#include <SimpleOxygenBasedCellCycleModel.hpp>

Inheritance diagram for SimpleOxygenBasedCellCycleModel:

Collaboration diagram for SimpleOxygenBasedCellCycleModel:

Public Member Functions
	SimpleOxygenBasedCellCycleModel ()

void	UpdateCellCyclePhase ()

void	UpdateHypoxicDuration ()

double	GetCurrentHypoxicDuration ()

double	GetCurrentHypoxiaOnsetTime ()

AbstractCellCycleModel *	CreateCellCycleModel ()

double	GetHypoxicConcentration ()

void	SetHypoxicConcentration (double hypoxicConcentration)

double	GetQuiescentConcentration ()

void	SetQuiescentConcentration (double quiescentConcentration)

double	GetCriticalHypoxicDuration ()

void	SetCriticalHypoxicDuration (double criticalHypoxicDuration)

void	SetCurrentHypoxiaOnsetTime (double currentHypoxiaOnsetTime)

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractSimpleCellCycleModel
	AbstractSimpleCellCycleModel ()

virtual	~AbstractSimpleCellCycleModel ()

virtual void	ResetForDivision ()

void	InitialiseDaughterCell ()

virtual void	Initialise ()

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 ()

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

Protected Attributes
double	mCurrentHypoxicDuration

double	mCurrentHypoxiaOnsetTime

double	mHypoxicConcentration

double	mQuiescentConcentration

double	mCriticalHypoxicDuration

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

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 AbstractSimpleCellCycleModel
virtual void	SetG1Duration ()

Detailed Description

Simple oxygen-based cell-cycle model.

A simple oxygen-dependent cell-cycle model that inherits from AbstractSimpleCellCycleModel. The duration of G1 phase depends on the local oxygen concentration. A prolonged period of acute hypoxia leads to the cell being labelled as apoptotic. This model allows for quiescence imposed by transient periods of hypoxia, followed by reoxygenation.

Definition at line 51 of file SimpleOxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel ( )

Constructor.

Definition at line 42 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), and mCurrentHypoxiaOnsetTime.

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * SimpleOxygenBasedCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: new cell-cycle model

Implements AbstractCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 89 of file SimpleOxygenBasedCellCycleModel.cpp.

double SimpleOxygenBasedCellCycleModel::GetCriticalHypoxicDuration ( )

Returns: mCriticalHypoxicDuration

Definition at line 185 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxiaOnsetTime ( )

Returns: mCurrentHypoxiaOnsetTime

Definition at line 56 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxicDuration ( )

Returns: mCurrentHypoxicDuration

Definition at line 51 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetHypoxicConcentration ( )

Returns: mHypoxicConcentration

Definition at line 161 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

double SimpleOxygenBasedCellCycleModel::GetQuiescentConcentration ( )

Returns: mQuiescentConcentration

Definition at line 173 of file SimpleOxygenBasedCellCycleModel.cpp.

References mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Outputs cell cycle model parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 202 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration, mHypoxicConcentration, mQuiescentConcentration, and AbstractSimpleCellCycleModel::OutputCellCycleModelParameters().

Referenced by StochasticOxygenBasedCellCycleModel::OutputCellCycleModelParameters().

template<class Archive >

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

inlineprivate

Boost Serialization method for archiving/checkpointing

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 62 of file SimpleOxygenBasedCellCycleModel.hpp.

References mCriticalHypoxicDuration, mCurrentHypoxiaOnsetTime, mCurrentHypoxicDuration, mHypoxicConcentration, and mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::SetCriticalHypoxicDuration ( double criticalHypoxicDuration )

Set method for mCriticalHypoxicDuration.

Parameters

criticalHypoxicDuration the new value of mCriticalHypoxicDuration

Definition at line 190 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleOxygenBasedCellCycleModel::SetCurrentHypoxiaOnsetTime ( double currentHypoxiaOnsetTime )

Set method for mCurrentHypoxiaOnsetTime.

Parameters

currentHypoxiaOnsetTime the new value of mCurrentHypoxiaOnsetTime

Definition at line 196 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleOxygenBasedCellCycleModel::SetHypoxicConcentration ( double hypoxicConcentration )

Set method for mHypoxicConcentration.

Parameters

hypoxicConcentration the new value of mHypoxicConcentration

Definition at line 166 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleOxygenBasedCellCycleModel::SetQuiescentConcentration ( double quiescentConcentration )

Set method for mQuiescentConcentration.

Parameters

quiescentConcentration the new value of mQuiescentConcentration

Definition at line 178 of file SimpleOxygenBasedCellCycleModel.cpp.

References mQuiescentConcentration.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase ( )

virtual

Overridden UpdateCellCyclePhase() method.

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 61 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimulationTime::GetTimeStep(), SimulationTime::Instance(), AbstractCellCycleModel::mCurrentCellCyclePhase, AbstractCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, mQuiescentConcentration, AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and UpdateHypoxicDuration().

void SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration ( )

Method for updating mCurrentHypoxicDuration, called at the start of ReadyToDivide().

Definition at line 123 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), RandomNumberGenerator::Instance(), mCriticalHypoxicDuration, mCurrentHypoxiaOnsetTime, mCurrentHypoxicDuration, mHypoxicConcentration, AbstractCellCycleModel::mpCell, and RandomNumberGenerator::ranf().

Referenced by UpdateCellCyclePhase().

Member Data Documentation

double SimpleOxygenBasedCellCycleModel::mCriticalHypoxicDuration

protected

Non-dimensionalized critical hypoxic duration. Has units of hours.

Definition at line 103 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetCriticalHypoxicDuration(), OutputCellCycleModelParameters(), serialize(), SetCriticalHypoxicDuration(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mCurrentHypoxiaOnsetTime

protected

The time when the current period of hypoxia began.

Definition at line 83 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetCurrentHypoxiaOnsetTime(), serialize(), SetCurrentHypoxiaOnsetTime(), SimpleOxygenBasedCellCycleModel(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mCurrentHypoxicDuration

protected

How long the current period of hypoxia has lasted. Has units of hours.

Definition at line 78 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by GetCurrentHypoxicDuration(), serialize(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mHypoxicConcentration

protected

Non-dimensionalized oxygen concentration below which cells are considered to be hypoxic. A prolonged period of hypoxia causes the cell to become apoptotic.

Definition at line 90 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetHypoxicConcentration(), OutputCellCycleModelParameters(), serialize(), SetHypoxicConcentration(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mQuiescentConcentration

protected

Non-dimensionalized oxygen concentration below which cells are considered to be quiescent and slow their progress through the G1 phase of the cell cycle.

Definition at line 97 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetQuiescentConcentration(), OutputCellCycleModelParameters(), serialize(), SetQuiescentConcentration(), and UpdateCellCyclePhase().

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

cell_based/src/cell/cycle/SimpleOxygenBasedCellCycleModel.hpp
cell_based/src/cell/cycle/SimpleOxygenBasedCellCycleModel.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation