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File List

Here is a list of all files with brief descriptions:

AcceptanceRatioFreeEnergyEstimator.cpp [code]
AcceptanceRatioFreeEnergyEstimator.h [code]
AlgebraicChemical.cpp [code]
AlgebraicChemical.h [code]
AlternateErkSubnetwork.cpp [code]
AlternateErkSubnetwork.h [code]
AlternateOneGeneInhibitoryNetwork.cpp [code]
AlternateOneGeneInhibitoryNetwork.h [code]
AlternateOneGeneInhibitoryNetworkMinimizableDirector.cpp [code]
AlternateOneGeneInhibitoryNetworkMinimizableDirector.h [code]
BasicQuenchMinimizer.cpp [code]
BasicQuenchMinimizer.h [code]
BinaryNetworkDataRelation.cpp [code]
BinaryNetworkDataRelation.h [code]
blas.h [code]
CatalyzedTranslationReaction.cpp [code]
CatalyzedTranslationReaction.h [code]
Cell.cpp [code]
Cell.h [code]
CellAverageObserver.cpp [code]
CellAverageObserver.h [code]
Chemical.cpp [code]
Chemical.h [code]
ChemicalSink.cpp [code]
ChemicalSink.h [code]
ChemicalSource.cpp [code]
ChemicalSource.h [code]
ChemicalTimeSeriesData.cpp [code]
ChemicalTimeSeriesData.h [code]
ChemicalTransportReaction.cpp [code]
ChemicalTransportReaction.h [code]
ClonalCommaES.cpp [code]
ClonalCommaES.h [code]
CombinatorialNetwork.cpp [code]
CombinatorialNetwork.h [code]
CombinatorialNetworkMinimizableDirector.cpp [code]
CombinatorialNetworkMinimizableDirector.h [code]
CombinatorialNetworksSloppyMinimizableDirector.cpp [code]
CombinatorialNetworksSloppyMinimizableDirector.h [code]
CombinatorialRunDirector.cpp [code]
CombinatorialRunDirector.h [code]
CommaStrategyOne.cpp [code]
CommaStrategyOne.h [code]
CompetitiveDegradationReaction.cpp [code]
CompetitiveDegradationReaction.h [code]
Components.cpp [code]
Components.h [code]
ConcentrationObserver.cpp [code]
ConcentrationObserver.h [code]
ConjugateGradientMinimizer.cpp [code]
ConjugateGradientMinimizer.h [code]
ConjugateGradientObserver.cpp [code]
ConjugateGradientObserver.h [code]
ConstantSinkReaction.cpp [code]
ConstantSinkReaction.h [code]
ConstantSourceReaction.cpp [code]
ConstantSourceReaction.h [code]
ContinuousTimeMonteCarloMover.cpp [code]
ContinuousTimeMonteCarloMover.h [code]
ConversionFactor.cpp [code]
ConversionFactor.h [code]
CoupledOneGeneNetworksMinimizableDirector.cpp [code]
CoupledOneGeneNetworksMinimizableDirector.h [code]
CoupledPC12NetworksMinimizableDirector.cpp [code]
CoupledPC12NetworksMinimizableDirector.h [code]
CoupledReplicasMinimizableDirector.cpp [code]
CoupledReplicasMinimizableDirector.h [code]
CurrentToCurrentRatioChemical.cpp [code]
CurrentToCurrentRatioChemical.h [code]
CurrentToInitialRatioChemical.cpp [code]
CurrentToInitialRatioChemical.h [code]
DataPoint.cpp [code]
DataPoint.h [code]
DifferentialEquationMover.cpp [code]
DifferentialEquationMover.h [code]
Director.cpp [code]
Director.h [code]
Display.cpp [code]
Display.h [code]
DNA.cpp [code]
DNA.h [code]
EGFRTraffickingCHOMinimizableDirector.cpp [code]
EGFRTraffickingCHOMinimizableDirector.h [code]
EGFRTraffickingCoupledMinimizableDirector.cpp [code]
EGFRTraffickingCoupledMinimizableDirector.h [code]
EGFRTraffickingEnsembleDirector.cpp [code]
EGFRTraffickingEnsembleDirector.h [code]
EGFRTraffickingIdealCellMinimizableDirector.cpp [code]
EGFRTraffickingIdealCellMinimizableDirector.h [code]
EGFRTraffickingMinimizableDirector.cpp [code]
EGFRTraffickingMinimizableDirector.h [code]
EGFRTraffickingNetwork.cpp [code]
EGFRTraffickingNetwork.h [code]
EGFRTraffickingNIH3T3MinimizableDirector.cpp [code]
EGFRTraffickingNIH3T3MinimizableDirector.h [code]
EGFRTraffickingPredictionNetwork.cpp [code]
EGFRTraffickingPredictionNetwork.h [code]
EGFRTraffickingRunDirector.cpp [code]
EGFRTraffickingRunDirector.h [code]
EnsembleCombinationDirector.cpp [code]
EnsembleCombinationDirector.h [code]
EnsembleMember.cpp [code]
EnsembleMember.h [code]
EnsembleRunDirector.cpp [code]
EnsembleRunDirector.h [code]
Equations.cpp [code]
Equations.h [code]
ErkSubnetwork.cpp [code]
ErkSubnetwork.h [code]
EvolutionStrategy.cpp [code]
EvolutionStrategy.h [code]
EvolutionStrategyChromosome.cpp [code]
EvolutionStrategyChromosome.h [code]
ExampleNetwork.cpp [code]
ExampleNetwork.h [code]
ExampleNetworkMinimizableDirector.cpp [code]
ExampleNetworkMinimizableDirector.h [code]
Experiment.cpp [code]
Experiment.h [code]
FirstOrderDestructionReaction.cpp [code]
FirstOrderDestructionReaction.h [code]
ForcesObserver.cpp [code]
ForcesObserver.h [code]
ForceVectorPoint.cpp [code]
ForceVectorPoint.h [code]
ForcingData.cpp [code]
ForcingData.h [code]
ForestNitrogenCycleNetwork.cpp [code]
ForestNitrogenCycleNetwork.h [code]
ForestNitrogenCyclingMinimizableDirector.cpp [code]
ForestNitrogenCyclingMinimizableDirector.h [code]
GenerationReaction.cpp [code]
GenerationReaction.h [code]
GeneticCode.cpp [code]
GeneticCode.h [code]
Geometry.cpp [code]
Geometry.h [code]
GnuPlotter.cpp [code]
GnuPlotter.h [code]
GnuPlotterCostObserver.cpp [code]
GnuPlotterCostObserver.h [code]
GnuPlotterDirectorObserver.cpp [code]
GnuPlotterDirectorObserver.h [code]
GnuPlotterEnsembleDataDirectorObserver.cpp [code]
GnuPlotterEnsembleDataDirectorObserver.h [code]
GnuPlotterEnsembleRunDirectorObserver.cpp [code]
GnuPlotterEnsembleRunDirectorObserver.h [code]
GnuPlotterMaster.h [code]
GnuPlotterParameterScatterPlot.cpp [code]
GnuPlotterParameterScatterPlot.h [code]
GnuPlotterResidualScatterPlot.cpp [code]
GnuPlotterResidualScatterPlot.h [code]
GnuPlotterRunnableObserver.cpp [code]
GnuPlotterRunnableObserver.h [code]
GnuPlotterSimulatedAnnealingObserver.cpp [code]
GnuPlotterSimulatedAnnealingObserver.h [code]
GnuPlotterSingleRun.cpp [code]
GnuPlotterSingleRun.h [code]
GnuPlotterTimeSeriesObserver.cpp [code]
GnuPlotterTimeSeriesObserver.h [code]
GnuPlotterTimeSeriesSharedBFactorObserver.cpp [code]
GnuPlotterTimeSeriesSharedBFactorObserver.h [code]
GnuPlotterTrajectoryObserver.cpp [code]
GnuPlotterTrajectoryObserver.h [code]
HeterodimerDissociationReaction.cpp [code]
HeterodimerDissociationReaction.h [code]
HeterodimerizationReaction.cpp [code]
HeterodimerizationReaction.h [code]
HomodimerDissociationReaction.cpp [code]
HomodimerDissociationReaction.h [code]
HomodimerizationReaction.cpp [code]
HomodimerizationReaction.h [code]
