EGFRTraffickingEnsembleDirector.cpp Source File

00001 #include "EGFRTraffickingEnsembleDirector.h"
00002 
00003 CEGFRTraffickingEnsembleDirector::CEGFRTraffickingEnsembleDirector(int ensembleSize)
00004 :CEnsembleCombinationDirector(ensembleSize)
00005 {
00006         double maxSimTime = 241.0;
00007         int intTime = (int) (maxSimTime + 2);
00008         double stepSize = 0.0001;
00009         double frequency = 1.0;
00010         double moveTol = 1.0e-6;
00011         bool rateFlag = true;
00012         bool chemFlag = false;
00013         bool logsFlag = false;
00014         double timeWeight = 1.0;
00015         double rateWeight = 0.0;
00016         double chemWeight = 0.0;
00017         int nCells = 1;
00018 
00019         int oldcnt = 0;
00020         int newcnt = 0;
00021         /*
00022         // NIH-3T3 cells
00023         // expt. 0 - NIH-3T3 cells transfected with 1.0(5) X 10^5 receptors, treated 
00024         //              with EGF at 100 nM concentration
00025         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00026         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 100 nM, Helin 1991"));
00027         // put data files here
00028         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/SurfaceEGFREGFHelin100nM.dat");
00029         // mover and plotter
00030         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00031         // minimizable
00032         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00033         // parameters
00034         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00035         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorFixed(true);
00036         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorValue(100.0/100000.0);
00037         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00038         // attach observer
00039         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00040         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 100 nM, Helin 1991 : ODE");
00041         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00042         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00043         oldcnt++;
00044 
00045         // expt. 1 - NIH-3T3's transfected w/ wild-type EGFR; measurements made
00046         //              with 10-30% of receptors initially occupied; cells express 
00047         //              1.0(5) X 10^5 receptors
00048         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00049         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"20 Percent Initial Occupancy, Helin 1991"));
00050         // put data files here
00051         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/EGFHelinOccupied.dat");
00052         // mover and plotter
00053         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00054         // minimizable
00055         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00056         // parameters
00057         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00058         m_vpMinimizables[oldcnt]->GetConversionFactor(48)->SetFactorFixed(true);
00059         m_vpMinimizables[oldcnt]->GetConversionFactor(48)->SetFactorValue(100.0/20000.0);
00060         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00061         // attach observer
00062         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00063         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("20 Percent Initial Occupancy, Helin 1991 : ODE");
00064         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00065         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00066         oldcnt++;
00067 
00068         // expt. 2 - NIH-3T3's transfected with wt EGFR; 1 X 10^5 receptors, EGF of
00069         //              100 ng/ml
00070         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00071         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 100 ng/ml wt1, Carter 1998"));
00072         // put data files here
00073         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/SurfaceEGFREGFwt1Carter.dat");
00074         // mover and plotter
00075         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00076         // minimizable
00077         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00078         // parameters
00079         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00080         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorFixed(true);
00081         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorValue(100.0/100000.0);
00082         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00083         // attach observer
00084         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00085         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 100 ng/ml wt1, Carter 1998 : ODE");
00086         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00087         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00088         oldcnt++;
00089 
00090         // expt. 3 - NIH-3T3's transfected with wt EGFR; 2.75 X 10^5 receptors, EGF of
00091         //              100 ng/ml
00092         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00093         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 100 ng/ml wt2, Carter 1998"));
00094         // put data files here
00095         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/SurfaceEGFREGFwt2Carter.dat");
00096         // mover and plotter
00097         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00098         // minimizable
00099         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00100         // parameters
00101         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00102         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorFixed(true);
00103         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorValue(100.0/275000.0);
00104         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00105         // attach observer
00106         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00107         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 100 ng/ml wt2, Carter 1998 : ODE");
00108         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00109         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00110         oldcnt++;
00111         */
00112         
00113         // CHO cells
00114         // expt. 0 - CHO cells transfected with ? receptors, treated with EGF at 5 ng/ml
00115         //              concentration
00116         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00117         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 5 ng/ml, Bao 2000"));
00118         // put data files here
00119         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/InternalizedEGFREGFYarden.dat");
00120         // mover and plotter
00121         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00122         // minimizable
00123         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00124         // parameters
00125         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00126         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00127         // attach observer
00128         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00129         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 5 ng/ml, Bao 2000 : ODE");
00130         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00131         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00132         oldcnt++;
00133 
00134         // expt. 1 - CHO cells transfected with 8.2(7) X 10^4 receptors, treated 
00135         //              with EGF at 100 nM concentration
00136         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00137         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 100 nM, Davis 1992"));
