl");
00566         rateConstants.push_back(kbCbl);
00567 
00568         // Cbl unbinding from a ubiquitinated receptor
00569         
00570         RateConstant *kuCblUbi = new RateConstant(1.0e-02,"kuCblUbi");
00571         rateConstants.push_back(kuCblUbi);
00572 
00573         // Cbl when bound to EGF receptor - activation and ubiquitination
00574 
00575         RateConstant *kCbl = new RateConstant(0.1/SecPerMin,"kCbl");
00576         rateConstants.push_back(kCbl);
00577 
00578         RateConstant *kUbi = new RateConstant(0.05/SecPerMin,"kUbi");
00579         rateConstants.push_back(kUbi);
00580 
00581         // Cool/Cbl and 42 binding/unbinding
00582 
00583         RateConstant *kbCbl42 = new RateConstant(1.0e-07,"kbCbl42");
00584         rateConstants.push_back(kbCbl42);
00585 
00586         RateConstant *kuCbl42 = new RateConstant(0.02,"kuCbl42");
00587         rateConstants.push_back(kuCbl42);
00588 
00589         RateConstant *kbCblActive42 = new RateConstant(1.0e-07,"kbCblActive42");
00590         rateConstants.push_back(kbCblActive42);
00591 
00592         RateConstant *kuCblActive42 = new RateConstant(0.02,"kuCblActive42");
00593         rateConstants.push_back(kuCblActive42);
00594 
00595         RateConstant *kuCool1Cbl42GDP = new RateConstant(0.1,"kuCool1Cbl42GDP");
00596         rateConstants.push_back(kuCool1Cbl42GDP);
00597 
00598         RateConstant *kuCool1CblActive42GDP = new RateConstant(0.1,"kuCool1CblActive42GDP");
00599         rateConstants.push_back(kuCool1CblActive42GDP);
00600 
00601         // COPI binding to EGFR
00602 
00603         RateConstant *kbCOPI = new RateConstant(1.0e-07,"kbCOPI");
00604         rateConstants.push_back(kbCOPI);
00605 
00606         // Active 42 binding to recycling vesicle
00607 
00608         RateConstant *kb42COPI = new RateConstant(2.0e-07,"kb42COPI");
00609         rateConstants.push_back(kb42COPI);
00610 
00611         // Inactive 42 unbinding
00612 
00613         RateConstant *ku42COPI = new RateConstant(0.02,"ku42COPI");
00614         rateConstants.push_back(ku42COPI);
00615 
00616         // COPI unbinding from recycled vesicle
00617 
00618         RateConstant *kuCOPI = new RateConstant(0.02,"kuCOPI");
00619         rateConstants.push_back(kuCOPI);
00620 
00621         // COPI-mediated recycling
00622 
00623         RateConstant *kRec = new RateConstant(25.0/SecPerMin,"kRec");
00624         rateConstants.push_back(kRec);
00625 
00626         
00627         // reactions
00628         // 0
00629         // EGF binding/unbinding
00630         Reaction *EGFBinding = new ReceptorBindingReaction(EGF,FreePMEGFR,BoundPMEGFR,kbEGF,"EGFBinding");
00631         reactions.push_back(EGFBinding);
00632 
00633         Reaction *EGFUnbinding = new ReceptorUnbindingReaction(BoundPMEGFR,FreePMEGFR,EGF,kuEGF,"EGFUnbinding");
00634         reactions.push_back(EGFUnbinding);
00635 
00636         // 42 activation
00637 
00638         Reaction *Cdc42PMActivation1 = new MichaelisMentenGProteinActivationReaction(BoundPMEGFR,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation1");
00639         reactions.push_back(Cdc42PMActivation1);
00640 
00641         Reaction *Cdc42PMActivation2 = new MichaelisMentenGProteinActivationReaction(BoundPMEGFRCoolCbl,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation2");
00642         reactions.push_back(Cdc42PMActivation2);
00643 
00644         Reaction *Cdc42PMActivation3 = new MichaelisMentenGProteinActivationReaction(BoundPMEGFRCoolCblActive,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation3");
00645         reactions.push_back(Cdc42PMActivation3);
00646 
00647         Reaction *Cdc42PMActivation4 = new MichaelisMentenGProteinActivationReaction(UbiBoundPMEGFRCoolCblActive,Cdc42GDP,Cdc42GTP,kEGFR42,KmEGFR42,"Cdc42PMActivation4");
00648         reactions.push_back(Cdc42PMActivation4);
00649 
00650         // gapping of free 42
00651 
00652         Reaction *Cdc42GAPHydrolysis = new MichaelisMentenGProteinActivationReaction(Cdc42GAP,Cdc42GTP,Cdc42GDP,kGAP,KmGAP,"Cdc42GAPHydrolysis");
00653         reactions.push_back(Cdc42GAPHydrolysis);
00654 
00655         // endocytosis
00656 
00657         Reaction *Endocytosis1 = new TransformationReaction(BoundPMEGFR,CCVEGFR,kEndo1,"Endocytosis1");
00658         reactions.push_back(Endocytosis1);
00659 
00660         Reaction *Endocytosis2 = new TransformationReaction(BoundPMEGFRCoolCblActive,CCVEGFRCoolCblActive,kEndo1,"Endocytosis2");
00661         reactions.push_back(Endocytosis2);
00662 
00663         Reaction *Endocytosis3 = new TransformationReaction(UbiBoundPMEGFRCoolCblActive,CCVUbiEGFRCoolCblActive,kEndo2,"Endocytosis3");
00664         reactions.push_back(Endocytosis3);
00665 
00666         // ACK2 and 42 cycle
00667         // 10
00668         Reaction *ACK42Binding = new HeterodimerizationReaction(ACK2,Cdc42GTP,ACK242GTP,kbACK2,"ACK42Binding");
00669         reactions.push_back(ACK42Binding);
00670 
00671         Reaction *ACK42Unbinding = new HeterodimerDissociationReaction(ACK242GTP,ACK2,Cdc42GTP,kuACK2,"ACK42Unbinding");
00672         reactions.push_back(ACK42Unbinding);
00673 
00674         Reaction *ACK2Active42Binding = new HeterodimerizationReaction(ACK2Active,Cdc42GTP,ACK2Active42GTP,kbACKActive,"ACK2Active42Binding");
00675         reactions.push_back(ACK2Active42Binding);
00676 
00677         Reaction *ACK2Active42Unbinding = new HeterodimerDissociationReaction(ACK2Active42GTP,ACK2Active,Cdc42GTP,kuACKActive,"ACK2Active42Unbinding");
00678         reactions.push_back(ACK2Active42Unbinding);
00679 
00680         Reaction *ACK2Activation = new TransformationReaction(ACK242GTP,ACK2Active42GTP,kACK2,"ACK2Activation");
00681         reactions.push_back(ACK2Activation);
00682 
00683         Reaction *ACK2Deactivation = new MichaelisMentenDephosphorylationReaction(YPPTase1,ACK2Active,ACK2,kdACK2,KmdACK2,"ACK2Deactivation");
00684         reactions.push_back(ACK2Deactivation);
00685 
00686         Reaction *ACK242GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,ACK242GTP,ACK242GDP,kGAP,KmGAP,"ACK242GAPing");
00687         reactions.push_back(ACK242GAPing);
00688 
00689         Reaction *ACK2Active42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,ACK2Active42GTP,ACK2Active42GDP,kGAP,KmGAP,"ACK2Active42GAPing");
00690         reactions.push_back(ACK2Active42GAPing);
00691 
00692         Reaction *ACK242GDPRelease = new HeterodimerDissociationReaction(ACK242GDP,ACK2,Cdc42GDP,kuACK242GDP,"ACK242GDPRelease");
00693         reactions.push_back(ACK242GDPRelease);
00694 
00695         Reaction *ACK2Active42GDPRelease = new HeterodimerDissociationReaction(ACK2Active42GDP,ACK2Active,Cdc42GDP,kuACK2Active42GDP,"ACK2Active42GDPRelease");
00696         reactions.push_back(ACK2Active42GDPRelease);
00697 
00698         // Cool/Cbl and 42 cycle
00699         // 20
00700         Reaction *CoolCbl42Binding = new HeterodimerizationReaction(Cool1Cbl,Cdc42GTP,Cool1Cbl42GTP,kbCbl42,"CoolCbl42Binding");
00701         reactions.push_back(CoolCbl42Binding);
00702 
00703         Reaction *CoolCbl42Unbinding = new HeterodimerDissociationReaction(Cool1Cbl42GTP,Cool1Cbl,Cdc42GTP,kuCbl42,"CoolCbl42Unbinding");
00704         reactions.push_back(CoolCbl42Unbinding);
00705 
00706         Reaction *CoolCblActive42Binding = new HeterodimerizationReaction(Cool1CblActive,Cdc42GTP,Cool1CblActive42GTP,kbCblActive42,"CoolCblActive42Binding");
00707         reactions.push_back(CoolCblActive42Binding);
00708 
00709         Reaction *CoolCblActive42Unbinding = new HeterodimerDissociationReaction(Cool1CblActive42GTP,Cool1CblActive,Cdc42GTP,kuCblActive42,"CoolCblActive42Unbinding");
00710         reactions.push_back(CoolCblActive42Unbinding);
00711 
00712         Reaction *CoolCbl42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,Cool1Cbl42GTP,Cool1Cbl42GDP,kGAP,KmGAP,"CoolCbl42GAPing");
00713         reactions.push_back(CoolCbl42GAPing);
00714 
00715         Reaction *CoolCblActive42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,Cool1CblActive42GTP,Cool1CblActive42GDP,kGAP,KmGAP,"CoolCblActive42GAPing");
00716         reactions.push_back(CoolCblActive42GAPing);
00717 
00718         Reaction *CoolCbl42GDPRelease = new HeterodimerDissociationReaction(Cool1Cbl42GDP,Cool1Cbl,Cdc42GDP,kuCool1Cbl42GDP,"CoolCbl42GDPRelease");
00719         reactions.push_back(CoolCbl42GDPRelease);
00720 
00721         Reaction *CoolCblActive42GDPRelease = new HeterodimerDissociationReaction(Cool1CblActive42GDP,Cool1CblActive,Cdc42GDP,kuCool1CblActive42GDP,"CoolCblActive42GDPRelease");
00722         reactions.push_back(CoolCblActive42GDPRelease);
00723 
00724         // sorting
00725 
00726         Reaction *ACKBinding1 = new HeterodimerizationReaction(ACK2Active,CCVEGFR,CCVEGFRACK2,kbACK2CCV,"ACKBinding1");
00727         reactions.push_back(ACKBinding1);
00728 
00729         Reaction *ACKBinding2 = new HeterodimerizationReaction(ACK2Active,CCVEGFRCoolCblActive,CCVEGFRCoolCblActiveACK2,kbACK2CCV,"ACKBinding2");
00730         reactions.push_back(ACKBinding2);
00731         // 30
00732         Reaction *ACKBinding3 = new HeterodimerizationReaction(ACK2Active,CCVUbiEGFRCoolCblActive,CCVUbiEGFRCoolCblActiveACK2,kbACK2CCV,"ACKBinding3");
00733         reactions.push_back(ACKBinding3);
00734 
00735         Reaction *Sorting1 = new TransformationReaction(CCVEGFRACK2,SortedEGFRACK2,kSort,"Sorting1");
00736         reactions.push_back(Sorting1);
00737 
00738         Reaction *Sorting2 = new TransformationReaction(CCVEGFRCoolCblActiveACK2,SortedEGFRCoolCblActiveACK2,kSort,"Sorting2");
00739         reactions.push_back(Sorting2);
00740 
00741         Reaction *Sorting3 = new TransformationReaction(CCVUbiEGFRCoolCblActiveACK2,SortedUbiEGFRCoolCblActiveACK2,kSort,"Sorting3");
00742         reactions.push_back(Sorting3);
00743 
00744         Reaction *ACKRelease1 = new HeterodimerDissociationReaction(SortedEGFRACK2,BoundEndoEGFR,ACK2Active,kuACK2CCV,"ACKRelease1");
00745         reactions.push_back(ACKRelease1);
00746 