IdentityParameterFilter.cpp [code]
IdentityParameterFilter.h [code]
ImprovedLevenbergMarquardtMinimizer.cpp [code]
ImprovedLevenbergMarquardtMinimizer.h [code]
InfrastructureMaster.h [code]
Integration.cpp [code]
Integration.h [code]
lapack.h [code]
LaubLoomisDictyNetwork.cpp [code]
LaubLoomisDictyNetwork.h [code]
LaubLoomisDictyNetworkEnsembleDirector.cpp [code]
LaubLoomisDictyNetworkEnsembleDirector.h [code]
LaubLoomisDictyNetworkMinimizableDirector.cpp [code]
LaubLoomisDictyNetworkMinimizableDirector.h [code]
LaubLoomisDictyRunDirector.cpp [code]
LaubLoomisDictyRunDirector.h [code]
LeastSquaresADMinimizer.cpp [code]
LeastSquaresADMinimizer.h [code]
LeastSquaresMinimizer.cpp [code]
LeastSquaresMinimizer.h [code]
LeastSquaresObserver.cpp [code]
LeastSquaresObserver.h [code]
LevenbergMarquardtMinimizer.cpp [code]
LevenbergMarquardtMinimizer.h [code]
LocateInputFileDirectory.cpp [code]
LocateInputFileDirectory.h [code]
LogChemical.cpp [code]
LogChemical.h [code]
LogParameterFilter.cpp [code]
LogParameterFilter.h [code]
LowDimensionalCostFunctionMapper.cpp [code]
LowDimensionalCostFunctionMapper.h [code]
OneGeneNetwork/main.cpp [code]
Quorum/main.cpp [code]
srcOld/main.cpp [code]
TranslationDynamics/main.cpp [code]
MartielGoldbeterDictyNetwork.cpp [code]
MartielGoldbeterDictyNetwork.h [code]
MartielGoldbeterDictyNetworkMinimizableDirector.cpp [code]
MartielGoldbeterDictyNetworkMinimizableDirector.h [code]
MatrixOperations.cpp [code]
MatrixOperations.h [code]
MDOChemical.cpp [code]
MDOChemical.h [code]
MichaelisMentenDephosphorylationReaction.cpp [code]
MichaelisMentenDephosphorylationReaction.h [code]
MichaelisMentenGProteinActivationReaction.cpp [code]
MichaelisMentenGProteinActivationReaction.h [code]
MichaelisMentenGProteinDeactivationReaction.cpp [code]
MichaelisMentenGProteinDeactivationReaction.h [code]
MichaelisMentenHeterodimerizationReaction.cpp [code]
MichaelisMentenHeterodimerizationReaction.h [code]
MichaelisMentenPhosphorylationReaction.cpp [code]
MichaelisMentenPhosphorylationReaction.h [code]
MichaelisMentenProteinProteinActivationReaction.cpp [code]
MichaelisMentenProteinProteinActivationReaction.h [code]
MichaelisMentenProteinProteinDeactivationReaction.cpp [code]
MichaelisMentenProteinProteinDeactivationReaction.h [code]
MichaelisMentenReaction.cpp [code]
MichaelisMentenReaction.h [code]
MichaelisMentenTransformationReaction.cpp [code]
MichaelisMentenTransformationReaction.h [code]
Minimizable.h [code]
Minimizer.cpp [code]
Minimizer.h [code]
MinimizerMaster.h [code]
MixedReactionMover.cpp [code]
MixedReactionMover.h [code]
MixedReactionNetwork.cpp [code]
MixedReactionNetwork.h [code]
MoverMaster.h [code]
NelderMeadSimplexMinimizer.cpp [code]
NelderMeadSimplexMinimizer.h [code]
NetworkMinimizable.cpp [code]
NetworkMinimizable.h [code]
NetworkMinimizableDirector.cpp [code]
NetworkMinimizableDirector.h [code]
NLLSMinimizable.cpp [code]
NLLSMinimizable.h [code]
NormalizedLinearAmplifier.cpp [code]
NormalizedLinearAmplifier.h [code]
NormalizedLinearAttenuator.cpp [code]
NormalizedLinearAttenuator.h [code]
