QuorumSensingEnsembleDirector.cpp Source File

00001 // QuorumSensingEnsembleDirector.cpp: implementation of the CQuorumSensingEnsembleDirector class.
00002 //
00004 
00005 #include "QuorumSensingEnsembleDirector.h"
00006 
00008 // Construction/Destruction
00010 
00011 CQuorumSensingEnsembleDirector::CQuorumSensingEnsembleDirector(int ensembleSize)
00012         :CEnsembleCombinationDirector(ensembleSize)
00013 {
00014         // counter for experiment number
00015         int expt = -1;
00016         int connid = -1;
00017         int obsrvr = -1;
00018 
00019         bool plotornot = true;
00020         int nChemicals;
00021 
00022         // create networks,experiments,observers,movers,minimizables
00023         double maxSimTime = 720.0;
00024         int intTime = (int) (maxSimTime + 2);
00025         double stepSize = 0.0001;
00026         double frequency = 1.0;
00027         int nCells = 1;
00028         double moveTol = 1.0e-06;
00029 
00030         // flags for all minimizables
00031         bool rateFlag = true;
00032         bool chemFlag = false;
00033         bool logsFlag = false;
00034         double timeWeight = 1.0;
00035         double rateWeight = 0.0;
00036         double chemWeight = 0.0;
00037 
00038 /*      // expt. - Steady State 1
00039         expt++;
00040         rateFlag = false;
00041         chemFlag = true;
00042         _networkList.push_back(new CQuorumSensingNetwork());
00043         _experimentList.push_back(new Experiment(_networkList[expt],"SteadyState1"));
00044         // put data files here
00045         _experimentList[expt]->AddDataFileToList("../DataFiles/SteadyState1.dat");
00046         // mover
00047         _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00048         // minimizable
00049         _minimizableList.push_back(new SingleNetworkMinimizable());
00050         // parameters
00051         _minimizableList[expt]->Initialize(_experimentList[expt],_moverList[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00052         //_minimizableList[0]->GetConversionFactor(7)->SetFactorFixed(true);
00053         //_minimizableList[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00054         _minimizableList[expt]->SetRateConstantsWeight(0.0);
00055 
00056         // expt.- Steady State 2
00057         expt++;
00058         rateFlag = false;
00059         chemFlag = true;
00060         _networkList.push_back(new CQuorumSensingNetwork());
00061         _experimentList.push_back(new Experiment(_networkList[expt],"SteadyState2"));
00062         // put data files here
00063         _experimentList[expt]->AddDataFileToList("../DataFiles/SteadyState2.dat");
00064         // mover
00065         _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00066         // minimizable
00067         _minimizableList.push_back(new SingleNetworkMinimizable());
00068         // parameters
00069         _minimizableList[expt]->Initialize(_experimentList[expt],_moverList[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00070         //_minimizableList[0]->GetConversionFactor(7)->SetFactorFixed(true);
00071         //_minimizableList[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00072         _minimizableList[expt]->SetRateConstantsWeight(0.0);
00073 */
00074         // expt. 0 - Addition of 100 nM OOHL, traR present at time 0
00075         expt++;
00076         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00077         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt],"OOHL Present, Zhu 1999"));
00078         // put data files here
00079         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu99_f7c_2.dat");
00080         m_vpExperiments[expt]->AddForcingFileToList("../DataFiles/zhu99_f7c_2forcing.dat");
00081         // mover
00082         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00083         // minimizable
00084         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00085         // parameters
00086         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00087         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00088         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00089         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00090 //      connid++;
00091 //      _largeconnectedList.push_back(new std::vector<int>);
00092 //      _largeconnectedList[connid]->push_back(expt);
00093 
00094 /*      // expt. 1 - No OOHL, traR present at time 0
00095         expt++;
00096         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00097         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt],"No OOHL, Zhu 1999"));
00098         // put data files here
00099         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu99_f7c_1.dat");
00100         m_vpExperiments[expt]->AddForcingFileToList("../DataFiles/zhu99_f7c_1forcing.dat");
00101         // mover and plotter
00102         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00103         // minimizable
00104         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00105         // parameters
00106         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00107         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00108         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00109         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00110         connid++;
00111         _largeconnectedList.push_back(new std::vector<int>);
00112         _largeconnectedList[connid]->push_back(expt);
00113 
00114         // expt. 2 - No octopine, no OOHL, traA present at time 0
00115         expt++;
00116         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00117         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt],"No OOHL or octopine, Fuqua 1994"));
00118         // put data files here
00119         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_1.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[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00126         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00127         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00128         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00129         connid++;
00130         _largeconnectedList.push_back(new std::vector<int>);
00131         _largeconnectedList[connid]->push_back(expt);
00132 
00133         // expt. 3 - octopine but no OOHL, traA present at time 0
00134         expt++;
00135         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00136         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "octopine but no OOHL, Fuqua 1994"));
00137         // put data files here
00138         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_2.dat");
00139         // mover and plotter
00140         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00141         // minimizable
00142         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00143         // parameters
00144         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00145         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00146         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00147         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00148         _largeconnectedList[connid]->push_back(expt);
00149 
00150         // expt. 4 - OOHL but no octopine, traA present at time 0
00151         expt++;
00152         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00153         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "OOHL but no octopine, Fuqua 1994"));
00154         // put data files here
00155         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_3.dat");
00156         // mover and plotter
00157         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00158         // minimizable
00159         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00160         // parameters
00161         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00162         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00163         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00164         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00165         _largeconnectedList[connid]->push_back(expt);
00166 
00167         // expt. 5 - OOHL and octopine, traA present at time 0
00168         expt++;
00169         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00170         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "OOHL and octopine, Fuqua 1994"));
00171         // put data files here
00172         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_4.dat");
00173         // mover and plotter
00174         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00175         // minimizable
00176         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00177         // parameters
00178         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00179         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00180         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00181         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00182         _largeconnectedList[connid]->push_back(expt);
