SimpleOxygenBasedCellCycleModel Class Reference

#include <SimpleOxygenBasedCellCycleModel.hpp>

Inherits AbstractSimpleCellCycleModel.

Inherited by StochasticOxygenBasedCellCycleModel.

Collaboration diagram for SimpleOxygenBasedCellCycleModel:
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List of all members.

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)

Protected Attributes

double mTimeSpentInG1Phase
double mCurrentHypoxicDuration
double mCurrentHypoxiaOnsetTime
double mHypoxicConcentration
double mQuiescentConcentration
double mCriticalHypoxicDuration

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 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 45 of file SimpleOxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel (  ) 

Constructor.

Definition at line 35 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.

Implements AbstractCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 108 of file SimpleOxygenBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCellProliferativeType, mCriticalHypoxicDuration, mCurrentHypoxiaOnsetTime, AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mG2Duration, mHypoxicConcentration, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, mQuiescentConcentration, AbstractCellCycleModel::mSDuration, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, AbstractCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetCellProliferativeType(), SetCriticalHypoxicDuration(), SetCurrentHypoxiaOnsetTime(), AbstractCellCycleModel::SetDimension(), AbstractCellCycleModel::SetG2Duration(), SetHypoxicConcentration(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), SetQuiescentConcentration(), AbstractCellCycleModel::SetSDuration(), AbstractCellCycleModel::SetStemCellG1Duration(), AbstractCellCycleModel::SetTransitCellG1Duration(), and SimpleOxygenBasedCellCycleModel().

double SimpleOxygenBasedCellCycleModel::GetCriticalHypoxicDuration (  ) 
Returns:
mCriticalHypoxicDuration

Definition at line 218 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxiaOnsetTime (  ) 
Returns:
mCurrentHypoxiaOnsetTime

Definition at line 50 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxicDuration (  ) 
Returns:
mCurrentHypoxicDuration

Definition at line 45 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetHypoxicConcentration (  ) 
Returns:
mHypoxicConcentration

Definition at line 194 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

double SimpleOxygenBasedCellCycleModel::GetQuiescentConcentration (  ) 
Returns:
mQuiescentConcentration

Definition at line 206 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 235 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration, mHypoxicConcentration, and mQuiescentConcentration.

template<class Archive >
void SimpleOxygenBasedCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archive the cell-cycle model.

Parameters:
archive the archive
version the current version of this class

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 51 of file SimpleOxygenBasedCellCycleModel.hpp.

References mCriticalHypoxicDuration, mCurrentHypoxiaOnsetTime, mCurrentHypoxicDuration, mHypoxicConcentration, mQuiescentConcentration, and mTimeSpentInG1Phase.

void SimpleOxygenBasedCellCycleModel::SetCriticalHypoxicDuration ( double  criticalHypoxicDuration  ) 

Set method for mCriticalHypoxicDuration.

Parameters:
criticalHypoxicDuration the new value of mCriticalHypoxicDuration

Definition at line 223 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 229 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 199 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 211 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 55 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimulationTime::GetTimeStep(), SimulationTime::Instance(), AbstractCellCycleModel::mCurrentCellCyclePhase, AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, mQuiescentConcentration, mTimeSpentInG1Phase, NEVER_REACHED, and UpdateHypoxicDuration().

void SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration (  ) 

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

Definition at line 143 of file SimpleOxygenBasedCellCycleModel.cpp.

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

Referenced by UpdateCellCyclePhase().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 49 of file SimpleOxygenBasedCellCycleModel.hpp.

Member Data Documentation

double SimpleOxygenBasedCellCycleModel::mCriticalHypoxicDuration [protected]

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

Definition at line 99 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 79 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 74 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 86 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 93 of file SimpleOxygenBasedCellCycleModel.hpp.

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

double SimpleOxygenBasedCellCycleModel::mTimeSpentInG1Phase [protected]

The time spent in G1 phase so far. Has units of hours.

Definition at line 68 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by serialize(), and UpdateCellCyclePhase().

The documentation for this class was generated from the following files:
Generated on Thu Dec 22 13:07:44 2011 for Chaste by  doxygen 1.6.3