00747         Reaction *ACKRelease2 = new HeterodimerDissociationReaction(SortedEGFRCoolCblActiveACK2,BoundEndoEGFRCoolCblActive,ACK2Active,kuACK2CCV,"ACKRelease2");
00748         reactions.push_back(ACKRelease2);
00749 
00750         Reaction *ACKRelease3 = new HeterodimerDissociationReaction(SortedUbiEGFRCoolCblActiveACK2,UbiBoundEndoEGFRCoolCblActive,ACK2Active,kuACK2CCV,"ACKRelease3");
00751         reactions.push_back(ACKRelease3);
00752 
00753         // Transfer to lysosomes
00754 
00755         Reaction *LysosomalTransfer = new TransformationReaction(UbiBoundEndoEGFRCoolCblActive,UbiBoundLysoEGFRCoolCblActive,kEndoLyso,"LysosomalTransfer");
00756         reactions.push_back(LysosomalTransfer);
00757 
00758         // EGF degradation
00759 
00760         Reaction *LigandDegradation1 = new ReceptorUnbindingReaction(UbiBoundLysoEGFR,UbiFreeLysoEGFR,DegradedEGF,kdegEGF,"EGFDegradation1");
00761         reactions.push_back(LigandDegradation1);
00762 
00763         Reaction *LigandDegradation2 = new ReceptorUnbindingReaction(UbiBoundLysoEGFRCoolCblActive,UbiFreeLysoEGFRCoolCblActive,DegradedEGF,kdegEGF,"EGFDegradation2");
00764         reactions.push_back(LigandDegradation2);
00765 
00766         // CoolCbl binding to receptor
00767         // 40
00768         Reaction *EGFRCoolCblBinding = new HeterodimerizationReaction(BoundPMEGFR,Cool1Cbl,BoundPMEGFRCoolCbl,kbCbl,"InactiveCblBinding");
00769         reactions.push_back(EGFRCoolCblBinding);
00770 
00771         Reaction *EGFRCoolCblActiveBinding = new HeterodimerizationReaction(BoundPMEGFR,Cool1CblActive,BoundPMEGFRCoolCblActive,kbCbl,"ActiveCblBinding");
00772         reactions.push_back(EGFRCoolCblActiveBinding);
00773 
00774         // CoolCbl phosphorylation
00775 
00776         Reaction *EGFRCoolCblActivation = new TransformationReaction(BoundPMEGFRCoolCbl,BoundPMEGFRCoolCblActive,kCbl,"EGFRCoolCblActivation");
00777         reactions.push_back(EGFRCoolCblActivation);
00778 
00779         // ubiquitination 
00780         Reaction *MembraneUbi = new TransformationReaction(BoundPMEGFRCoolCblActive,UbiBoundPMEGFRCoolCblActive,kUbi,"MembraneUbi");
00781         reactions.push_back(MembraneUbi);
00782 
00783         Reaction *VesicleUbi = new TransformationReaction(CCVEGFRCoolCblActive,CCVUbiEGFRCoolCblActive,kUbi,"VesicleUbi");
00784         reactions.push_back(VesicleUbi);
00785 
00786         Reaction *EndoUbi = new TransformationReaction(BoundEndoEGFRCoolCblActive,UbiBoundEndoEGFRCoolCblActive,kUbi,"EndoUbi");
00787         reactions.push_back(EndoUbi);
00788 
00789         // CoolCbl release
00790 
00791         Reaction *CoolCblDissociation1 = new HeterodimerDissociationReaction(UbiBoundLysoEGFRCoolCblActive,UbiBoundLysoEGFR,Cool1CblActive,kuCblUbi,"CoolCblDissociation1");
00792         reactions.push_back(CoolCblDissociation1);
00793 
00794         Reaction *CoolCblDissociation2 = new HeterodimerDissociationReaction(UbiFreeLysoEGFRCoolCblActive,UbiFreeLysoEGFR,Cool1CblActive,kuCblUbi,"CoolCblDissociation2");
00795         reactions.push_back(CoolCblDissociation2);
00796 
00797         // EGFR proteolysis 
00798 
00799         Reaction *FreeEGFRProteolysis = new TransformationReaction(UbiFreeLysoEGFR,DegradedEGFR,kProt,"FreeEGFRProteolysis");
00800         reactions.push_back(FreeEGFRProteolysis);
00801 