00183 
00184         // expt. 2b - traR null mutant No octopine, no OOHL, traA present at time 0
00185         expt++;
00186         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00187         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt],"traR null mutant No OOHL or octopine, Fuqua 1994"));
00188         // put data files here
00189         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_5.dat");
00190         // mover and plotter
00191         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00192         // minimizable
00193         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00194         // parameters
00195         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00196         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00197         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00198         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00199         connid++;
00200         _largeconnectedList.push_back(new std::vector<int>);
00201         _largeconnectedList[connid]->push_back(expt);
00202 
00203         // expt. 3b - traR null mutant octopine but no OOHL, traA present at time 0
00204         expt++;
00205         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00206         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "traR null mutant octopine but no OOHL, Fuqua 1994"));
00207         // put data files here
00208         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_6.dat");
00209         // mover and plotter
00210         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00211         // minimizable
00212         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00213         // parameters
00214         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00215         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00216         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00217         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00218         _largeconnectedList[connid]->push_back(expt);
00219 
00220         // expt. 4b - traR null mutant OOHL but no octopine, traA present at time 0
00221         expt++;
00222         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00223         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "traR null mutant OOHL but no octopine, Fuqua 1994"));
00224         // put data files here
00225         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_7.dat");
00226         // mover and plotter
00227         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00228         // minimizable
00229         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00230         // parameters
00231         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00232         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00233         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00234         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00235         _largeconnectedList[connid]->push_back(expt);
00236 
00237         // expt. 5b - traR null mutant OOHL and octopine, traA present at time 0
00238         expt++;
00239         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00240         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "traR null mutant OOHL and octopine, Fuqua 1994"));
00241         // put data files here
00242         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_8.dat");
00243         // mover and plotter
00244         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00245         // minimizable
00246         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00247         // parameters
00248         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00249         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00250         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00251         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00252         _largeconnectedList[connid]->push_back(expt);
00253 
00254         // expt. 2c - occR null mutant No octopine, no OOHL, traA present at time 0
00255         expt++;
00256         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00257         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt],"occR null mutant No OOHL or octopine, Fuqua 1994"));
00258         // put data files here
00259         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_9.dat");
00260         // mover and plotter
00261         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00262         // minimizable
00263         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00264         // parameters
00265         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00266         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00267         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00268         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00269         connid++;
00270         _largeconnectedList.push_back(new std::vector<int>);
00271         _largeconnectedList[connid]->push_back(expt);
00272 
00273         // expt. 3c - occR null mutant octopine but no OOHL, traA present at time 0
00274         expt++;
00275         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00276         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "occR null mutant octopine but no OOHL, Fuqua 1994"));
00277         // put data files here
00278         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_10.dat");
00279         // mover and plotter
00280         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00281         // minimizable
00282         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00283         // parameters
00284         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00285         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00286         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00287         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00288         _largeconnectedList[connid]->push_back(expt);
00289 
00290         // expt. 4c - occR null mutant OOHL but no octopine, traA present at time 0
00291         expt++;
00292         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00293         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "occR null mutant OOHL but no octopine, Fuqua 1994"));
00294         // put data files here
00295         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_11.dat");
00296         // mover and plotter
00297         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00298         // minimizable
00299         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00300         // parameters
00301         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00302         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00303         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00304         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00305         _largeconnectedList[connid]->push_back(expt);
00306 
00307         // expt. 5c - occR null mutant OOHL and octopine, traA present at time 0
00308         expt++;
00309         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00310         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "occR null mutant OOHL and octopine, Fuqua 1994"));
00311         // put data files here
00312         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t4_12.dat");
00313         // mover and plotter
00314         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00315         // minimizable
00316         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00317         // parameters
00318         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00319         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00320         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00321         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00322         _largeconnectedList[connid]->push_back(expt);
00323 
00324         // expt. 6 - no octopine, traR-lacZ fusion
00325         expt++;
00326         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00327         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "no octopine, traR-lacZ fusion, Fuqua 1994"));
00328         // put data files here
00329         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t3_1.dat");
00330         // mover and plotter
00331         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00332         // minimizable
00333         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00334         // parameters
00335         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00336         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00337         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00338         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00339         connid++;
