#include <AbstractWntOdeBasedCellCycleModel.hpp>

Inheritance diagram for AbstractWntOdeBasedCellCycleModel:

Collaboration diagram for AbstractWntOdeBasedCellCycleModel:

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

virtual	~AbstractWntOdeBasedCellCycleModel ()

void	ResetForDivision ()

void	UpdateCellProliferativeType ()

virtual void	ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ()=0

double	GetAverageTransitCellCycleTime ()

double	GetAverageStemCellCycleTime ()

virtual bool	CanCellTerminallyDifferentiate ()

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 ()

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)

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

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
double	GetWntLevel () const

void	UpdateCellCyclePhase ()

	AbstractWntOdeBasedCellCycleModel (const AbstractWntOdeBasedCellCycleModel &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)

virtual void	AdjustOdeParameters (double currentTime)

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

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

This class contains all the things common to the Wnt cell cycle ODE based models, the resetting method and updating of cell types etc.

The concrete models all need to operate with a WntConcentration singleton object.

These models have a constant length M phase, run ODEs to decide when to finish G1 phase, then add time for S and G2 phases (in some classes, random periods of time). The CellProliferativeType is updated dependent on the concentration of beta-catenin (given by one of the ODEs).

Definition at line 58 of file AbstractWntOdeBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel ( const AbstractWntOdeBasedCellCycleModel & 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 47 of file AbstractWntOdeBasedCellCycleModel.cpp.

AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel ( 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 38 of file AbstractWntOdeBasedCellCycleModel.cpp.

AbstractWntOdeBasedCellCycleModel::~AbstractWntOdeBasedCellCycleModel ( )

virtual

Destructor.

Definition at line 43 of file AbstractWntOdeBasedCellCycleModel.cpp.

Member Function Documentation

bool AbstractWntOdeBasedCellCycleModel::CanCellTerminallyDifferentiate ( )

virtual

Overridden CanCellTerminallyDifferentiate() method.

Returns: whether cell can terminally differentiate

Reimplemented from AbstractCellCycleModel.

Definition at line 141 of file AbstractWntOdeBasedCellCycleModel.cpp.

virtual void AbstractWntOdeBasedCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ( )

pure virtual

Change cell type to reflect current levels of beta-catenin.

As this method is pure virtual, it must be overridden in subclasses.

Implemented in WntCellCycleModel, and AbstractVanLeeuwen2009WntSwatCellCycleModel.

Referenced by UpdateCellProliferativeType().

double AbstractWntOdeBasedCellCycleModel::GetAverageStemCellCycleTime ( )

virtual

Overridden GetAverageStemCellCycleTime() method.

Returns: time

Reimplemented from AbstractPhaseBasedCellCycleModel.

Definition at line 136 of file AbstractWntOdeBasedCellCycleModel.cpp.

double AbstractWntOdeBasedCellCycleModel::GetAverageTransitCellCycleTime ( )

virtual

Overridden GetAverageTransitCellCycleTime() method.

Returns: time

Reimplemented from AbstractPhaseBasedCellCycleModel.

Definition at line 131 of file AbstractWntOdeBasedCellCycleModel.cpp.

double AbstractWntOdeBasedCellCycleModel::GetWntLevel ( ) const

protected

Returns: the Wnt level experienced by the cell.

Definition at line 65 of file AbstractWntOdeBasedCellCycleModel.cpp.

References WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::Instance(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, and NEVER_REACHED.

Referenced by AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(), WntCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), WntCellCycleModel::Initialise(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::VanLeeuwen2009WntSwatCellCycleModelHypothesisOne(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo(), and WntCellCycleModel::WntCellCycleModel().

void AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.

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

Definition at line 146 of file AbstractWntOdeBasedCellCycleModel.cpp.

References AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters().

Referenced by WntCellCycleModel::OutputCellCycleModelParameters(), and AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters().

void AbstractWntOdeBasedCellCycleModel::ResetForDivision ( )

virtual

Resets the Wnt 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 Wnt pathway proteins maintain their current values.

Should only be called by the Cell::Divide() method.

Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.

Reimplemented in StochasticWntCellCycleModel.

Definition at line 97 of file AbstractWntOdeBasedCellCycleModel.cpp.

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

Referenced by StochasticWntCellCycleModel::ResetForDivision().

template<class Archive >

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

inlineprivate

Archive the cell-cycle model, never used directly - boost uses this.

Parameters

archive	the archive
version	the current version of this class

Definition at line 71 of file AbstractWntOdeBasedCellCycleModel.hpp.

void AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase ( )

protectedvirtual

Call base class UpdateCellCyclePhase, then UpdateCellProliferativeType.

Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.

Definition at line 113 of file AbstractWntOdeBasedCellCycleModel.cpp.

References AbstractOdeBasedPhaseBasedCellCycleModel::GetOdeStopTime(), SimulationTime::Instance(), CellCycleModelOdeHandler::mLastTime, AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase(), and UpdateCellProliferativeType().

void AbstractWntOdeBasedCellCycleModel::UpdateCellProliferativeType ( )

Updates the current cell type to reflect whether the beta-catenin level has dropped low enough to make it stop dividing. This should only be called when the cell-cycle model has been evaluated to the current time, or it may give misleading results.

Definition at line 124 of file AbstractWntOdeBasedCellCycleModel.cpp.

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

Referenced by UpdateCellCyclePhase().

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 63 of file AbstractWntOdeBasedCellCycleModel.hpp.

The documentation for this class was generated from the following files:

crypt/src/cell/cycle/AbstractWntOdeBasedCellCycleModel.hpp
crypt/src/cell/cycle/AbstractWntOdeBasedCellCycleModel.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation