SimpleOxygenBasedCellCycleModel Class Reference

#include <SimpleOxygenBasedCellCycleModel.hpp>

Inheritance diagram for SimpleOxygenBasedCellCycleModel:

Collaboration diagram for SimpleOxygenBasedCellCycleModel:

Public Member Functions
	SimpleOxygenBasedCellCycleModel ()
void	UpdateCellCyclePhase ()
void	UpdateHypoxicDuration ()
double	GetCurrentHypoxicDuration () const
double	GetCurrentHypoxiaOnsetTime () const
AbstractCellCycleModel *	CreateCellCycleModel ()
double	GetHypoxicConcentration () const
void	SetHypoxicConcentration (double hypoxicConcentration)
double	GetQuiescentConcentration () const
void	SetQuiescentConcentration (double quiescentConcentration)
double	GetCriticalHypoxicDuration () const
void	SetCriticalHypoxicDuration (double criticalHypoxicDuration)
void	SetCurrentHypoxiaOnsetTime (double currentHypoxiaOnsetTime)
virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel ()
virtual	~AbstractSimplePhaseBasedCellCycleModel ()
virtual void	ResetForDivision ()
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
	SimpleOxygenBasedCellCycleModel (const SimpleOxygenBasedCellCycleModel &rModel)
Protected Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
virtual void	SetG1Duration ()
	AbstractSimplePhaseBasedCellCycleModel (const AbstractSimplePhaseBasedCellCycleModel &rModel)
Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)
Protected Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel (const AbstractCellCycleModel &rModel)

Protected Attributes
double	mCurrentHypoxicDuration
double	mCurrentHypoxiaOnsetTime
double	mHypoxicConcentration
double	mQuiescentConcentration
double	mCriticalHypoxicDuration
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

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

Friends
class	boost::serialization::access

Detailed Description

Simple oxygen-based cell-cycle model.

A simple oxygen-dependent cell-cycle model that inherits from AbstractSimplePhaseBasedCellCycleModel. 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 ( const SimpleOxygenBasedCellCycleModel &  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 87 of file SimpleOxygenBasedCellCycleModel.cpp.

SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel

(

)

Constructor.

Definition at line 40 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 111 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimpleOxygenBasedCellCycleModel().

double SimpleOxygenBasedCellCycleModel::GetCriticalHypoxicDuration

(

)

const

Returns

mCriticalHypoxicDuration

Definition at line 178 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxiaOnsetTime

(

)

const

Returns

mCurrentHypoxiaOnsetTime

Definition at line 54 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxicDuration

(

)

const

Returns

mCurrentHypoxicDuration

Definition at line 49 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetHypoxicConcentration

(

)

const

Returns

mHypoxicConcentration

Definition at line 154 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

double SimpleOxygenBasedCellCycleModel::GetQuiescentConcentration

(

)

const

Returns

mQuiescentConcentration

Definition at line 166 of file SimpleOxygenBasedCellCycleModel.cpp.

References mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 195 of file SimpleOxygenBasedCellCycleModel.cpp.

References CHASTE_CLASS_EXPORT, mCriticalHypoxicDuration, mHypoxicConcentration, mQuiescentConcentration, and AbstractSimplePhaseBasedCellCycleModel::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 183 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

void SimpleOxygenBasedCellCycleModel::SetCurrentHypoxiaOnsetTime

(

double

currentHypoxiaOnsetTime

)

Set method for mCurrentHypoxiaOnsetTime.

Parameters

currentHypoxiaOnsetTime

the new value of mCurrentHypoxiaOnsetTime

Definition at line 189 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

void SimpleOxygenBasedCellCycleModel::SetHypoxicConcentration

(

double

hypoxicConcentration

)

Set method for mHypoxicConcentration.

Parameters

hypoxicConcentration

the new value of mHypoxicConcentration

Definition at line 159 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

void SimpleOxygenBasedCellCycleModel::SetQuiescentConcentration

(

double

quiescentConcentration

)

Set method for mQuiescentConcentration.

Parameters

quiescentConcentration

the new value of mQuiescentConcentration

Definition at line 171 of file SimpleOxygenBasedCellCycleModel.cpp.

References mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase ( )

virtual

Overridden UpdateCellCyclePhase() method.

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 59 of file SimpleOxygenBasedCellCycleModel.cpp.

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

void SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration

(

)

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

Definition at line 116 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 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 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 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 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