00802         // assembly of recycling vesicle
00803 
00804         Reaction *COPIBinding1 = new HeterodimerizationReaction(COPI,BoundEndoEGFR,COPIEndoBoundEGFR,kbCOPI,"COPIBinding1");
00805         reactions.push_back(COPIBinding1);
00806         // 50
00807         Reaction *COPIBinding2 = new HeterodimerizationReaction(COPI,BoundEndoEGFRCoolCblActive,COPIEndoBoundEGFRCoolCblActive,kbCOPI,"COPIBinding2");
00808         reactions.push_back(COPIBinding2);
00809 
00810         Reaction *VesicleAssembly1 = new HeterodimerizationReaction(COPIEndoBoundEGFR,Cdc42GTP,RecyclingVesicle1,kb42COPI,"VesicleAssembly1");
00811         reactions.push_back(VesicleAssembly1);
00812 
00813         Reaction *VesicleAssembly2 = new HeterodimerizationReaction(COPIEndoBoundEGFRCoolCblActive,Cdc42GTP,RecyclingVesicle2,kb42COPI,"VesicleAssembly2");
00814         reactions.push_back(VesicleAssembly2);
00815 
00816         // recycling
00817 
00818         Reaction *Recycling1 = new TransformationReaction(RecyclingVesicle1,RecycledVesicle1,kRec,"Recycling1");
00819         reactions.push_back(Recycling1);
00820 
00821         Reaction *Recycling2 = new TransformationReaction(RecyclingVesicle2,RecycledVesicle2,kRec,"Recycling2");
00822         reactions.push_back(Recycling2);
00823 
00824         // uncoating and fusion
00825 
00826         Reaction *VesicleGAPing1 = new MichaelisMentenTransformationReaction(Cdc42GAP,RecycledVesicle1,Vesicle1Cdc42GDP,kGAP,KmGAP,"VesicleGAPing1");
00827         reactions.push_back(VesicleGAPing1);
00828 
00829         Reaction *VesicleGAPing2 = new MichaelisMentenTransformationReaction(Cdc42GAP,RecycledVesicle2,Vesicle2Cdc42GDP,kGAP,KmGAP,"VesicleGAPing2");
00830         reactions.push_back(VesicleGAPing2);
00831 
00832         Reaction *Cdc42COPIUnbinding1 = new HeterodimerDissociationReaction(Vesicle1Cdc42GDP,COPIPMBoundEGFR,Cdc42GDP,ku42COPI,"Cdc42COPIUnbinding1");
00833         reactions.push_back(Cdc42COPIUnbinding1);
00834 
00835         Reaction *Cdc42COPIUnbinding2 = new HeterodimerDissociationReaction(Vesicle2Cdc42GDP,COPIPMBoundEGFRCoolCblActive,Cdc42GDP,ku42COPI,"Cdc42COPIUnbinding2");
00836         reactions.push_back(Cdc42COPIUnbinding2);
00837 
00838         Reaction *VesicleFusion1 = new HeterodimerDissociationReaction(COPIPMBoundEGFR,COPI,BoundPMEGFR,kuCOPI,"VesicleFusion1");
00839         reactions.push_back(VesicleFusion1);
00840 
00841         // 60
00842         Reaction *VesicleFusion2 = new HeterodimerDissociationReaction(COPIPMBoundEGFRCoolCblActive,COPI,BoundPMEGFRCoolCblActive,kuCOPI,"VesicleFusion2");
00843         reactions.push_back(VesicleFusion2);
00844 
00845         
00846         // reactions with mutant 42
00847 
00848         Reaction *MutACK42Binding = new HeterodimerizationReaction(ACK2,MutCdc42GTP,MutACK242GTP,kbACK2,"MutACK42Binding");
00849         reactions.push_back(MutACK42Binding);
00850 
00851         Reaction *MutACK42Unbinding = new HeterodimerDissociationReaction(MutACK242GTP,ACK2,MutCdc42GTP,kuACK2,"MutACK42Unbinding");
00852         reactions.push_back(MutACK42Unbinding);
00853 
00854         Reaction *MutACK2Active42Binding = new HeterodimerizationReaction(ACK2Active,MutCdc42GTP,MutACK2Active42GTP,kbACKActive,"MutACK2Active42Binding");
00855         reactions.push_back(MutACK2Active42Binding);
00856 