00340         _largeconnectedList.push_back(new std::vector<int>);
00341         _largeconnectedList[connid]->push_back(expt);
00342 
00343         // expt. 7 - 400 ug/ml octopine, traR-lacZ fusion
00344         expt++;
00345         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00346         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "Octopine, traR-lacZ fusion, Fuqua 1994"));
00347         // put data files here
00348         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t3_2.dat");
00349         // mover and plotter
00350         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00351         // minimizable
00352         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00353         // parameters
00354         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00355         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00356         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00357         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00358         _largeconnectedList[connid]->push_back(expt);
00359 
00360         // expt. 8 - no octopine, traR-lacZ fusion, no occR
00361         expt++;
00362         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00363         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "no octopine, no occR, traR-lacZ fusion, Fuqua 1994"));
00364         // put data files here
00365         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t3_3.dat");
00366         // mover and plotter
00367         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00368         // minimizable
00369         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00370         // parameters
00371         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00372         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00373         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00374         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00375         connid++;
00376         _largeconnectedList.push_back(new std::vector<int>);
00377         _largeconnectedList[connid]->push_back(expt);
00378 
00379         // expt. 9 - 400ug/ml octopine, traR-lacZ fusion, no occR
00380         expt++;
00381         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00382         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "400 ug/ml octopine, no occR, traR-lacZ fusion, Fuqua 1994"));
00383         // put data files here
00384         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t3_4.dat");
00385         // mover and plotter
00386         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00387         // minimizable
00388         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00389         // parameters
00390         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00391         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00392         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00393         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00394         _largeconnectedList[connid]->push_back(expt);
00395 */
00396 /* Not using expts 10,11 because I'm not certain of the implementation of 
00397    multiple gene copies with only fused to a reporter -JJW 1/7/03
00398         // expt. 10 - no octopine, traR-lacZ fusion, traR multicopies
00399         expt++;
00400         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00401         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "no octopine, traR multipcopies, traR-lacZ fusion, Fuqua 1994"));
00402         // put data files here
00403         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t3_5.dat");
00404         // mover and plotter
00405         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00406         // minimizable
00407         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00408         // parameters
00409         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00410         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00411         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00412         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00413         connid++;
00414         _largeconnectedList.push_back(new std::vector<int>);
00415         _largeconnectedList[connid]->push_back(expt);
00416 
00417         // expt. 11 - 400ug/ml octopine, traR-lacZ fusion, traR multipcopies
00418         expt++;
00419         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00420         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "400 ug/ml octopine, traR multicopies, traR-lacZ fusion, Fuqua 1994"));
00421         // put data files here
00422         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua94_t3_6.dat");
00423         // mover and plotter
00424         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00425         // minimizable
00426         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00427         // parameters
00428         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00429         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorFixed(true);
00430         //m_vpMinimizables[0]->GetConversionFactor(7)->SetFactorValue(100.0/100000.0);
00431         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00432         _largeconnectedList[connid]->push_back(expt);
00433 */
00434 /*      // expt. 12 - 0.1 nM OOHL, traI-lacZ fusion
00435         expt++;
00436         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00437         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "0.1 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00438         // put data files here
00439         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_1.dat");
00440         // mover and plotter
00441         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00442         // minimizable
00443         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00444         // parameters
00445         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00446 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00447 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00448         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00449         connid++;
00450         _largeconnectedList.push_back(new std::vector<int>);
00451         _largeconnectedList[connid]->push_back(expt);
00452         
00453         // expt. 13 - 0.2 nM OOHL, traI-lacZ fusion
00454         expt++;
00455         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00456         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "0.2 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00457         // put data files here
00458         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_2.dat");
00459         // mover and plotter
00460         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00461         // minimizable
00462         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00463         // parameters
00464         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00465 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00466 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00467         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00468         _largeconnectedList[connid]->push_back(expt);
00469         
00470         // expt. 14 - 1.0 nM OOHL, traI-lacZ fusion
00471         expt++;
00472         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00473         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "1.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00474         // put data files here
00475         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_3.dat");
00476         // mover and plotter
00477         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00478         // minimizable
00479         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00480         // parameters
00481         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00482 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00483 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00484         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00485         _largeconnectedList[connid]->push_back(expt);
00486 
00487         // expt. 15 - 2.0 nM OOHL, traI-lacZ fusion
00488         expt++;
00489         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00490         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "2.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00491         // put data files here
00492         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_4.dat");
00493         // mover and plotter
00494         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00495         // minimizable
00496         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00497         // parameters
