Chaste  Release::2018.1
Alarcon2004OxygenBasedCellCycleModel Class Reference

#include <Alarcon2004OxygenBasedCellCycleModel.hpp>

+ Inheritance diagram for Alarcon2004OxygenBasedCellCycleModel:
+ Collaboration diagram for Alarcon2004OxygenBasedCellCycleModel:

Public Member Functions

 Alarcon2004OxygenBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual void ResetForDivision ()
 
AbstractCellCycleModelCreateCellCycleModel ()
 
void Initialise ()
 
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 ()
 
virtual void UpdateCellCyclePhase ()
 
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)
 
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)
 
virtual void InitialiseDaughterCell ()
 
CellPtr GetCell ()
 
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
 
- Public Member Functions inherited from CellCycleModelOdeHandler
 CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual ~CellCycleModelOdeHandler ()
 
AbstractOdeSystemGetOdeSystem () 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< doubleGetProteinConcentrations () const
 
void SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
 

Protected Member Functions

 Alarcon2004OxygenBasedCellCycleModel (const Alarcon2004OxygenBasedCellCycleModel &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)
 

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
 
void AdjustOdeParameters (double currentTime)
 

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
 
AbstractOdeSystemmpOdeSystem
 
boost::shared_ptr
< AbstractCellCycleModelOdeSolver
mpOdeSolver
 
double mLastTime
 
bool mFinishedRunningOdes
 

Detailed Description

Oxygen-dependent ODE-based cell-cycle model.

Published by Alarcon et al. (doi:10.1016/j.jtbi.2004.04.016).

Definition at line 52 of file Alarcon2004OxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel ( const Alarcon2004OxygenBasedCellCycleModel 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
rModelthe cell cycle model to copy.

Definition at line 51 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References CellCycleModelOdeHandler::GetOdeSystem(), AbstractCellCycleModel::mpCell, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), CellCycleModelOdeHandler::SetOdeSystem(), and CellCycleModelOdeHandler::SetStateVariables().

Referenced by CreateCellCycleModel().

Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>())

Default constructor.

Parameters
pOdeSolverAn optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 40 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Member Function Documentation

void Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters ( double  currentTime)
privatevirtual

Adjust any ODE parameters needed before solving until currentTime.

Parameters
currentTimethe time up to which the system will be solved.

Reimplemented from CellCycleModelOdeHandler.

Definition at line 105 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

AbstractCellCycleModel * Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel ( )
virtual

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

Returns
new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 74 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References Alarcon2004OxygenBasedCellCycleModel().

void Alarcon2004OxygenBasedCellCycleModel::Initialise ( void  )
virtual

Initialise the cell-cycle model at the start of a simulation.

This overridden method sets up a new ODE system.

Reimplemented from AbstractCellCycleModel.

Definition at line 93 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

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

void Alarcon2004OxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Overridden OutputCellCycleModelParameters() method.

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.

Definition at line 115 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters().

void Alarcon2004OxygenBasedCellCycleModel::ResetForDivision ( )
virtual

Resets the oxygen-based 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 oxygen concentration maintains its current value.

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

Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.

Definition at line 79 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

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

template<class Archive >
void Alarcon2004OxygenBasedCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Archive the cell-cycle model and ODE system.

Parameters
archivethe archive
versionthe archive version

Definition at line 65 of file Alarcon2004OxygenBasedCellCycleModel.hpp.

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 57 of file Alarcon2004OxygenBasedCellCycleModel.hpp.


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