00001 // EGFRTraffickingRunDirector.cpp: implementation of the CEGFRTraffickingRunDirector class. 00002 // 00004 00005 #include "EGFRTraffickingRunDirector.h" 00006 00008 // Construction/Destruction 00010 00011 CEGFRTraffickingRunDirector::CEGFRTraffickingRunDirector() 00012 { 00013 double maxSimTime = 240.0; 00014 int intTime = (int) maxSimTime + 2; 00015 double stepSize = 0.001; 00016 double frequency = 1.0; 00017 double moveTol = 1.0e-06; 00018 00019 int cnt = 0; 00020 00021 // EGF at 100 ng/ml, 8000 EGFRs 00022 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00023 //m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00024 m_vpRxnMovers.push_back(new CStiffBulirschStoerMover(frequency,stepSize,moveTol)); 00025 int nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00026 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00027 m_vpRunnables.push_back(new CRunnable()); 00028 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00029 // create an observer for the runnable 00030 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00031 00032 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(70); 00033 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(71); 00034 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(72); 00035 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(77); 00036 /* 00037 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(32); 00038 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(33); 00039 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(34); 00040 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(35); 00041 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(55); 00042 */ 00043 // attach the observer 00044 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00045 cnt++; 00046 00047 /* 00048 // EGF at 100 ng/ml, 50000 EGFRs 00049 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00050 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00051 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00052 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00053 m_vpRunnables.push_back(new CRunnable()); 00054 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00055 // create an observer for the runnable 00056 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00057 00058 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(54); 00059 00060 // attach the observer 00061 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00062 cnt++; 00063 00064 // EGF at 100 ng/ml, 100000 EGFRs 00065 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00066 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00067 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00068 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00069 m_vpRunnables.push_back(new CRunnable()); 00070 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00071 // create an observer for the runnable 00072 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00073 00074 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(54); 00075 00076 // attach the observer 00077 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00078 cnt++; 00079 00080 // EGF at 100 ng/ml, 300000 EGFRs 00081 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00082 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00083 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00084 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00085 m_vpRunnables.push_back(new CRunnable()); 00086 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00087 // create an observer for the runnable 00088 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00089 00090 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(54); 00091 00092 // attach the observer 00093 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00094 cnt++; 00095 */ 00096 /* 00097 // EGF at 100 ng/ml, EGFR overexpressed 00098 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00099 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00100 int nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00101 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00102 m_vpRunnables.push_back(new CRunnable()); 00103 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00104 // create an observer for the runnable 00105 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00106 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00107 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00108 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00109 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00110 // attach the observer 00111 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00112 cnt++; 00113 00114 00115 // EGF at 100 ng/ml, EGFR overexpressed, Cdc42 wt overexpressed 00116 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00117 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00118 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00119 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00120 m_vpRunnables.push_back(new CRunnable()); 00121 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00122 // create an observer for the runnable 00123 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00124 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00125 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00126 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00127 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00128 // attach the observer 00129 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00130 cnt++; 00131 00132 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(Q61L) 00133 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00134 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00135 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00136 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00137 m_vpRunnables.push_back(new CRunnable()); 00138 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00139 // create an observer for the runnable 00140 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00141 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00142 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00143 