#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 AbstractOdeBasedPhaseBasedCellCycleModel
	AbstractOdeBasedPhaseBasedCellCycleModel (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractOdeBasedPhaseBasedCellCycleModel ()

virtual void	UpdateCellCyclePhase ()

double	GetOdeStopTime ()

void	SetBirthTime (double birthTime)

Public Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel ()

virtual	~AbstractPhaseBasedCellCycleModel ()

virtual bool	ReadyToDivide ()

CellCyclePhase	GetCurrentCellCyclePhase () const

virtual double	GetG1Duration () const

double	GetStemCellG1Duration () const

double	GetTransitCellG1Duration () const

double	GetSG2MDuration () const

virtual double	GetSDuration () const

virtual double	GetG2Duration () const

virtual double	GetMDuration () const

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 ()

double	GetMinimumGapDuration () const

void	SetMinimumGapDuration (double minimumGapDuration)

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetDimension (unsigned dimension)

unsigned	GetDimension () const

double	GetBirthTime () const

double	GetAge ()

virtual bool	CanCellTerminallyDifferentiate ()

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)

std::vector< double >	GetProteinConcentrations () const

void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)

Protected Member Functions
	Alarcon2004OxygenBasedCellCycleModel (const Alarcon2004OxygenBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractOdeBasedPhaseBasedCellCycleModel
	AbstractOdeBasedPhaseBasedCellCycleModel (const AbstractOdeBasedPhaseBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel (const AbstractCellCycleModel &rModel)

Protected Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler)

bool	SolveOdeToTime (double currentTime)

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 Attributes inherited from AbstractOdeBasedPhaseBasedCellCycleModel
double	mDivideTime

double	mG2PhaseStartTime

Protected Attributes inherited from AbstractPhaseBasedCellCycleModel
CellCyclePhase	mCurrentCellCyclePhase

double	mG1Duration

double	mMinimumGapDuration

double	mStemCellG1Duration

double	mTransitCellG1Duration

double	mSDuration

double	mG2Duration

double	mMDuration

Protected Attributes inherited from AbstractCellCycleModel
CellPtr	mpCell

double	mBirthTime

bool	mReadyToDivide

unsigned	mDimension

Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr < AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

bool	mFinishedRunningOdes

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 52 of file Alarcon2004OxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel ( const Alarcon2004OxygenBasedCellCycleModel & rModel )

protected

Protected copy-constructor for use by CreateCellCycleModel. The only way for external code to create a copy of a cell cycle model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.

This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent cell cycle model will have had ResetForDivision() called just before CreateCellCycleModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Parameters

rModel the cell cycle model to copy.

Definition at line 51 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References CellCycleModelOdeHandler::GetOdeSystem(), AbstractCellCycleModel::mpCell, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), CellCycleModelOdeHandler::SetOdeSystem(), and CellCycleModelOdeHandler::SetStateVariables().

Referenced by CreateCellCycleModel().

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

Default constructor.

Parameters

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

Definition at line 40 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

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

Member Function Documentation

void Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters ( double currentTime )

privatevirtual

Adjust any ODE parameters needed before solving until currentTime.

Parameters

currentTime the time up to which the system will be solved.

Reimplemented from CellCycleModelOdeHandler.

Definition at line 105 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 74 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References Alarcon2004OxygenBasedCellCycleModel().

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 93 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractCellCycleModel::Initialise(), AbstractCellCycleModel::mpCell, and CellCycleModelOdeHandler::mpOdeSystem.

void Alarcon2004OxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.

Definition at line 115 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractOdeBasedPhaseBasedCellCycleModel::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 AbstractOdeBasedPhaseBasedCellCycleModel.

Definition at line 79 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

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

template<class Archive >