#include <UniformG1GenerationalCellCycleModel.hpp>

Inheritance diagram for UniformG1GenerationalCellCycleModel:

Collaboration diagram for UniformG1GenerationalCellCycleModel:

Public Member Functions
	UniformG1GenerationalCellCycleModel ()

AbstractCellCycleModel *	CreateCellCycleModel ()

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractSimpleGenerationalCellCycleModel
	AbstractSimpleGenerationalCellCycleModel ()

virtual	~AbstractSimpleGenerationalCellCycleModel ()

void	ResetForDivision ()

void	InitialiseDaughterCell ()

void	SetGeneration (unsigned generation)

unsigned	GetGeneration () const

void	SetMaxTransitGenerations (unsigned maxTransitGenerations)

unsigned	GetMaxTransitGenerations () const

Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel ()

virtual	~AbstractSimplePhaseBasedCellCycleModel ()

virtual void	UpdateCellCyclePhase ()

void	InitialiseDaughterCell ()

virtual void	Initialise ()

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)

CellPtr	GetCell ()

virtual void	SetBirthTime (double birthTime)

void	SetDimension (unsigned dimension)

unsigned	GetDimension () const

double	GetBirthTime () const

double	GetAge ()

virtual bool	CanCellTerminallyDifferentiate ()

void	OutputCellCycleModelInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
void	SetG1Duration ()

	UniformG1GenerationalCellCycleModel (const UniformG1GenerationalCellCycleModel &rModel)

Protected Member Functions inherited from AbstractSimpleGenerationalCellCycleModel
	AbstractSimpleGenerationalCellCycleModel (const AbstractSimpleGenerationalCellCycleModel &rModel)

Protected Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel (const AbstractSimplePhaseBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel (const AbstractCellCycleModel &rModel)

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

Friends
class	TestSimpleCellCycleModels

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractSimpleGenerationalCellCycleModel
unsigned	mGeneration

unsigned	mMaxTransitGenerations

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

Detailed Description

A stochastic cell-cycle model employed by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x). Cells that are proliferating are assigned G1 phase durations drawn from a uniform distribution, which differs between stem and transit amplifying cells. All other cell-cycle phases are held constant.

Definition at line 49 of file UniformG1GenerationalCellCycleModel.hpp.

Constructor & Destructor Documentation

UniformG1GenerationalCellCycleModel::UniformG1GenerationalCellCycleModel ( const UniformG1GenerationalCellCycleModel & 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 45 of file UniformG1GenerationalCellCycleModel.cpp.

UniformG1GenerationalCellCycleModel::UniformG1GenerationalCellCycleModel ( )

Constructor - just a default, mBirthTime is set in the AbstractCellCycleModel class. mG1Duration is set very high, it is set for the individual cells when InitialiseDaughterCell is called

Definition at line 41 of file UniformG1GenerationalCellCycleModel.cpp.

Referenced by CreateCellCycleModel(), and serialize().

Member Function Documentation

AbstractCellCycleModel * UniformG1GenerationalCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 66 of file UniformG1GenerationalCellCycleModel.cpp.

References UniformG1GenerationalCellCycleModel().

Referenced by serialize().

void UniformG1GenerationalCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractSimpleGenerationalCellCycleModel.

Definition at line 95 of file UniformG1GenerationalCellCycleModel.cpp.

References CHASTE_CLASS_EXPORT, and AbstractSimpleGenerationalCellCycleModel::OutputCellCycleModelParameters().

Referenced by serialize().

template<class Archive >

void UniformG1GenerationalCellCycleModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the cell-cycle model and random number generator, never used directly - boost uses this.

Parameters

archive	the archive
version	the current version of this class

Definition at line 64 of file UniformG1GenerationalCellCycleModel.hpp.

References CHASTE_CLASS_EXPORT, CreateCellCycleModel(), SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), RandomNumberGenerator::Instance(), OutputCellCycleModelParameters(), SetG1Duration(), and UniformG1GenerationalCellCycleModel().

void UniformG1GenerationalCellCycleModel::SetG1Duration ( )

protectedvirtual

Set the duration of G1 phase. This method is called on each cell at the start of a simulation, and for both daughter cells immediately following cell division.

If the cell associated with this cell-cycle model has stem proliferative type, then the G1 phase duration is drawn from the uniform distribution U[14,18]. If the cell has transit proliferative type (semi-differentiated), then the G1 phase duration is drawn from the uniform distribution U[4,6]. These two distributions, proposed by Meineke et al (doi:10.1046/j.0960-7722.2001.00216.x), reflect indirect biological observations that stem cells cycle more slowly than their progeny.

If the cell is differentiated, then the G1 phase duration is set to DBL_MAX, so that the cell will never reach the end of G1 phase.

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 71 of file UniformG1GenerationalCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::GetStemCellG1Duration(), AbstractPhaseBasedCellCycleModel::GetTransitCellG1Duration(), RandomNumberGenerator::Instance(), AbstractPhaseBasedCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, NEVER_REACHED, and RandomNumberGenerator::ranf().

Referenced by serialize().