00138         // put data files here
00139         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/SurfaceEGFREGFDavis100nM.dat");
00140         // mover and plotter
00141         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00142         // minimizable
00143         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00144         // parameters
00145         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00146         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorFixed(true);
00147         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorValue(100.0/82000.0);
00148         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00149         // attach observer
00150         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00151         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 100 nM, Davis 1992 : ODE");
00152         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00153         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00154         oldcnt++;
00155 
00156         // expt. 2 - CHO cells transfected with 8.2(7) X 10^4 receptors, treated 
00157         //              with EGF at 10 nM concentration
00158         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00159         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 10 nM, Davis 1992"));
00160         // put data files here
00161         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/SurfaceEGFREGFDavis10nM.dat");
00162         // mover and plotter
00163         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00164         // minimizable
00165         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00166         // parameters
00167         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00168         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorFixed(true);
00169         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorValue(100.0/82000.0);
00170         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00171         // attach observer
00172         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00173         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 10 nM, Davis 1992 : ODE");
00174         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00175         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00176         oldcnt++;
00177 
00178         // expt. 3 - CHO cells transfected with 8.2(7) X 10^4 receptors, treated 
00179         //              with EGF at 1 nM concentration
00180         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00181         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 1 nM, Davis 1992"));
00182         // put data files here
00183         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/SurfaceEGFREGFDavis1nM.dat");
00184         // mover and plotter
00185         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00186         // minimizable
00187         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00188         // parameters
00189         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00190         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorFixed(true);
00191         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorValue(100.0/82000.0);
00192         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00193         // attach observer
00194         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00195         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 1 nM, Davis 1992 : ODE");
00196         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00197         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00198         oldcnt++;
00199         
00200         // expt. 4 - CHO cells transfected with ? EGFR and treated with EGF at 
00201         //              100 ng/ml concentration
00202         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00203         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 100 ng/ml, Levkowitz 1999"));
00204         // put data files here
00205         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/SurfaceEGFREGFLevkowitz.dat");
00206         // mover and plotter
00207         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00208         // minimizable
00209         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00210         // parameters
00211         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00212         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorFixed(true);
00213         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorValue(100.0/80000.0);
00214         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00215         // attach observer
00216         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00217         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 100 ng/ml, Levkowitz 1999 : ODE");
00218         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00219         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00220         oldcnt++;
00221         
00222         // expt. 5 - CHO cells transfected with ? EGFR Y1045F and treated with EGF at
00223         //              100 ng/ml concentration
00224         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00225         m_vpExperiments.push_back(new Experiment(m_vpNetworks[oldcnt],"EGF at 100 ng/ml, Y1045F EGFR, Levkowitz 1999"));
00226         // put data files here
00227         m_vpExperiments[oldcnt]->AddDataFileToList("../DataFiles/TimeSeries/SurfaceEGFREGFY1045FLevkowitz.dat");
00228         // mover and plotter
00229         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00230         // minimizable
00231         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00232         // parameters
00233         m_vpMinimizables[oldcnt]->Initialize(m_vpExperiments[oldcnt],m_vpMovers[oldcnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00234         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorFixed(true);
00235         m_vpMinimizables[oldcnt]->GetConversionFactor(47)->SetFactorValue(100.0/80000.0);
00236         m_vpMinimizables[oldcnt]->SetRateConstantsWeight(0.0);
00237         // attach observer
00238         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00239         m_vpEnsembleDataPlotters[oldcnt]->SetTitle("EGF at 100 ng/ml, Y1045 EGFR, Levkowitz 1999 : ODE");
00240         m_vpEnsembleDataPlotters[oldcnt]->FixMinimizable(oldcnt);
00241         this->Attach(m_vpEnsembleDataPlotters[oldcnt]);
00242         oldcnt++;
00243 
00244         // Runnables, common to CHO and 3T3
00245         // EGF at 100 ng/ml, EGFR overexpressed
00246         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00247         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00248         int nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00249         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00250         m_vpRunnables.push_back(new CRunnable());
00251         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00252         // attach the observer
00253         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00254         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR overexpressed, EGF at 100 ng/ml : ODE");
00255         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00256         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00257         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00258         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00259         oldcnt++;
00260         newcnt++;
00261         
00262         // EGF at 100 ng/ml, EGFR overexpressed, Cdc42 wt overexpressed