00857         Reaction *MutACK2Active42Unbinding = new HeterodimerDissociationReaction(MutACK2Active42GTP,ACK2Active,MutCdc42GTP,kuACKActive,"MutACK2Active42Unbinding");
00858         reactions.push_back(MutACK2Active42Unbinding);
00859 
00860         Reaction *MutACK2Activation = new TransformationReaction(MutACK242GTP,MutACK2Active42GTP,kACK2,"MutACK2Activation");
00861         reactions.push_back(MutACK2Activation);
00862 
00863         Reaction *MutACK242GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,MutACK242GTP,MutACK242GDP,kGAP,KmGAP,"MutACK242GAPing");
00864         reactions.push_back(MutACK242GAPing);
00865 
00866         Reaction *MutACK2Active42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,MutACK2Active42GTP,MutACK2Active42GDP,kGAP,KmGAP,"MutACK2Active42GAPing");
00867         reactions.push_back(MutACK2Active42GAPing);
00868 
00869         Reaction *MutACK242GDPRelease = new HeterodimerDissociationReaction(MutACK242GDP,ACK2,MutCdc42GDP,kuACK242GDP,"MutACK242GDPRelease");
00870         reactions.push_back(MutACK242GDPRelease);
00871 
00872         Reaction *MutACK2Active42GDPRelease = new HeterodimerDissociationReaction(MutACK2Active42GDP,ACK2Active,MutCdc42GDP,kuACK2Active42GDP,"MutACK2Active42GDPRelease");
00873         reactions.push_back(MutACK2Active42GDPRelease);
00874         // 70
00875         Reaction *MutCoolCbl42Binding = new HeterodimerizationReaction(Cool1Cbl,MutCdc42GTP,MutCool1Cbl42GTP,kbCbl42,"MutCoolCbl42Binding");
00876         reactions.push_back(MutCoolCbl42Binding);
00877 
00878         Reaction *MutCoolCbl42Unbinding = new HeterodimerDissociationReaction(MutCool1Cbl42GTP,Cool1Cbl,MutCdc42GTP,kuCbl42,"MutCoolCbl42Unbinding");
00879         reactions.push_back(MutCoolCbl42Unbinding);
00880 
00881         Reaction *MutCoolCblActive42Binding = new HeterodimerizationReaction(Cool1CblActive,MutCdc42GTP,MutCool1CblActive42GTP,kbCblActive42,"MutCoolCblActive42Binding");
00882         reactions.push_back(MutCoolCblActive42Binding);
00883 
00884         Reaction *MutCoolCblActive42Unbinding = new HeterodimerDissociationReaction(MutCool1CblActive42GTP,Cool1CblActive,MutCdc42GTP,kuCblActive42,"MutCoolCblActive42Unbinding");
00885         reactions.push_back(MutCoolCblActive42Unbinding);
00886 
00887         Reaction *MutCoolCbl42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,MutCool1Cbl42GTP,MutCool1Cbl42GDP,kGAP,KmGAP,"MutCoolCbl42GAPing");
00888         reactions.push_back(MutCoolCbl42GAPing);
00889 
00890         Reaction *MutCoolCblActive42GAPing = new MichaelisMentenGProteinDeactivationReaction(Cdc42GAP,MutCool1CblActive42GTP,MutCool1CblActive42GDP,kGAP,KmGAP,"MutCoolCblActive42GAPing");
00891         reactions.push_back(MutCoolCblActive42GAPing);
00892 
00893         Reaction *MutCoolCbl42GDPRelease = new HeterodimerDissociationReaction(MutCool1Cbl42GDP,Cool1Cbl,MutCdc42GDP,kuCool1Cbl42GDP,"MutCoolCbl42GDPRelease");
00894         reactions.push_back(MutCoolCbl42GDPRelease);
00895 
00896         Reaction *MutCoolCblActive42GDPRelease = new HeterodimerDissociationReaction(MutCool1CblActive42GDP,Cool1CblActive,MutCdc42GDP,kuCool1CblActive42GDP,"MutCoolCblActive42GDPRelease");
00897         reactions.push_back(MutCoolCblActive42GDPRelease);
00898 
00899         Reaction *MutVesicleAssembly1 = new HeterodimerizationReaction(COPIEndoBoundEGFR,MutCdc42GTP,MutRecyclingVesicle1,kb42COPI,"MutVesicleAssembly1");