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00144 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00145 // attach the observer 00146 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00147 cnt++; 00148 00149 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(T17N) 00150 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00151 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00152 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00153 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00154 m_vpRunnables.push_back(new CRunnable()); 00155 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00156 // create an observer for the runnable 00157 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00158 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00159 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00160 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00161 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00162 // attach the observer 00163 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00164 cnt++; 00165 00166 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42dL8 00167 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00168 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00169 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00170 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00171 m_vpRunnables.push_back(new CRunnable()); 00172 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00173 // create an observer for the runnable 00174 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00175 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00176 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00177 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00178 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00179 // attach the observer 00180 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00181 cnt++; 00182 00183 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42Lss 00184 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00185 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00186 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00187 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00188 m_vpRunnables.push_back(new CRunnable()); 00189 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00190 // create an observer for the runnable 00191 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00192 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00193 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00194 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00195 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00196 // attach the observer 00197 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00198 cnt++; 00199 00200 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(Q61L/dL8) 00201 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00202 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00203 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00204 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00205 m_vpRunnables.push_back(new CRunnable()); 00206 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00207 // create an observer for the runnable 00208 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00209 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00210 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00211 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00212 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00213 // attach the observer 00214 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00215 cnt++; 00216 00217 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(Q61L/Lss) 00218 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00219 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00220 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00221 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00222 m_vpRunnables.push_back(new CRunnable()); 00223 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00224 // create an observer for the runnable 00225 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00226 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00227 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00228 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00229 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00230 // attach the observer 00231 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00232 cnt++; 00233 00234 00235 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(F28L) 00236 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00237 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00238 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00239 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00240 m_vpRunnables.push_back(new CRunnable()); 00241 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00242 // create an observer for the runnable 00243 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00244 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00245 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00246 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00247 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00248 // attach the observer 00249 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00250 cnt++; 00251 00252 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(F28L/dL8) 00253 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00254 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00255 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00256 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00257 m_vpRunnables.push_back(new CRunnable()); 00258 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00259 // create an observer for the runnable 00260 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00261 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00262 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00263 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00264 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00265 // attach the observer 00266 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00267 cnt++; 00268 00269 // EGF at 100 ng/ml, EGFR overexpressed + Cdc42(F28L/Lss) 00270 m_vpRxnNetworks.push_back(new CEGFRTraffickingNetwork()); 00271 m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol)); 00272 nChemicals = m_vpRxnNetworks[cnt]->GetNumberOfChemicals(); 00273 m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1)); 00274 m_vpRunnables.push_back(new CRunnable()); 00275 m_vpRunnables[cnt]->SetComponents(m_vpRxnNetworks[cnt],m_vpRxnMovers[cnt],m_vpCellObservers[cnt]); 00276 // create an observer for the runnable 00277 m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver()); 00278 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(1); 00279 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(47); 00280 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(49); 00281 m_vpGnuPlotters[cnt]->AddChemicalNumberToList(58); 00282 // attach the observer 00283 m_vpRunnables[cnt]->Attach(m_vpGnuPlotters[cnt]); 00284 cnt++; 00285 */ 00286 DefineRuns(); 00287 } 00288 00289 CEGFRTraffickingRunDirector::~CEGFRTraffickingRunDirector() 00290 { 00291 00292 } 00293 00294 void CEGFRTraffickingRunDirector::DefineRuns() 00295 { 00296 // set parameters in the runnables to those read from a previous 00297 // optimization pass; assumes all runnables have same number of 00298 // rate constants 00299 ParameterReader *pReader = new ParameterReader("traffic_restart.par"); 00300 int nRC = m_vpRunnables[0]->GetReactionNetwork()->GetNumberOfRateConstants(); 00301 for(int j = 0; j < nRC; j++) 00302 { 00303 double rate = pReader->ReadParameter(); 00304 for(int i = 0; i < m_vpRunnables.size(); i++) 00305 { 00306 m_vpRunnables[i]->GetReactionNetwork()->GetRateConstant(j)->SetRateConstant(rate); 00307 } 00308 } 00309 00310 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00311 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(3)->SetInitialAmount(8000); 00312 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(45)->SetInitialAmount(pReader->ReadParameter()); 00313 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(46)->SetInitialAmount(pReader->ReadParameter()); 00314 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(48)->SetInitialAmount(pReader->ReadParameter()); 00315 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(51)->SetInitialAmount(pReader->ReadParameter()); 00316 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(57)->SetInitialAmount(pReader->ReadParameter()); 00317 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(58)->SetInitialAmount(pReader->ReadParameter()); 00318 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(63)->SetInitialAmount(pReader->ReadParameter()); 00319 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(71)->SetInitialAmount(pReader->ReadParameter()); 00320 m_vpRunnables[0]->GetReactionNetwork()->ChemicalReset(); 00321 m_vpGnuPlotters[0]->SetTitle("100 ng/ml EGF + 8000 EGFRs"); 00322 00323 delete pReader; 00324 00325 /* 00326 m_vpRunnables[1]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00327 m_vpRunnables[1]->GetReactionNetwork()->GetChemical(3)->SetInitialAmount(50000); 00328 m_vpRunnables[1]->GetReactionNetwork()->ChemicalReset(); 00329 m_vpGnuPlotters[1]->SetTitle("100 ng/ml EGF + 50000 EGFRs"); 00330 00331 m_vpRunnables[2]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00332 m_vpRunnables[2]->GetReactionNetwork()->GetChemical(3)->SetInitialAmount(100000); 00333 m_vpRunnables[2]->GetReactionNetwork()->ChemicalReset(); 00334 m_vpGnuPlotters[2]->SetTitle("100 ng/ml EGF + 100000 EGFRs"); 00335 00336 m_vpRunnables[3]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00337 m_vpRunnables[3]->GetReactionNetwork()->GetChemical(3)->SetInitialAmount(300000); 00338 m_vpRunnables[3]->GetReactionNetwork()->ChemicalReset(); 00339 m_vpGnuPlotters[3]->SetTitle("100 ng/ml EGF + 300000 EGFRs"); 00340 */ 00341 /* 00342 // 100,000 receptors, EGF at 100 ng/ml 00343 m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(64); 00344 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00345 m_vpRunnables[0]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00346 m_vpRunnables[0]->GetReactionNetwork()->ChemicalReset(); 00347 m_vpGnuPlotters[0]->SetTitle("100 ng/ml EGF + EGFR"); 00348 00349 // 100,000 receptors, EGF at 100 ng/ml, Cdc42wt 2-fold overexpressed 00350 m_vpRunnables[1]->GetReactionNetwork()->RemoveReaction(64); 00351 m_vpRunnables[1]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00352 m_vpRunnables[1]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00353 m_vpRunnables[1]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(2*600000); 00354 m_vpRunnables[1]->GetReactionNetwork()->ChemicalReset(); 00355 m_vpGnuPlotters[1]->SetTitle("100 ng/ml EGF + EGFR + Cdc42wt"); 00356 00357 // 100,000 receptors, EGF at 100 ng/ml, Cdc42(Q61L) 00358 m_vpRunnables[2]->GetReactionNetwork()->RemoveReaction(64); 00359 m_vpRunnables[2]->GetReactionNetwork()->RemoveReaction(59); 00360 m_vpRunnables[2]->GetReactionNetwork()->RemoveReaction(58); 00361 m_vpRunnables[2]->GetReactionNetwork()->RemoveReaction(25); 00362 m_vpRunnables[2]->GetReactionNetwork()->RemoveReaction(24); 00363 m_vpRunnables[2]->GetReactionNetwork()->RemoveReaction(17); 00364 m_vpRunnables[2]->GetReactionNetwork()->RemoveReaction(16); 00365 m_vpRunnables[2]->GetReactionNetwork()->RemoveReaction(6); 00366 m_vpRunnables[2]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00367 m_vpRunnables[2]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00368 // start with all mutant 42 active 00369 m_vpRunnables[2]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0); 00370 m_vpRunnables[2]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000); 00371 m_vpRunnables[2]->GetReactionNetwork()->ChemicalReset(); 00372 m_vpGnuPlotters[2]->SetTitle("100 ng/ml EGF + EGFR + Cdc42(Q61L)"); 00373 00374 // 100,000 receptors, EGF at 100 ng/ml, Cdc42(T17N) 00375 m_vpRunnables[3]->GetReactionNetwork()->RemoveReaction(64); 00376 m_vpRunnables[3]->GetReactionNetwork()->RemoveReaction(5); 00377 m_vpRunnables[3]->GetReactionNetwork()->RemoveReaction(4); 00378 m_vpRunnables[3]->GetReactionNetwork()->RemoveReaction(3); 00379 m_vpRunnables[3]->GetReactionNetwork()->RemoveReaction(2); 