00498         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00499 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00500 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00501         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00502         _largeconnectedList[connid]->push_back(expt);
00503 
00504         // expt. 16 - 10.0 nM OOHL, traI-lacZ fusion
00505         expt++;
00506         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00507         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "10.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00508         // put data files here
00509         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_5.dat");
00510         // mover and plotter
00511         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00512         // minimizable
00513         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00514         // parameters
00515         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00516 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00517 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00518         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00519         _largeconnectedList[connid]->push_back(expt);
00520 
00521         // expt. 17 - 20.0 nM OOHL, traI-lacZ fusion
00522         expt++;
00523         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00524         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "20.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00525         // put data files here
00526         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_6.dat");
00527         // mover and plotter
00528         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00529         // minimizable
00530         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00531         // parameters
00532         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00533 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00534 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00535         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00536         _largeconnectedList[connid]->push_back(expt);
00537 
00538         // expt. 18 - 100.0 nM OOHL, traI-lacZ fusion
00539         expt++;
00540         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00541         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "100.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00542         // put data files here
00543         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_7.dat");
00544         // mover and plotter
00545         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00546         // minimizable
00547         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00548         // parameters
00549         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00550 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00551 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00552         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00553         _largeconnectedList[connid]->push_back(expt);
00554 
00555         // expt. 19 - 200.0 nM OOHL, traI-lacZ fusion
00556         expt++;
00557         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00558         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "200.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00559         // put data files here
00560         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_8.dat");
00561         // mover and plotter
00562         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00563         // minimizable
00564         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00565         // parameters
00566         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00567 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00568 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00569         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00570         _largeconnectedList[connid]->push_back(expt);
00571 
00572         // expt. 20 - 1000.0 nM OOHL, traI-lacZ fusion
00573         expt++;
00574         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00575         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "1000.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00576         // put data files here
00577         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_9.dat");
00578         // mover and plotter
00579         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00580         // minimizable
00581         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00582         // parameters
00583         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00584 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00585 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00586         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00587         _largeconnectedList[connid]->push_back(expt);
00588 
00589         // expt. 21 - 2000.0 nM OOHL, traI-lacZ fusion
00590         expt++;
00591         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00592         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "2000.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00593         // put data files here
00594         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_10.dat");
00595         // mover and plotter
00596         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00597         // minimizable
00598         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00599         // parameters
00600         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00601 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00602 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00603         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00604         _largeconnectedList[connid]->push_back(expt);
00605 
00606         // expt. 22 - 10000.0 nM OOHL, traI-lacZ fusion
00607         expt++;
00608         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00609         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "10000.0 nM OOHL, traI-lacZ fusion, Zhu 1998"));
00610         // put data files here
00611         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/zhu98_f2_11.dat");
00612         // mover and plotter
00613         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00614         // minimizable
00615         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00616         // parameters
00617         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00618 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorFixed(true);
00619 //      m_vpMinimizables[expt]->GetConversionFactor(32)->SetFactorValue(1.0);
00620         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00621         _largeconnectedList[connid]->push_back(expt);
00622 */
00623         // runnable 0 - no OOHL, no octopine R10 (pCF372)
00624         expt++;
00625         obsrvr++;
00626         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00627         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00628         nChemicals = m_vpNetworks[expt]->GetNumberOfChemicals();
00629         m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
00630         m_vpRunnables.push_back(new CRunnable());
00631         m_vpRunnables[obsrvr]->SetComponents(m_vpNetworks[expt],m_vpMovers[expt],m_vpCellObservers[obsrvr]);
00632         //m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00633         //m_vpEnsembleRunPlotters[1]->SetTitle("MAPK Cascade : 50 ng/ml NGF + DN Ras : ODE");
00634         //m_vpEnsembleRunPlotters[1]->FixRunnable(1);
00635         //m_vpEnsembleRunPlotters[1]->AddChemicalToList(20);
00636         //this->Attach(m_vpEnsembleRunPlotters[1]);
00637 
00638 
00639 
00640 /*      // expt. 23 - no octopine, WT, Conjugal Transfer Efficiency
00641         expt++;
00642         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00643         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "No octopine, WT, Conjugal transfer efficiency, Fuqua 1995"));
00644         // put data files here
00645         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua95_t2_1.dat");
00646         // mover and plotter
00647         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00648         // minimizable
00649         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00650         // parameters
00651         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00652         m_vpMinimizables[expt]->GetConversionFactor(38)->SetFactorFixed(true);
00653         m_vpMinimizables[expt]->GetConversionFactor(38)->SetFactorValue(1.0);
00654         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00655 
00656         // expt. 24 - 2 mg/ml octopine, WT, Conjugal Transfer Efficiency
00657         expt++;
00658         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00659         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "2 mg/ml octopine, WT, Conjugal transfer efficiency, Fuqua 1995"));