OneGeneEnsembleDirector.cpp [code]
OneGeneEnsembleDirector.h [code]
OneGeneEnsembleRunDirector.cpp [code]
OneGeneEnsembleRunDirector.h [code]
OneGeneInhibitoryAveragingDirector.cpp [code]
OneGeneInhibitoryAveragingDirector.h [code]
OneGeneInhibitoryNetwork.cpp [code]
OneGeneInhibitoryNetwork.h [code]
OneGeneInhibitoryNetworkMinimizableDirector.cpp [code]
OneGeneInhibitoryNetworkMinimizableDirector.h [code]
OneGeneInhibitoryNetworkMinimizableDirectorOLD.cpp [code]
OneGeneInhibitoryNetworkRunDirector.cpp [code]
OneGeneInhibitoryNetworkRunDirector.h [code]
OneGeneMaster.h [code]
OneGeneReplicaMinimizableDirector.cpp [code]
OneGeneReplicaMinimizableDirector.h [code]
OneGeneStochasticNetworkMinimizableDirector.cpp [code]
OneGeneStochasticNetworkMinimizableDirector.h [code]
OneGeneStochasticNetworkRunDirector.cpp [code]
OneGeneStochasticNetworkRunDirector.h [code]
ParameterFilter.cpp [code]
ParameterFilter.h [code]
ParameterRandomizer.cpp [code]
ParameterRandomizer.h [code]
ParameterReader.cpp [code]
ParameterReader.h [code]
ParameterTranslator.cpp [code]
ParameterTranslator.h [code]
PC12AlternateEnsembleDirector.cpp [code]
PC12AlternateEnsembleDirector.h [code]
PC12AlternateMinimizableDirector.cpp [code]
PC12AlternateMinimizableDirector.h [code]
PC12EGFNGFEnsembleDirector.cpp [code]
PC12EGFNGFEnsembleDirector.h [code]
PC12EGFNGFMinimizableDirector.cpp [code]
PC12EGFNGFMinimizableDirector.h [code]
PC12EGFNGFRunDirector.cpp [code]
PC12EGFNGFRunDirector.h [code]
PC12ParameterTranslator.cpp [code]
PC12ParameterTranslator.h [code]
PC12RapMinusEnsembleDirector.cpp [code]
PC12RapMinusEnsembleDirector.h [code]
PC12RapMinusMinimizableDirector.cpp [code]
PC12RapMinusMinimizableDirector.h [code]
PC12RapMinusNetwork.cpp [code]
PC12RapMinusNetwork.h [code]
PeriodicQuenchMinimizer.cpp [code]
PeriodicQuenchMinimizer.h [code]
PlasmidReplicationReaction.cpp [code]
PlasmidReplicationReaction.h [code]
PoolTransitionReaction.cpp [code]
PoolTransitionReaction.h [code]
PositiveDefiniteLevenbergMarquardtMinimizer.cpp [code]
PositiveDefiniteLevenbergMarquardtMinimizer.h [code]
PromoterBindingReaction.cpp [code]
PromoterBindingReaction.h [code]
PromoterUnbindingReaction.cpp [code]
PromoterUnbindingReaction.h [code]
ProteinTranslationReaction.cpp [code]
ProteinTranslationReaction.h [code]
QualityControlCashKarpMover.cpp [code]
QualityControlCashKarpMover.h [code]
QualityControlRK2TMover.cpp [code]
QualityControlRK2TMover.h [code]
QualityControlRungeKuttaMover.cpp [code]
QualityControlRungeKuttaMover.h [code]
QuorumMaster.h [code]
QuorumSensingEnsembleDirector.cpp [code]
QuorumSensingEnsembleDirector.h [code]
QuorumSensingNetwork.cpp [code]
QuorumSensingNetwork.h [code]
QuorumSensingNetworkMinimizableDirector.cpp [code]
QuorumSensingNetworkMinimizableDirector.h [code]
QuorumSensingRunDirector.cpp [code]
QuorumSensingRunDirector.h [code]
Rand.h [code]
RateConstant.cpp [code]
RateConstant.h [code]
Reaction.cpp [code]
Reaction.h [code]
ReactionMover.cpp [code]
ReactionMover.h [code]
ReactionNetwork.cpp [code]
ReactionNetwork.h [code]
ReactionsMaster.h [code]
