#include <AbstractOdeBasedPhaseBasedCellCycleModel.hpp>

Inheritance diagram for AbstractOdeBasedPhaseBasedCellCycleModel:

Collaboration diagram for AbstractOdeBasedPhaseBasedCellCycleModel:

Public Member Functions
	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)

virtual void	ResetForDivision ()

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

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	Initialise ()

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetDimension (unsigned dimension)

unsigned	GetDimension () const

double	GetBirthTime () const

double	GetAge ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0

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
	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)

virtual void	AdjustOdeParameters (double currentTime)

Protected Attributes
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

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

Detailed Description

This class contains all the functionality shared by 'ODE-based' cell-cycle models, where the duration of one or more cell cycle phases are evaluated 'on the fly' as the cell ages, according to a system of ordinary differential equations (ODEs) governing (for example) the concentrations of key intracellular proteins. To determine when cell division should occur, one or more stopping conditions for this ODE system may be specified.

This class of cell-cycle models is distinct from 'simple' cell-cycle models, where the duration of each cell cycle phase is determined when the cell-cycle model is created.

Definition at line 61 of file AbstractOdeBasedPhaseBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractOdeBasedPhaseBasedCellCycleModel::AbstractOdeBasedPhaseBasedCellCycleModel ( const AbstractOdeBasedPhaseBasedCellCycleModel & 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 AbstractOdeBasedPhaseBasedCellCycleModel.cpp.

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

Creates an AbstractOdeBasedPhaseBasedCellCycleModel, calls SetBirthTime on the AbstractPhaseBasedCellCycleModel to make sure that can be set 'back in time' for cells which did not divide at the current time.

Parameters

lastTime	The birth time of the cell / last time model was evaluated (defaults to the current SimulationTime)
pOdeSolver	An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 38 of file AbstractOdeBasedPhaseBasedCellCycleModel.cpp.

References AbstractCellCycleModel::SetBirthTime().

AbstractOdeBasedPhaseBasedCellCycleModel::~AbstractOdeBasedPhaseBasedCellCycleModel ( )

virtual

Destructor.

Definition at line 47 of file AbstractOdeBasedPhaseBasedCellCycleModel.cpp.

Member Function Documentation

double AbstractOdeBasedPhaseBasedCellCycleModel::GetOdeStopTime ( )

Get the time at which the ODE stopping event occurred. Only called in those subclasses for which stopping events are defined.

Returns: the time at which the ODE system reached its stopping event

Definition at line 159 of file AbstractOdeBasedPhaseBasedCellCycleModel.cpp.

References DOUBLE_UNSET, and CellCycleModelOdeHandler::mpOdeSolver.

Referenced by AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase(), and UpdateCellCyclePhase().

void AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Outputs cell cycle model parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractPhaseBasedCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, WntCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.

Definition at line 169 of file AbstractOdeBasedPhaseBasedCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::OutputCellCycleModelParameters().

Referenced by Alarcon2004OxygenBasedCellCycleModel::OutputCellCycleModelParameters(), and AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters().

void AbstractOdeBasedPhaseBasedCellCycleModel::ResetForDivision ( )

virtual

For a naturally cycling model this does not need to be overridden in the subclasses. But most models should override this function and then call AbstractOdeBasedPhaseBasedCellCycleModel::ResetForDivision() from inside their version.

Reimplemented from AbstractPhaseBasedCellCycleModel.

Reimplemented in StochasticWntCellCycleModel, AbstractWntOdeBasedCellCycleModel, and Alarcon2004OxygenBasedCellCycleModel.

Definition at line 148 of file AbstractOdeBasedPhaseBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mBirthTime, mDivideTime, CellCycleModelOdeHandler::mFinishedRunningOdes, AbstractPhaseBasedCellCycleModel::mG1Duration, CellCycleModelOdeHandler::mLastTime, and AbstractPhaseBasedCellCycleModel::ResetForDivision().

Referenced by Alarcon2004OxygenBasedCellCycleModel::ResetForDivision(), and AbstractWntOdeBasedCellCycleModel::ResetForDivision().

template<class Archive >

void AbstractOdeBasedPhaseBasedCellCycleModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the cell-cycle model and member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 74 of file AbstractOdeBasedPhaseBasedCellCycleModel.hpp.

References mDivideTime, and mG2PhaseStartTime.

void AbstractOdeBasedPhaseBasedCellCycleModel::SetBirthTime ( double birthTime )

virtual

This overrides the AbstractPhaseBasedCellCycleModel::SetBirthTime(double birthTime) because an ODE based cell-cycle model has more to reset...

Parameters

birthTime the simulation time when the cell was born

Reimplemented from AbstractCellCycleModel.

Definition at line 70 of file AbstractOdeBasedPhaseBasedCellCycleModel.cpp.

References mDivideTime, CellCycleModelOdeHandler::mLastTime, and AbstractCellCycleModel::SetBirthTime().

void AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase ( )

virtual

Default UpdateCellCyclePhase() method for an ODE-based cell-cycle model. This method calls SolveOdeToTime() for G1 phase and adds time for the other phases.

Can be overridden if they should do something more subtle.

Implements AbstractPhaseBasedCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel.

Definition at line 77 of file AbstractOdeBasedPhaseBasedCellCycleModel.cpp.

References EXCEPTION, AbstractCellCycleModel::GetAge(), AbstractPhaseBasedCellCycleModel::GetG2Duration(), AbstractPhaseBasedCellCycleModel::GetMDuration(), AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetOdeStopTime(), AbstractPhaseBasedCellCycleModel::GetSDuration(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellCycleModel::mBirthTime, AbstractPhaseBasedCellCycleModel::mCurrentCellCyclePhase, mDivideTime, CellCycleModelOdeHandler::mFinishedRunningOdes, AbstractPhaseBasedCellCycleModel::mG1Duration, mG2PhaseStartTime, CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SolveOdeToTime().