00660         // put data files here
00661         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua95_t2_2.dat");
00662         // mover and plotter
00663         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00664         // minimizable
00665         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00666         // parameters
00667         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00668         m_vpMinimizables[expt]->GetConversionFactor(38)->SetFactorFixed(true);
00669         m_vpMinimizables[expt]->GetConversionFactor(38)->SetFactorValue(1.0);
00670         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00671 
00672         // expt. 25 - no octopine, traM null mutant, Conjugal Transfer Efficiency
00673         expt++;
00674         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00675         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "No octopine, traM null mutant, Conjugal transfer efficiency, Fuqua 1995"));
00676         // put data files here
00677         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua95_t2_3.dat");
00678         // mover and plotter
00679         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00680         // minimizable
00681         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00682         // parameters
00683         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00684         m_vpMinimizables[expt]->GetConversionFactor(38)->SetFactorFixed(true);
00685         m_vpMinimizables[expt]->GetConversionFactor(38)->SetFactorValue(1.0);
00686         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00687 
00688     // expt. 26 - 2 mg/ml octopine, traM null mutant, Conjugal Transfer Efficiency
00689         expt++;
00690         m_vpNetworks.push_back(new CQuorumSensingNetwork());
00691         m_vpExperiments.push_back(new Experiment(m_vpNetworks[expt], "2 mg/ml octopine, traM null mutant, Conjugal transfer efficiency, Fuqua 1995"));
00692         // put data files here
00693         m_vpExperiments[expt]->AddDataFileToList("../DataFiles/fuqua95_t2_4.dat");
00694         // mover and plotter
00695         m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
00696         // minimizable
00697         m_vpMinimizables.push_back(new SingleNetworkMinimizable());
00698         // parameters
00699         m_vpMinimizables[expt]->Initialize(m_vpExperiments[expt],m_vpMovers[expt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
00700         m_vpMinimizables[expt]->GetConversionFactor(38)->SetFactorFixed(true);
00701         m_vpMinimizables[expt]->GetConversionFactor(38)->SetFactorValue(1.0);
00702         m_vpMinimizables[expt]->SetRateConstantsWeight(0.0);
00703 */
00704 
00705         if (plotornot == 1) {
00706                 cout << "setting up plots\n";
00707 //Plot Commands
00708                 expt = -1;
00709 
00710 /*      //expt steadystate1
00711         expt++;
00712         _plotterList.push_back(new GnuPlotterTimeSeriesObserver());
00713         _plotterList[expt]->SetTitle("SteadyState1");
00714         m_vpMinimizables[expt]->Attach(_plotterList[expt]);
00715 
00716         //expt steadystate2
00717         expt++;
00718         _plotterList.push_back(new GnuPlotterTimeSeriesObserver());
00719         _plotterList[expt]->SetTitle("SteadyState2");
00720         m_vpMinimizables[expt]->Attach(_plotterList[expt]);
00721 */
00722                 //expt 0
00723                 expt++;
00724                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00725                 m_vpEnsembleDataPlotters[expt]->SetTitle("OOHL Present:Zhu 1999:ODE");
00726                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00727                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00728                 
00729 /*              //expt 1
00730                 expt++;
00731                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00732                 m_vpEnsembleDataPlotters[expt]->SetTitle("No OOHL:Zhu 1999:ODE");
00733                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00734                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00735 
00736                 //expt 2
00737                 expt++;
00738                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00739                 m_vpEnsembleDataPlotters[expt]->SetTitle("No OOHL or octopine:Fuqua 1994:ODE");
00740                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00741                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00742         
00743                 //expt 3
00744                 expt++;
00745                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00746                 m_vpEnsembleDataPlotters[expt]->SetTitle("octopine but no OOHL:Fuqua 1994:ODE");
00747                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00748                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00749                 
00750                 //expt 4
00751                 expt++;
00752                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00753                 m_vpEnsembleDataPlotters[expt]->SetTitle("OOHL but no octopine:Fuqua 1994:ODE");
00754                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00755                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00756                 
00757                 //expt 5
00758                 expt++;
00759                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00760                 m_vpEnsembleDataPlotters[expt]->SetTitle("OOHL and octopine:Fuqua 1994:ODE");
00761                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00762                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00763                 
00764                 //expt 2b
00765                 expt++;
00766                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00767                 m_vpEnsembleDataPlotters[expt]->SetTitle("traR null mutant No OOHL or octopine:Fuqua 1994:ODE");
00768                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00769                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00770                 
00771                 //expt 3b
00772                 expt++;
00773                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00774                 m_vpEnsembleDataPlotters[expt]->SetTitle("traR null mutant octopine but no OOHL:Fuqua 1994:ODE");
00775                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00776                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00777                 
00778                 //expt 4b
00779                 expt++;
00780                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00781                 m_vpEnsembleDataPlotters[expt]->SetTitle("traR null mutant OOHL but no octopine:Fuqua 1994:ODE");
00782                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00783                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00784                 
00785                 //expt 5b
00786                 expt++;
00787                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00788                 m_vpEnsembleDataPlotters[expt]->SetTitle("traR null mutant OOHL and octopine:Fuqua 1994:ODE");
00789                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00790                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00791                 
00792                 //expt 2c
00793                 expt++;
00794                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00795                 m_vpEnsembleDataPlotters[expt]->SetTitle("occR null mutant No OOHL or octopine:Fuqua 1994:ODE");
00796                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00797                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00798                 
00799                 //expt 3c
00800                 expt++;
00801                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00802                 m_vpEnsembleDataPlotters[expt]->SetTitle("occR null mutant octopine but no OOHL:Fuqua 1994:ODE");
00803                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00804                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00805                 
00806                 //expt 4c
00807                 expt++;
00808                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00809                 m_vpEnsembleDataPlotters[expt]->SetTitle("occR null mutant OOHL but no octopine:Fuqua 1994:ODE");
00810                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00811                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00812                 
00813                 //expt 5c
00814                 expt++;
00815                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00816                 m_vpEnsembleDataPlotters[expt]->SetTitle("occR null mutant OOHL and octopine:Fuqua 1994:ODE");
00817                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00818                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00819                 
00820                 //expt 6
00821                 expt++;
00822                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00823                 m_vpEnsembleDataPlotters[expt]->SetTitle("No octopine, traR-lacZ fusion:Fuqua 1994:ODE");
00824                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00825                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00826 
00827                 //expt 7
00828                 expt++;
00829                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00830                 m_vpEnsembleDataPlotters[expt]->SetTitle("octopine, traR-lacZ fusion:Fuqua 1994:ODE");
00831                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00832                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00833                 
00834                 //expt 8
00835                 expt++;
00836                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00837                 m_vpEnsembleDataPlotters[expt]->SetTitle("no octopine, no occR, traR-lacZ fusion:Fuqua 1994:ODE");
00838                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00839                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00840                 
00841                 //expt 9
00842                 expt++;
00843                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00844                 m_vpEnsembleDataPlotters[expt]->SetTitle("400 ug/ml octopine, no occR, traR-lacZ fusion:Fuqua 1994:ODE");
00845                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00846                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00847 */
00848 /* see above for why 10,11 are commented out
00849                 //expt 10
00850                 expt++;
00851                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00852                 m_vpEnsembleDataPlotters[expt]->SetTitle("No octopine, traR multicopies, traR-lacZ fusion:Fuqua 1994:ODE");
00853                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00854                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00855 
00856                 //expt 11
00857                 expt++;
00858                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00859                 m_vpEnsembleDataPlotters[expt]->SetTitle("octopine, traR multicopies, traR-lacZ fusion:Fuqua 1994:ODE");
00860                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00861                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00862 */
00863 /*              //expt 12
00864                 expt++;
00865                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00866                 m_vpEnsembleDataPlotters[expt]->SetTitle("0.1 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00867                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00868                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00869                 
00870                 //expt 13
00871                 expt++;
00872                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00873                 m_vpEnsembleDataPlotters[expt]->SetTitle("0.2 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00874                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00875                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00876                 
00877                 //expt 14
00878                 expt++;
00879                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00880                 m_vpEnsembleDataPlotters[expt]->SetTitle("1.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00881                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00882                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00883                 
00884                 //expt 15
00885                 expt++;
00886                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00887                 m_vpEnsembleDataPlotters[expt]->SetTitle("2.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00888                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00889                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00890                 
00891                 //expt 16
00892                 expt++;
00893                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00894                 m_vpEnsembleDataPlotters[expt]->SetTitle("10.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00895                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00896                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00897                 
00898                 //expt 17
00899                 expt++;
00900                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00901                 m_vpEnsembleDataPlotters[expt]->SetTitle("20.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00902                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00903                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00904                 
00905                 //expt 18
00906                 expt++;
00907                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00908                 m_vpEnsembleDataPlotters[expt]->SetTitle("100.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00909                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00910                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00911                 
00912                 //expt 19
00913                 expt++;
00914                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00915                 m_vpEnsembleDataPlotters[expt]->SetTitle("200.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00916                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00917                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00918                 
00919                 //expt 20
00920                 expt++;
00921                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00922                 m_vpEnsembleDataPlotters[expt]->SetTitle("1000.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00923                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00924                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00925                 
00926                 //expt 21
00927                 expt++;
00928                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00929                 m_vpEnsembleDataPlotters[expt]->SetTitle("2000.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00930                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00931                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00932                 
00933                 //expt 22
00934                 expt++;
00935                 m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00936                 m_vpEnsembleDataPlotters[expt]->SetTitle("10000.0 nM OOHL, traI-lacZ fusion:Zhu 1998:ODE");
00937                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00938                 this->Attach(m_vpEnsembleDataPlotters[expt]);
00939 */
00940 
00941                 m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
00942                 m_vpEnsembleRunPlotters[expt]->SetTitle("R10(pCF372) -/-");
00943                 m_vpEnsembleRunPlotters[expt]->FixRunnable(expt);
00944                 m_vpEnsembleRunPlotters[expt]->AddChemicalToList(32);
00945                 this->Attach(m_vpEnsembleRunPlotters[expt]);
00946 
00947 
00948 /*      //expt 23
00949         expt++;
00950         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00951         m_vpEnsembleDataPlotters[expt]->SetTitle("No octopine, WT, Conjugal transfer efficiency, Fuqua 1995:ODE");
00952                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00953         this->Attach(m_vpEnsembleDataPlotters[expt]);
00954 
00955         //expt 24
00956         expt++;
00957         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00958         m_vpEnsembleDataPlotters[expt]->SetTitle("2 mg/ml octopine, WT, Conjugal transfer efficiency, Fuqua 1995:ODE");
00959                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00960         this->Attach(m_vpEnsembleDataPlotters[expt]);
00961 
00962         //expt 25
00963         expt++;
00964         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00965         m_vpEnsembleDataPlotters[expt]->SetTitle("No octopine, traM null mutant, Conjugal transfer efficiency, Fuqua 1995:ODE");
00966                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00967         this->Attach(m_vpEnsembleDataPlotters[expt]);
00968 
00969         //expt 26
00970         expt++;
00971         m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
00972         m_vpEnsembleDataPlotters[expt]->SetTitle("2 mg/ml octopine, traM null mutant, Conjugal transfer efficiency, Fuqua 1995:ODE");
00973                 m_vpEnsembleDataPlotters[expt]->FixMinimizable(expt);
00974         this->Attach(m_vpEnsembleDataPlotters[expt]);
00975 */
00976         } //end of plotornot
00977 
00978         // allocate space to accumulate statistics
00979         SumAllocate();
00980 
00981         // Define runs
00982         DefineRuns();
00983 
00984         // define the experiments
00985         DefineExperiments();
00986 
00987         // Load in the ensemble information
00988         LoadEnsembleInfo("ensemble.par");
00989 
00990 }
00991 
00992 CQuorumSensingEnsembleDirector::~CQuorumSensingEnsembleDirector()
00993 {
00994         for(int i = 0; i < m_vpEnsembleDataPlotters.size(); i++)
00995         {
00996                 m_vpMinimizables[i]->Detach(m_vpEnsembleDataPlotters[i]);
00997                 delete m_vpEnsembleDataPlotters[i];
00998         }
00999 }
01000 
01001 void CQuorumSensingEnsembleDirector::DefineRuns()
01002 {
01003         int expt = -1;
01004         // R10(pCF372) -/-
01005         expt++;
01006         m_vpRunnables[expt]->GetReactionNetwork()->RemoveReaction(18);
01007 //      m_vpRunnables[expt]->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(228000.0);
01008         m_vpRunnables[expt]->GetReactionNetwork()->ChemicalReset();
01009 
01010 }
01011 
01012 void CQuorumSensingEnsembleDirector::DefineExperiments()
01013 {       
01014         int expt = -1;
01015 
01016 /*      // Steady State 1
01017         expt++;
01018         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01019 
01020         // Steady State 2
01021         expt++;
01022         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01023 */
01024         // OOHL present -> 200 molecules of BoundtraR
01025         expt++;
01026 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(13)->SetInitialAmount(200.0);
01027 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(5);
01028 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01029         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(10.6e07);
01030         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01031 
01032 /*      // No OOHL -> 100 molecules of FreetraR
01033         expt++;
01034 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(12)->SetInitialAmount(100.0);
01035 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(5);
01036 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01037         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01038 
01039         // no octopine no OOHL ->
01040         expt++;
01041 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(45);
01042         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01043 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(8);
01044         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01045 
01046         // octopine but No OOHL -> 
01047         expt++;
01048         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(5.0e07);
01049 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(45);
01050         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01051 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(8);
01052         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01053         
01054         // OOHL but No octopine -> 
01055         expt++;
01056         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.3e04);
01057 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(45);
01058         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01059 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(8);
01060         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01061         
01062         // OOHL and octopine -> 
01063         expt++;
01064         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(5.0e07);
01065         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.3e04);
01066 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(45);
01067         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01068 //      m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(8);
01069         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01070 
01071         //traR null mutant no octopine no OOHL ->
01072         expt++;
01073         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01074         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01075         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(0);
01076         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(12)->SetInitialAmount(0.0);
01077         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(11)->SetInitialAmount(0.0);
01078         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(0.0);
01079         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01080 
01081         // traR null mutant octopine but No OOHL -> 
01082         expt++;
01083         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(5.0e07);
01084         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01085         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01086         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(0);
01087         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(12)->SetInitialAmount(0.0);
01088         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(11)->SetInitialAmount(0.0);
01089         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(0.0);
01090         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01091         
01092         // traR null mutant OOHL but No octopine -> 
01093         expt++;
01094         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.3e04);
01095         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01096         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01097         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(0);
01098         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(12)->SetInitialAmount(0.0);
01099         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(11)->SetInitialAmount(0.0);
01100         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(0.0);
01101         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01102         
01103         // traR null mutant OOHL and octopine -> 
01104         expt++;
01105         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(5.0e07);
01106         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.3e04);
01107         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01108         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01109         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(0);
01110         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(12)->SetInitialAmount(0.0);
01111         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(11)->SetInitialAmount(0.0);
01112         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(0.0);
01113         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01114 
01115         //occR null mutant no octopine no OOHL ->
01116         expt++;
01117         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01118         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01119         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(0.0);
01120         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01121 
01122         //occR null mutant octopine but No OOHL -> 
01123         expt++;
01124         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(5.0e07);
01125         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01126         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01127         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(0.0);
01128         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01129         
01130         //occR null mutant OOHL but No octopine -> 
01131         expt++;
01132         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.3e04);
01133         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01134         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01135         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(0.0);
01136         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01137         
01138         //occR null mutant OOHL and octopine -> 
01139         expt++;
01140         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(5.0e07);
01141         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.3e04);
01142         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(41);
01143         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01144         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(0.0);
01145         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01146 