00263         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00264         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00265         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00266         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00267         m_vpRunnables.push_back(new CRunnable());
00268         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00269         // attach the observer
00270         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00271         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + wt Cdc42, EGF at 100 ng/ml : ODE");
00272         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00273         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00274         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00275         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00276         oldcnt++;
00277         newcnt++;
00278         
00279         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(Q61L)
00280         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00281         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00282         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00283         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00284         m_vpRunnables.push_back(new CRunnable());
00285         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00286         // attach the observer
00287         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00288         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(Q61L), EGF at 100 ng/ml : ODE");
00289         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00290         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00291         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00292         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00293         oldcnt++;
00294         newcnt++;
00295         
00296         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(T17N)
00297         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00298         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00299         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00300         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00301         m_vpRunnables.push_back(new CRunnable());
00302         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00303         // attach the observer
00304         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00305         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(T17N), EGF at 100 ng/ml : ODE");
00306         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00307         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00308         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00309         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00310         oldcnt++;
00311         newcnt++;
00312         
00313         
00314         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42dL8
00315         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00316         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00317         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00318         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00319         m_vpRunnables.push_back(new CRunnable());
00320         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00321         // attach the observer
00322         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00323         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(dL8), EGF at 100 ng/ml : ODE");
00324         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00325         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00326         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00327         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00328         oldcnt++;
00329         newcnt++;
00330 
00331         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42Lss
00332         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00333         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00334         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00335         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00336         m_vpRunnables.push_back(new CRunnable());
00337         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00338         // attach the observer
00339         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00340         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(Lss), EGF at 100 ng/ml : ODE");
00341         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00342         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00343         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00344         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00345         oldcnt++;
00346         newcnt++;
00347 
00348         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(Q61L/dL8)
00349         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00350         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00351         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00352         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00353         m_vpRunnables.push_back(new CRunnable());
00354         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00355         // attach the observer
00356         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00357         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(Q61L/dL8), EGF at 100 ng/ml : ODE");
00358         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00359         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00360         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00361         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00362         oldcnt++;
00363         newcnt++;
00364 
00365         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(Q61L/Lss)
00366         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00367         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00368         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00369         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00370         m_vpRunnables.push_back(new CRunnable());
00371         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00372         // attach the observer
00373         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00374         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(Q61L/Lss), EGF at 100 ng/ml : ODE");
00375         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00376         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00377         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00378         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00379         oldcnt++;
00380         newcnt++;
00381                 
00382         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(F28L)
00383         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00384         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00385         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00386         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00387         m_vpRunnables.push_back(new CRunnable());
00388         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00389         // attach the observer
00390         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00391         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(F28L), EGF at 100 ng/ml : ODE");
00392         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00393         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00394         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00395         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00396         oldcnt++;
00397         newcnt++;
00398         
00399         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(F28L/dL8)
00400         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00401         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00402         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00403         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00404         m_vpRunnables.push_back(new CRunnable());
00405         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00406         // attach the observer
00407         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00408         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(F28L/dL8), EGF at 100 ng/ml : ODE");
00409         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00410         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00411         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00412         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00413         oldcnt++;
00414         newcnt++;
00415         
00416         // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(F28L/Lss)
00417         m_vpNetworks.push_back(new CEGFRTraffickingNetwork());
00418         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00419         nChemicals = m_vpNetworks[oldcnt]->GetNumberOfChemicals();
00420         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00421         m_vpRunnables.push_back(new CRunnable());
00422         m_vpRunnables[newcnt]->SetComponents(m_vpNetworks[oldcnt],m_vpMovers[oldcnt],m_vpCellObservers[newcnt]);
00423         // create an observer for the runnable
00424         m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00425         m_vpEnsembleRunPlotters[newcnt]->SetTitle("EGFR + Cdc42(F28L/Lss), EGF at 100 ng/ml : ODE");
00426         m_vpEnsembleRunPlotters[newcnt]->FixRunnable(newcnt);
00427         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(58);
00428         m_vpEnsembleRunPlotters[newcnt]->AddChemicalToList(59);
00429         this->Attach(m_vpEnsembleRunPlotters[newcnt]);
00430         
00431         
00432         // allocate space to accumulate statistics
00433         SumAllocate();
00434 
00435         // Define runs
00436         DefineRuns();
00437 
00438         // Define experiments
00439         DefineExperiments();
00440 
00441         // Load in the ensemble info
00442         LoadEnsembleInfo("ensemble.par");
00443 }
00444 
00445 CEGFRTraffickingEnsembleDirector::~CEGFRTraffickingEnsembleDirector(void)
00446 {
00447         for(int i = 0; i < m_vpEnsembleRunPlotters.size(); i++)
00448         {
00449                 this->Detach(m_vpEnsembleRunPlotters[i]);
00450         }
00451         for(i = 0; i < m_vpEnsembleDataPlotters.size(); i++)
00452         {
00453                 this->Detach(m_vpEnsembleDataPlotters[i]);
00454         }
00455 }
00456 
00457 
00458 void CEGFRTraffickingEnsembleDirector::DefineRuns()
00459 {
00460         int cnt = 0;
00461         // 100,000 receptors, EGF at 100 ng/ml
00462         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(64);
00463         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00464         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00465         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00466         cnt++;
00467 
00468         
00469         // 100,000 receptors, EGF at 100 ng/ml, Cdc42wt 2-fold overexpressed
00470         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(64);
00471         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00472         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00473         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(2*600000);
00474         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00475         cnt++;
00476         
00477         // 100,000 receptors, EGF at 100 ng/ml, Cdc42(Q61L)
00478         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(64);
00479         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(59);
00480         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(58);
00481         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(25);
00482         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(24);
00483         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(17);
00484         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(16);
00485         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(6);
00486         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00487         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00488         // start with all mutant 42 active
00489         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0);
00490         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000);
00491         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00492         cnt++;
00493 
00494         // 100,000 receptors, EGF at 100 ng/ml, Cdc42(T17N)
00495         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(64);
00496         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(5);
00497         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(4);
00498         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(3);
00499         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(2);
00500         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00501         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00502         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(2*600000);
00503         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00504         cnt++;
00505 
00506         // 100,000 receptors, EGF at 100 ng/ml, Cdc42dL8
00507         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(64);
00508         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(22);
00509         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(20);
00510         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00511         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00512         // start with all 42 active
00513         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(2*600000);
00514         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00515         cnt++;
00516 
00517         // 100,000 receptors, EGF at 100 ng/ml, Cdc42Lss
00518         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(64);
00519         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(55);
00520         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(54);
00521         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00522         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00523         // start with all 42 active
00524         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(2*600000);
00525         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00526         cnt++;
00527 
00528         // 100,000 receptors, EGF at 100 ng/ml, Cdc42(Q61L/dL8)
00529         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(64);
00530         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(59);
00531         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(58);
00532         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(25);
00533         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(24);
00534         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(22);
00535         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(20);
00536         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(17);
00537         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(16);
00538         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(6);
00539         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00540         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00541         // start with all 42 active
00542         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0);