00900         reactions.push_back(MutVesicleAssembly1);
00901 
00902         Reaction *MutVesicleAssembly2 = new HeterodimerizationReaction(COPIEndoBoundEGFRCoolCblActive,MutCdc42GTP,MutRecyclingVesicle2,kb42COPI,"MutVesicleAssembly2");
00903         reactions.push_back(MutVesicleAssembly2);
00904         // 80
00905         Reaction *MutRecycling1 = new TransformationReaction(MutRecyclingVesicle1,MutRecycledVesicle1,kRec,"MutRecycling1");
00906         reactions.push_back(MutRecycling1);
00907 
00908         Reaction *MutRecycling2 = new TransformationReaction(MutRecyclingVesicle2,MutRecycledVesicle2,kRec,"MutRecycling2");
00909         reactions.push_back(MutRecycling2);
00910 
00911         Reaction *MutVesicleGAPing1 = new MichaelisMentenTransformationReaction(Cdc42GAP,MutRecycledVesicle1,MutVesicle1Cdc42GDP,kGAP,KmGAP,"MutVesicleGAPing1");
00912         reactions.push_back(MutVesicleGAPing1);
00913 
00914         Reaction *MutVesicleGAPing2 = new MichaelisMentenTransformationReaction(Cdc42GAP,MutRecycledVesicle2,MutVesicle2Cdc42GDP,kGAP,KmGAP,"MutVesicleGAPing2");
00915         reactions.push_back(MutVesicleGAPing2);
00916 
00917         Reaction *MutCdc42COPIUnbinding1 = new HeterodimerDissociationReaction(MutVesicle1Cdc42GDP,COPIPMBoundEGFR,MutCdc42GDP,ku42COPI,"MutCdc42COPIUnbinding1");
00918         reactions.push_back(MutCdc42COPIUnbinding1);
00919 
00920         Reaction *MutCdc42COPIUnbinding2 = new HeterodimerDissociationReaction(MutVesicle2Cdc42GDP,COPIPMBoundEGFRCoolCblActive,MutCdc42GDP,ku42COPI,"MutCdc42COPIUnbinding2");
00921         reactions.push_back(MutCdc42COPIUnbinding2);
00922         
00923         // activation by receptor
00924         Reaction *MutCdc42PMActivation1 = new MichaelisMentenGProteinActivationReaction(BoundPMEGFR,MutCdc42GDP,MutCdc42GTP,kEGFR42,KmEGFR42,"MutCdc42PMActivation1");
00925         reactions.push_back(MutCdc42PMActivation1);
00926 
00927         Reaction *MutCdc42PMActivation2 = new MichaelisMentenGProteinActivationReaction(BoundPMEGFRCoolCbl,MutCdc42GDP,MutCdc42GTP,kEGFR42,KmEGFR42,"MutCdc42PMActivation2");
00928         reactions.push_back(MutCdc42PMActivation2);
00929 
00930         Reaction *MutCdc42PMActivation3 = new MichaelisMentenGProteinActivationReaction(BoundPMEGFRCoolCblActive,MutCdc42GDP,MutCdc42GTP,kEGFR42,KmEGFR42,"MutCdc42PMActivation3");
00931         reactions.push_back(MutCdc42PMActivation3);
00932 
00933         Reaction *MutCdc42PMActivation4 = new MichaelisMentenGProteinActivationReaction(UbiBoundPMEGFRCoolCblActive,MutCdc42GDP,MutCdc42GTP,kEGFR42,KmEGFR42,"MutCdc42PMActivation4");
00934         reactions.push_back(MutCdc42PMActivation4);
00935         
00936         Reaction *MutCdc42GAPHydrolysis = new MichaelisMentenGProteinActivationReaction(Cdc42GAP,MutCdc42GTP,MutCdc42GDP,kGAP,KmGAP,"MutCdc42GAPHydrolysis");
00937         reactions.push_back(MutCdc42GAPHydrolysis);
00938 
00939         // 91
00940         // autoactivation (fast cycler)
00941         Reaction *AutoActivation = new TransformationReaction(MutCdc42GDP,MutCdc42GTP,kEGFR42,"AutoActivation");
00942         reactions.push_back(AutoActivation);
00943         
00944 
00945 }
00946 
00947 CEGFRTraffickingPredictionNetwork::~CEGFRTraffickingPredictionNetwork()
00948 {
00949 
00950 }