01147         // no octopine, traR-lacZ fusion -> 
01148         expt++;
01149         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(7);
01150         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(6);
01151         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01152 
01153         //400ug/ml octopine, traR-lacZ fusion -> 
01154         expt++;
01155         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.0e7);
01156         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(7);
01157         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(6);
01158         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01159 
01160         // no octopine, no occR, traR-lacZ fusion -> 
01161         expt++;
01162         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(7);
01163         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(6);
01164         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01165         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01166 
01167         // 400 ug/ml octopine, no occR, traR-lacZ fusion -> 
01168         expt++;
01169         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.0e7);
01170         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(7);
01171         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(6);
01172         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
01173         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01174 */
01175 /* see above for why 10,11 are commented out
01176         // no octopine, traR multicopies, traR-lacZ fusion -> 
01177         expt++;
01178         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(7);
01179         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(6);
01180         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(5.0);
01181         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01182 
01183         //400ug/ml octopine, traR multicopies, traR-lacZ fusion -> 
01184         expt++;
01185         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.0e7);
01186         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(7);
01187         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(6);
01188         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(8)->SetInitialAmount(5.0);
01189         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01190 */
01191 /*      // 0.1nM OOHL, traI-lacZ fusion -> 
01192         expt++;
01193         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01194         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1.1e04);
01195         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01196         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01197         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01198 
01199         // 0.2nM OOHL, traI-lacZ fusion -> 
01200         expt++;
01201         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01202         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.5e04);
01203         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01204         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01205         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01206 
01207         // 1.0nM OOHL, traI-lacZ fusion -> 
01208         expt++;
01209         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01210         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1.1e05);
01211         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01212         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01213         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01214 
01215         // 2.0nM OOHL, traI-lacZ fusion -> 
01216         expt++;
01217         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01218         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.5e05);
01219         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01220         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01221         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01222 
01223         // 10.0nM OOHL, traI-lacZ fusion -> 
01224         expt++;
01225         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01226         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1.1e06);
01227         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01228         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01229         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01230 
01231         // 20.0nM OOHL, traI-lacZ fusion -> 
01232         expt++;
01233         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01234         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.5e06);
01235         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01236         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01237         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01238 
01239         // 100.0nM OOHL, traI-lacZ fusion -> 
01240         expt++;
01241         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01242         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1.1e07);
01243         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01244         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01245         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01246 
01247         // 200.0nM OOHL, traI-lacZ fusion -> 
01248         expt++;
01249         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01250         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.5e07);
01251         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01252         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01253         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01254 
01255         // 1000.0nM OOHL, traI-lacZ fusion -> 
01256         expt++;
01257         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01258         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1.1e08);
01259         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01260         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01261         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01262 
01263         // 2000.0nM OOHL, traI-lacZ fusion -> 
01264         expt++;
01265         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01266         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(5.5e08);
01267         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01268         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01269         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01270 
01271         // 10000.0nM OOHL, traI-lacZ fusion -> 
01272         expt++;
01273         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.8e11);
01274         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1.1e09);
01275         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01276         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(18);
01277         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01278 */
01279 /*      //No octopine, WT, Conjugal transfer efficiency ->
01280         expt++;
01281         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01282 
01283         //2 mg/ml octopine, WT, Conjugal transfer efficiency ->
01284         expt++;
01285         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(9.0e11);
01286         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01287 
01288         //No octopine, traM null mutant, Conjugal transfer efficiency ->
01289         expt++;
01290         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(19)->SetInitialAmount(0.0);
01291         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(18)->SetInitialAmount(0.0);
01292         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(21);
01293         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(20);
01294         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01295         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(10);
01296         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01297 
01298         //2 mg/ml octopine, traM null mutant, Conjugal transfer efficiency ->
01299         expt++;
01300         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(9.0e11);
01301         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(19)->SetInitialAmount(0.0);
01302         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->GetChemical(18)->SetInitialAmount(0.0);
01303         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(21);
01304         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(20);
01305         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(19);
01306         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->RemoveReaction(10);
01307         m_vpMinimizables[expt]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
01308 */
01309 }
01310 
01311