00543         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000);
00544         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00545         cnt++;
00546 
00547         // 100,000 receptors, EGF at 100 ng/ml, Cdc42(Q61L/Lss)
00548         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(64);
00549         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(59);
00550         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(58);
00551         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(55);
00552         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(54);
00553         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(25);
00554         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(24);
00555         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(17);
00556         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(16);
00557         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(6);
00558         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00559         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00560         // start with all 42 active
00561         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0);
00562         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000);
00563         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00564         cnt++;
00565 
00566         // 100,000 receptors, EGF at 100 ng/ml, Cdc42(F28L)
00567         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00568         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00569         // start with all 42 active
00570         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0);
00571         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000);
00572         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00573         cnt++;
00574 
00575         // 100,000 receptors, EGF at 100 ng/ml, Cdc42(F28L/dL8)
00576         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(22);
00577         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(20);
00578         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00579         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00580         // start with all 42 active
00581         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0);
00582         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000);
00583         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00584         cnt++;
00585 
00586         // 100,000 receptors, EGF at 100 ng/ml, Cdc42(F28L/Lss)
00587         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(55);
00588         m_vpRunnables[cnt]->GetReactionNetwork()->RemoveReaction(54);
00589         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00590         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00591         // start with all 42 active
00592         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0);
00593         m_vpRunnables[cnt]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000);
00594         m_vpRunnables[cnt]->GetReactionNetwork()->ChemicalReset();
00595         cnt++;
00596 
00597 
00598         return;
00599 }
00600 
00601 void CEGFRTraffickingEnsembleDirector::DefineExperiments()
00602 {       
00603         /*
00604         // 3T3 cells
00605         // 100,000 receptors, EGF at 100 nM
00606         m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00607         m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(7.2e+007);
00608         m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00609         m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00610 
00611         // No EGF, 20% of receptors on surface initially occupied
00612         m_vpMinimizables[1]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00613         m_vpMinimizables[1]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(80000.0);
00614         m_vpMinimizables[1]->GetExperiment()->GetReactionNetwork()->GetChemical(3)->SetInitialAmount(20000.0);
00615         m_vpMinimizables[1]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00616 
00617         // 100,000 receptors assumed, EGF at 100 ng/ml
00618         m_vpMinimizables[2]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00619         m_vpMinimizables[2]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00620         m_vpMinimizables[2]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000);
00621         m_vpMinimizables[2]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00622 
00623         // 275,000 receptors assumed, EGF at 100 ng/ml
00624         m_vpMinimizables[3]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00625         m_vpMinimizables[3]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00626         m_vpMinimizables[3]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(275000);
00627         m_vpMinimizables[3]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00628         */
00629         // CHO cells
00630         // 80,000 receptors assumed, EGF at 5 ng/ml
00631         m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00632         m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(600000.0);
00633         m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(80000.0);
00634         m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00635 
00636         // 82,000 receptors, EGF at 100 nM
00637         m_vpMinimizables[1]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00638         m_vpMinimizables[1]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(7.2e+007);
00639         m_vpMinimizables[1]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(82000);
00640         m_vpMinimizables[1]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00641 
00642         // 82,000 receptors, EGF at 10 nM
00643         m_vpMinimizables[2]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00644         m_vpMinimizables[2]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(7.2e+006);
00645         m_vpMinimizables[2]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(82000);
00646         m_vpMinimizables[2]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00647 
00648         // 82,000 receptors, EGF at 1 nM
00649         m_vpMinimizables[3]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64); 
00650         m_vpMinimizables[3]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(7.2e+005);
00651         m_vpMinimizables[3]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(82000);
00652         m_vpMinimizables[3]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00653 
00654         // 80,000 receptors assumed, EGF at 100 ng/ml
00655         m_vpMinimizables[4]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00656         m_vpMinimizables[4]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00657         m_vpMinimizables[4]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(80000);
00658         m_vpMinimizables[4]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00659         
00660         // 80,000 receptors assumed, EGF at 100 ng/ml, Y1045F can't bind to Cbl
00661         m_vpMinimizables[5]->GetExperiment()->GetReactionNetwork()->RemoveReaction(64);
00662         m_vpMinimizables[5]->GetExperiment()->GetReactionNetwork()->RemoveReaction(42);
00663         m_vpMinimizables[5]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
00664         m_vpMinimizables[5]->GetExperiment()->GetReactionNetwork()->RemoveReaction(40); 
00665         m_vpMinimizables[5]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007);
00666         m_vpMinimizables[5]->GetExperiment()->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(80000);
00667         m_vpMinimizables[5]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
00668 }