#include <AbstractOdeBasedCellCycleModel.hpp>

Inheritance diagram for AbstractOdeBasedCellCycleModel:

Collaboration diagram for AbstractOdeBasedCellCycleModel:

Public Member Functions
	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)

virtual void	ResetForDivision ()

void	SetFinishedRunningOdes (bool finishedRunningOdes)

void	SetDivideTime (double divideTime)

void	SetG2PhaseStartTime (double g2PhaseStartTime)

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

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 ()

double	GetBirthTime () const

double	GetAge ()

virtual bool	ReadyToDivide ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0

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)

Protected Attributes
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

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

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from CellCycleModelOdeHandler
bool	SolveOdeToTime (double currentTime)

virtual void	AdjustOdeParameters (double currentTime)

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 AbstractOdeBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

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

Creates an AbstractOdeBasedCellCycleModel, calls SetBirthTime on the AbstractCellCycleModel 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 41 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::SetBirthTime().

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel ( )

virtual

Destructor.

Definition at line 51 of file AbstractOdeBasedCellCycleModel.cpp.

Member Function Documentation

double AbstractOdeBasedCellCycleModel::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 158 of file AbstractOdeBasedCellCycleModel.cpp.

References DOUBLE_UNSET, and CellCycleModelOdeHandler::mpOdeSolver.

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

std::vector< double > AbstractOdeBasedCellCycleModel::GetProteinConcentrations ( ) const

Returns: the protein concentrations at the current time (useful for tests)

NB: Will copy the vector - you can't use this to modify the concentrations.

Definition at line 62 of file AbstractOdeBasedCellCycleModel.cpp.

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

Referenced by CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

void AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Outputs cell cycle model parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellCycleModel.

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

Definition at line 183 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::OutputCellCycleModelParameters().

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

void AbstractOdeBasedCellCycleModel::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 AbstractOdeBasedCellCycleModel::ResetForDivision() from inside their version.

Reimplemented from AbstractCellCycleModel.

Reimplemented in StochasticWntCellCycleModel, AbstractWntOdeBasedCellCycleModel, TysonNovakCellCycleModel, and Alarcon2004OxygenBasedCellCycleModel.

Definition at line 147 of file AbstractOdeBasedCellCycleModel.cpp.

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

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

template<class Archive >

void AbstractOdeBasedCellCycleModel::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 AbstractOdeBasedCellCycleModel.hpp.

References mDivideTime, mFinishedRunningOdes, and mG2PhaseStartTime.

void AbstractOdeBasedCellCycleModel::SetBirthTime ( double birthTime )

virtual

This overrides the AbstractCellCycleModel::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 55 of file AbstractOdeBasedCellCycleModel.cpp.

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

Referenced by VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and WntCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetDivideTime ( double divideTime )

Set mDivideTime.

Parameters

divideTime the new value of mDivideTime

Definition at line 173 of file AbstractOdeBasedCellCycleModel.cpp.

References mDivideTime.

Referenced by VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and WntCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes ( bool finishedRunningOdes )

Set mFinishedRunningOdes. Used in CreateCellCycleModel().

Parameters

finishedRunningOdes the new value of mFinishedRunningOdes

Definition at line 168 of file AbstractOdeBasedCellCycleModel.cpp.

References mFinishedRunningOdes.

Referenced by VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and WntCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime ( double g2PhaseStartTime )

Set mG2PhaseStartTime. Used in CreateCellCycleModel().

Parameters

g2PhaseStartTime the new value of mG2PhaseStartTime

Definition at line 178 of file AbstractOdeBasedCellCycleModel.cpp.

References mG2PhaseStartTime.

Referenced by VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and WntCellCycleModel::CreateCellCycleModel().

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

Sets the protein concentrations and time when the model was last evaluated - should only be called by tests

Parameters

lastTime	the SimulationTime at which the protein concentrations apply
proteinConcentrations	a standard vector of doubles of protein concentrations

Definition at line 68 of file AbstractOdeBasedCellCycleModel.cpp.

References CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().

void AbstractOdeBasedCellCycleModel::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 AbstractCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel.

Definition at line 76 of file AbstractOdeBasedCellCycleModel.cpp.

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