#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 ()

double	GetOdeStopTime ()

void	SetBirthTime (double birthTime)

virtual bool	ReadyToDivide ()

virtual void	ResetForDivision ()

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 () const

double	GetBirthTime () const

double	GetAge ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0

virtual bool	CanCellTerminallyDifferentiate ()

virtual double	GetAverageTransitCellCycleTime ()=0

virtual double	GetAverageStemCellCycleTime ()=0

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
	AbstractOdeBasedCellCycleModel (const AbstractOdeBasedCellCycleModel &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

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 the cell cycle is 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 the cell cycle is determined when the cell-cycle model is created.

Definition at line 61 of file AbstractOdeBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel ( const AbstractOdeBasedCellCycleModel & 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 50 of file AbstractOdeBasedCellCycleModel.cpp.

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

Creates an AbstractOdeBasedCellCycleModel, 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 AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::SetBirthTime().

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel ( )

virtual

Destructor.

Definition at line 46 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 115 of file AbstractOdeBasedCellCycleModel.cpp.

References DOUBLE_UNSET, and CellCycleModelOdeHandler::mpOdeSolver.

Referenced by ReadyToDivide().

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.

Definition at line 125 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::OutputCellCycleModelParameters().

Referenced by TysonNovakCellCycleModel::OutputCellCycleModelParameters().

bool AbstractOdeBasedCellCycleModel::ReadyToDivide ( )

virtual

See AbstractCellCycleModel::ResetForDivision()

Returns: whether the cell is ready to divide (enter M phase).

Implements AbstractCellCycleModel.

Definition at line 70 of file AbstractOdeBasedCellCycleModel.cpp.

References EXCEPTION, AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetOdeStopTime(), SimulationTime::GetTime(), SimulationTime::Instance(), mDivideTime, CellCycleModelOdeHandler::mLastTime, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, AbstractCellCycleModel::mReadyToDivide, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SolveOdeToTime().

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 TysonNovakCellCycleModel.

Definition at line 106 of file AbstractOdeBasedCellCycleModel.cpp.

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

Referenced by TysonNovakCellCycleModel::ResetForDivision().

template<class Archive >