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Alarcon2004OxygenBasedCellCycleModel Class Reference

#include <Alarcon2004OxygenBasedCellCycleModel.hpp>

+ Inheritance diagram for Alarcon2004OxygenBasedCellCycleModel:
+ Collaboration diagram for Alarcon2004OxygenBasedCellCycleModel:

Public Member Functions

 Alarcon2004OxygenBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual void ResetForDivision ()
 
AbstractCellCycleModel * CreateCellCycleModel ()
 
void Initialise ()
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractOdeBasedCellCycleModel
 AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual ~AbstractOdeBasedCellCycleModel ()
 
virtual void UpdateCellCyclePhase ()
 
double GetOdeStopTime ()
 
void SetBirthTime (double birthTime)
 
std::vector< double > GetProteinConcentrations () const
 
void SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
 
void SetFinishedRunningOdes (bool finishedRunningOdes)
 
void SetDivideTime (double divideTime)
 
void SetG2PhaseStartTime (double g2PhaseStartTime)
 
- Public Member Functions inherited from AbstractCellCycleModel
 AbstractCellCycleModel ()
 
virtual ~AbstractCellCycleModel ()
 
void SetCell (CellPtr pCell)
 
virtual void InitialiseDaughterCell ()
 
CellPtr GetCell ()
 
void SetDimension (unsigned dimension)
 
unsigned GetDimension ()
 
double GetBirthTime () const
 
double GetAge ()
 
virtual bool ReadyToDivide ()
 
CellCyclePhase GetCurrentCellCyclePhase ()
 
virtual double GetG1Duration ()
 
double GetStemCellG1Duration ()
 
double GetTransitCellG1Duration ()
 
double GetSG2MDuration ()
 
virtual double GetSDuration ()
 
virtual double GetG2Duration ()
 
virtual double GetMDuration ()
 
virtual void SetStemCellG1Duration (double stemCellG1Duration)
 
virtual void SetTransitCellG1Duration (double transitCellG1Duration)
 
void SetSDuration (double sDuration)
 
void SetG2Duration (double g2Duration)
 
void SetMDuration (double mDuration)
 
virtual double GetAverageTransitCellCycleTime ()
 
virtual double GetAverageStemCellCycleTime ()
 
virtual bool CanCellTerminallyDifferentiate ()
 
double GetMinimumGapDuration ()
 
void SetMinimumGapDuration (double minimumGapDuration)
 
void OutputCellCycleModelInfo (out_stream &rParamsFile)
 
- Public Member Functions inherited from Identifiable
virtual ~Identifiable ()
 
std::string GetIdentifier () const
 
- Public Member Functions inherited from CellCycleModelOdeHandler
 CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual ~CellCycleModelOdeHandler ()
 
AbstractOdeSystem * GetOdeSystem () const
 
void SetOdeSystem (AbstractOdeSystem *pOdeSystem)
 
const boost::shared_ptr
< AbstractCellCycleModelOdeSolver > 		GetOdeSolver () const
 
void SetLastTime (double lastTime)
 
double GetDt ()
 
void SetDt (double timeStep)
 
void SetStateVariables (const std::vector< double > &rStateVariables)
 

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
 
void AdjustOdeParameters (double currentTime)
 

Friends

class boost::serialization::access
 

Additional Inherited Members

- Protected Member Functions inherited from CellCycleModelOdeHandler
bool SolveOdeToTime (double currentTime)
 
- Protected Attributes inherited from AbstractOdeBasedCellCycleModel
double mDivideTime
 
bool mFinishedRunningOdes
 
double mG2PhaseStartTime
 
- Protected Attributes inherited from AbstractCellCycleModel
CellPtr mpCell
 
double mBirthTime
 
CellCyclePhase mCurrentCellCyclePhase
 
double mG1Duration
 
bool mReadyToDivide
 
unsigned mDimension
 
double mMinimumGapDuration
 
double mStemCellG1Duration
 
double mTransitCellG1Duration
 
double mSDuration
 
double mG2Duration
 
double mMDuration
 
- Protected Attributes inherited from CellCycleModelOdeHandler
double mDt
 
AbstractOdeSystem * mpOdeSystem
 
boost::shared_ptr
< AbstractCellCycleModelOdeSolver > 		mpOdeSolver
 
double mLastTime
 

Detailed Description

Oxygen-dependent ODE-based cell-cycle model.

Published by Alarcon et al. (doi:10.1016/j.jtbi.2004.04.016).

Definition at line 54 of file Alarcon2004OxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver >  pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>())

Default constructor.

Parameters
pOdeSolverAn optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 41 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Referenced by CreateCellCycleModel().

Member Function Documentation

void Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters ( double  currentTime)
privatevirtual

Adjust any ODE parameters needed before solving until currentTime.

Parameters
currentTimethe time up to which the system will be solved.

Reimplemented from CellCycleModelOdeHandler.

Definition at line 120 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

AbstractCellCycleModel * Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel ( )
virtual

Overridden builder method to create new copies of this cell-cycle model.

Returns
new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 66 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References Alarcon2004OxygenBasedCellCycleModel(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mDimension, AbstractOdeBasedCellCycleModel::mDivideTime, AbstractOdeBasedCellCycleModel::mFinishedRunningOdes, AbstractCellCycleModel::mG2Duration, AbstractOdeBasedCellCycleModel::mG2PhaseStartTime, CellCycleModelOdeHandler::mLastTime, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSolver, CellCycleModelOdeHandler::mpOdeSystem, AbstractCellCycleModel::mSDuration, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), AbstractOdeBasedCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetDimension(), AbstractOdeBasedCellCycleModel::SetDivideTime(), AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes(), AbstractCellCycleModel::SetG2Duration(), AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime(), CellCycleModelOdeHandler::SetLastTime(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), CellCycleModelOdeHandler::SetOdeSystem(), AbstractCellCycleModel::SetSDuration(), CellCycleModelOdeHandler::SetStateVariables(), AbstractCellCycleModel::SetStemCellG1Duration(), and AbstractCellCycleModel::SetTransitCellG1Duration().

void Alarcon2004OxygenBasedCellCycleModel::Initialise ( void  )
virtual

Initialise the cell-cycle model at the start of a simulation.

This overridden method sets up a new ODE system.

Reimplemented from AbstractCellCycleModel.

Definition at line 108 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mpCell, and CellCycleModelOdeHandler::mpOdeSystem.

void Alarcon2004OxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Outputs cell cycle model parameters to files.

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 131 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters().

void Alarcon2004OxygenBasedCellCycleModel::ResetForDivision ( )
virtual

Resets the oxygen-based model to the start of the cell cycle (this model does not cycle naturally). Cells are given a new birth time and cell cycle proteins are reset. Note that the oxygen concentration maintains its current value.

Should only be called by the Cell Divide() method.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 52 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), CellCycleModelOdeHandler::mpOdeSystem, AbstractOdeBasedCellCycleModel::ResetForDivision(), and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

template<class Archive >
void Alarcon2004OxygenBasedCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Archive the cell-cycle model and ODE system.

Parameters
archivethe archive
versionthe archive version

Definition at line 67 of file Alarcon2004OxygenBasedCellCycleModel.hpp.

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 59 of file Alarcon2004OxygenBasedCellCycleModel.hpp.

The documentation for this class was generated from the following files: