#include <SingleOdeWntCellCycleModel.hpp>

Inheritance diagram for SingleOdeWntCellCycleModel:

Collaboration diagram for SingleOdeWntCellCycleModel:

Public Member Functions
	SingleOdeWntCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

void	Initialise ()

void	UpdateCellCyclePhase ()

AbstractCellCycleModel *	CreateCellCycleModel ()

double	GetBetaCateninConcentration ()

void	SetBetaCateninDivisionThreshold (double betaCateninDivisionThreshold)

double	GetBetaCateninDivisionThreshold ()

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from SimpleWntCellCycleModel
	SimpleWntCellCycleModel ()

virtual void	InitialiseDaughterCell ()

void	SetUseCellProliferativeTypeDependentG1Duration (bool useCellProliferativeTypeDependentG1Duration=true)

virtual bool	CanCellTerminallyDifferentiate ()

double	GetWntStemThreshold ()

void	SetWntStemThreshold (double wntStemThreshold)

double	GetWntTransitThreshold ()

void	SetWntTransitThreshold (double wntTransitThreshold)

double	GetWntLabelledThreshold ()

void	SetWntLabelledThreshold (double wntLabelledThreshold)

Public Member Functions inherited from AbstractSimpleCellCycleModel
	AbstractSimpleCellCycleModel ()

virtual	~AbstractSimpleCellCycleModel ()

virtual void	ResetForDivision ()

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

CellPtr	GetCell ()

virtual void	SetBirthTime (double birthTime)

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 ()

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	ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ()

virtual void	AdjustOdeParameters (double currentTime)

Private Attributes
double	mBetaCateninDivisionThreshold

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from SimpleWntCellCycleModel
double	GetWntLevel ()

WntConcentrationType	GetWntType ()

void	SetG1Duration ()

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

Protected Attributes inherited from SimpleWntCellCycleModel
bool	mUseCellProliferativeTypeDependentG1Duration

double	mWntStemThreshold

double	mWntTransitThreshold

double	mWntLabelledThreshold

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

Wnt-dependent cell-cycle model. Needs to operate with a WntConcentration singleton object.

This model has a constant length M phase, runs ODEs to decide when to finish G1 phase then adds time for S and G2 phases. The CellProliferativeType is updated dependent on the concentration of beta-catenin (given by one of the ODEs).

Definition at line 58 of file SingleOdeWntCellCycleModel.hpp.

Constructor & Destructor Documentation

SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel ( 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 41 of file SingleOdeWntCellCycleModel.cpp.

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

Referenced by CreateCellCycleModel().

Member Function Documentation

void SingleOdeWntCellCycleModel::AdjustOdeParameters ( double currentTime )

privatevirtual

Adjust any ODE parameters needed before solving until currentTime. Defaults to do nothing.

Parameters

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

Reimplemented from CellCycleModelOdeHandler.

Definition at line 132 of file SingleOdeWntCellCycleModel.cpp.

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

void SingleOdeWntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ( )

private

Called by Initialise() and UpdateCellProliferativeType() only. Updates the mpCell::mCellProliferativeType to match mpOdeSystem's beta-catenin levels

This carries out the work for UpdateCellProliferativeType(); But does not check the current time so it can be used by the initialise method.

Definition at line 141 of file SingleOdeWntCellCycleModel.cpp.

References GetBetaCateninConcentration(), GetBetaCateninDivisionThreshold(), AbstractCellCycleModel::mpCell, and CellCycleModelOdeHandler::mpOdeSystem.

Referenced by Initialise(), and UpdateCellCyclePhase().

AbstractCellCycleModel * SingleOdeWntCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: the new cell-cycle model

Reimplemented from SimpleWntCellCycleModel.

Definition at line 60 of file SingleOdeWntCellCycleModel.cpp.

double SingleOdeWntCellCycleModel::GetBetaCateninConcentration ( )

Returns: the total beta-catenin concentration

Definition at line 169 of file SingleOdeWntCellCycleModel.cpp.

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

Referenced by ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel().

double SingleOdeWntCellCycleModel::GetBetaCateninDivisionThreshold ( )

Returns: mBetaCateninDivisionThreshold.

Definition at line 179 of file SingleOdeWntCellCycleModel.cpp.

References mBetaCateninDivisionThreshold.

Referenced by ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel().

void SingleOdeWntCellCycleModel::Initialise ( void )

virtual

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

This overridden method sets up a new WntCellCycleOdeSystem, sets the cell type according to the current beta catenin level and sets a random G2 duration.

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 112 of file SingleOdeWntCellCycleModel.cpp.

References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), SimpleWntCellCycleModel::GetWntLevel(), AbstractSimpleCellCycleModel::Initialise(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, CellCycleModelOdeHandler::SetLastTime(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().