ReceptorBindingReaction.cpp [code]
ReceptorBindingReaction.h [code]
ReceptorUnbindingReaction.cpp [code]
ReceptorUnbindingReaction.h [code]
ReplicaMinimizableDirector.cpp [code]
ReplicaMinimizableDirector.h [code]
RK2ExplicitEulerHybridMover.cpp [code]
RK2ExplicitEulerHybridMover.h [code]
RK2TMover.cpp [code]
RK2TMover.h [code]
RK4Mover.cpp [code]
RK4Mover.h [code]
RNADegradationReaction.cpp [code]
RNADegradationReaction.h [code]
RobustLevenbergMarquardtMinimizer.cpp [code]
RobustLevenbergMarquardtMinimizer.h [code]
RowColumnSparseMatrix.cpp [code]
RowColumnSparseMatrix.h [code]
RunDirector.cpp [code]
RunDirector.h [code]
RungeKuttaMover.cpp [code]
RungeKuttaMover.h [code]
Runnable.cpp [code]
Runnable.h [code]
ScaleInvariantMarquardtMinimizer.cpp [code]
ScaleInvariantMarquardtMinimizer.h [code]
SharedBFactorNetworkMinimizable.cpp [code]
SharedBFactorNetworkMinimizable.h [code]
SharedParametersMinimizableDirector.cpp [code]
SharedParametersMinimizableDirector.h [code]
SharedPC12NetworksMinimizableDirector.cpp [code]
SharedPC12NetworksMinimizableDirector.h [code]
SimulatedAnnealingStrategy.cpp [code]
SimulatedAnnealingStrategy.h [code]
SingleNetworkMinimizable.cpp [code]
SingleNetworkMinimizable.h [code]
SingleNetworkMinimizableOLD.cpp [code]
SingleNetworkMinimizableOLD.h [code]
SloppyDataMinimizableDirector.cpp [code]
SloppyDataMinimizableDirector.h [code]
SmallErkSubnetwork.cpp [code]
SmallErkSubnetwork.h [code]
SparseMatrix.cpp [code]
SparseMatrix.h [code]
SquareRootParameterFilter.cpp [code]
SquareRootParameterFilter.h [code]
StdAfx.cpp [code]
StdAfx.h [code]
StiffBulirschStoerMover.cpp [code]
StiffBulirschStoerMover.h [code]
StochasticSensitivityAnalysis.cpp [code]
StochasticSensitivityAnalysis.h [code]
SubjectObserver.h [code]
SumChemical.cpp [code]
SumChemical.h [code]
SynchronizedCashKarpMover.cpp [code]
SynchronizedCashKarpMover.h [code]
SynchronizedRungeKuttaMover.cpp [code]
SynchronizedRungeKuttaMover.h [code]
TauNetwork.cpp [code]
TauNetwork.h [code]
TauReaction.cpp [code]
TauReaction.h [code]
Tester.cpp [code]
TimeVectorPoint.cpp [code]
TimeVectorPoint.h [code]
TranscriptionInducedByBindingReaction.cpp [code]
TranscriptionInducedByBindingReaction.h [code]
TranscriptionInhibitedByBindingReaction.cpp [code]
TranscriptionInhibitedByBindingReaction.h [code]
TranscriptionReaction.cpp [code]
TranscriptionReaction.h [code]
TransformationReaction.cpp [code]
TransformationReaction.h [code]
TranslationModelMinimizable.cpp [code]
TranslationModelMinimizable.h [code]
TrimerDissociation.cpp [code]
TrimerDissociation.h [code]
TrimerFormation.cpp [code]
TrimerFormation.h [code]
typedefs.h [code]
UnaryDegradationReaction.cpp [code]
UnaryDegradationReaction.h [code]
UnstableProteinDegradationReaction.cpp [code]
UnstableProteinDegradationReaction.h [code]
VariableStepsizeAnnealMinimizer.cpp [code]
VariableStepsizeAnnealMinimizer.h [code]
XYPoint.cpp [code]
XYPoint.h [code]
XYVector.cpp [code]
XYVector.h [code]
ZeroTAnnealMinimizer.cpp [code]
ZeroTAnnealMinimizer.h [code]

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