00380 m_vpRunnables[3]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00381 m_vpRunnables[3]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00382 m_vpRunnables[3]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(2*600000); 00383 m_vpRunnables[3]->GetReactionNetwork()->ChemicalReset(); 00384 m_vpGnuPlotters[3]->SetTitle("100 ng/ml EGF + EGFR + Cdc42(T17N)"); 00385 00386 // 100,000 receptors, EGF at 100 ng/ml, Cdc42dL8 00387 m_vpRunnables[4]->GetReactionNetwork()->RemoveReaction(64); 00388 m_vpRunnables[4]->GetReactionNetwork()->RemoveReaction(22); 00389 m_vpRunnables[4]->GetReactionNetwork()->RemoveReaction(20); 00390 m_vpRunnables[4]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00391 m_vpRunnables[4]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00392 // start with all 42 active 00393 m_vpRunnables[4]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(2*600000); 00394 m_vpRunnables[4]->GetReactionNetwork()->ChemicalReset(); 00395 m_vpGnuPlotters[4]->SetTitle("100 ng/ml EGF + EGFR + Cdc42dL8"); 00396 00397 // 100,000 receptors, EGF at 100 ng/ml, Cdc42Lss 00398 m_vpRunnables[5]->GetReactionNetwork()->RemoveReaction(64); 00399 m_vpRunnables[5]->GetReactionNetwork()->RemoveReaction(55); 00400 m_vpRunnables[5]->GetReactionNetwork()->RemoveReaction(54); 00401 m_vpRunnables[5]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00402 m_vpRunnables[5]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00403 // start with all 42 active 00404 m_vpRunnables[5]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(2*600000); 00405 m_vpRunnables[5]->GetReactionNetwork()->ChemicalReset(); 00406 m_vpGnuPlotters[5]->SetTitle("100 ng/ml EGF + EGFR + Cdc42Lss"); 00407 00408 // 100,000 receptors, EGF at 100 ng/ml, Cdc42(Q61L/dL8) 00409 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(64); 00410 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(59); 00411 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(58); 00412 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(25); 00413 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(24); 00414 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(22); 00415 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(20); 00416 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(17); 00417 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(16); 00418 m_vpRunnables[6]->GetReactionNetwork()->RemoveReaction(6); 00419 m_vpRunnables[6]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00420 m_vpRunnables[6]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00421 // start with all 42 active 00422 m_vpRunnables[6]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0); 00423 m_vpRunnables[6]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000); 00424 m_vpRunnables[6]->GetReactionNetwork()->ChemicalReset(); 00425 m_vpGnuPlotters[6]->SetTitle("100 ng/ml EGF + EGFR + Cdc42(Q61L/dL8)"); 00426 00427 00428 // 100,000 receptors, EGF at 100 ng/ml, Cdc42(Q61L/Lss) 00429 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(64); 00430 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(59); 00431 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(58); 00432 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(55); 00433 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(54); 00434 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(25); 00435 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(24); 00436 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(17); 00437 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(16); 00438 m_vpRunnables[7]->GetReactionNetwork()->RemoveReaction(6); 00439 m_vpRunnables[7]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00440 m_vpRunnables[7]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00441 // start with all 42 active 00442 m_vpRunnables[7]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0); 00443 m_vpRunnables[7]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000); 00444 m_vpRunnables[7]->GetReactionNetwork()->ChemicalReset(); 00445 m_vpGnuPlotters[7]->SetTitle("100 ng/ml EGF + EGFR + Cdc42(Q61L/Lss)"); 00446 00447 00448 // 100,000 receptors, EGF at 100 ng/ml, Cdc42(F28L) 00449 m_vpRunnables[8]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00450 m_vpRunnables[8]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00451 // start with all 42 active 00452 m_vpRunnables[8]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0); 00453 m_vpRunnables[8]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000); 00454 m_vpRunnables[8]->GetReactionNetwork()->ChemicalReset(); 00455 m_vpGnuPlotters[8]->SetTitle("100 ng/ml EGF + EGFR + Cdc42(F28L)"); 00456 00457 00458 // 100,000 receptors, EGF at 100 ng/ml, Cdc42(F28L/dL8) 00459 m_vpRunnables[9]->GetReactionNetwork()->RemoveReaction(22); 00460 m_vpRunnables[9]->GetReactionNetwork()->RemoveReaction(20); 00461 m_vpRunnables[9]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00462 m_vpRunnables[9]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00463 // start with all 42 active 00464 m_vpRunnables[9]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0); 00465 m_vpRunnables[9]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000); 00466 m_vpRunnables[9]->GetReactionNetwork()->ChemicalReset(); 00467 m_vpGnuPlotters[9]->SetTitle("100 ng/ml EGF + EGFR + Cdc42(F28L/dL8)"); 00468 00469 00470 // 100,000 receptors, EGF at 100 ng/ml, Cdc42(F28L/Lss) 00471 m_vpRunnables[10]->GetReactionNetwork()->RemoveReaction(55); 00472 m_vpRunnables[10]->GetReactionNetwork()->RemoveReaction(54); 00473 m_vpRunnables[10]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.2e+007); 00474 m_vpRunnables[10]->GetReactionNetwork()->GetChemical(2)->SetInitialAmount(100000); 00475 // start with all 42 active 00476 m_vpRunnables[10]->GetReactionNetwork()->GetChemical(35)->SetInitialAmount(0.0); 00477 m_vpRunnables[10]->GetReactionNetwork()->GetChemical(36)->SetInitialAmount(2*600000); 00478 m_vpRunnables[10]->GetReactionNetwork()->ChemicalReset(); 00479 m_vpGnuPlotters[10]->SetTitle("100 ng/ml EGF + EGFR + Cdc42(F28L/Lss)"); 00480 */ 00481 }
1.2.14 written by Dimitri van Heesch,
© 1997-2002