#include <TysonNovakCellCycleModel.hpp>

Inheritance diagram for TysonNovakCellCycleModel:

Collaboration diagram for TysonNovakCellCycleModel:

Public Member Functions
	TysonNovakCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

void	Initialise ()

void	ResetForDivision ()

AbstractCellCycleModel *	CreateCellCycleModel ()

double	GetSDuration ()

double	GetG2Duration ()

double	GetMDuration ()

void	InitialiseDaughterCell ()

double	GetAverageTransitCellCycleTime ()

double	GetAverageStemCellCycleTime ()

bool	CanCellTerminallyDifferentiate ()

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractOdeBasedCellCycleModel
	AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractOdeBasedCellCycleModel ()

virtual void	UpdateCellCyclePhase ()

double	GetOdeStopTime ()

void	SetBirthTime (double birthTime)

std::vector< double >	GetProteinConcentrations () const

void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)

void	SetFinishedRunningOdes (bool finishedRunningOdes)

void	SetDivideTime (double divideTime)

void	SetG2PhaseStartTime (double g2PhaseStartTime)

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

CellPtr	GetCell ()

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 void	SetStemCellG1Duration (double stemCellG1Duration)

virtual void	SetTransitCellG1Duration (double transitCellG1Duration)

void	SetSDuration (double sDuration)

void	SetG2Duration (double g2Duration)

void	SetMDuration (double mDuration)

double	GetMinimumGapDuration ()

void	SetMinimumGapDuration (double minimumGapDuration)

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 ()

AbstractOdeSystem *	GetOdeSystem () 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)

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

Friends
class	TestOdeBasedCellCycleModels

class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from CellCycleModelOdeHandler
bool	SolveOdeToTime (double currentTime)

virtual void	AdjustOdeParameters (double currentTime)

Protected Attributes inherited from AbstractOdeBasedCellCycleModel
double	mDivideTime

bool	mFinishedRunningOdes

double	mG2PhaseStartTime

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

Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr < AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

Detailed Description

Tyson-Novak 2001 cell-cycle model, taken from the version at doi:10.1006/jtbi.2001.2293

Note that this is not a model for murine or human colonic-cell cycling, but is included in chaste as one of the most commonly known ODE based cell-cycle models.

Time taken to progress through the cycle is deterministic and given by an ODE system independent of external factors.

Definition at line 55 of file TysonNovakCellCycleModel.hpp.

Constructor & Destructor Documentation

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

Default constructor.

Parameters

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

Definition at line 40 of file TysonNovakCellCycleModel.cpp.

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

Referenced by CreateCellCycleModel().

Member Function Documentation

bool TysonNovakCellCycleModel::CanCellTerminallyDifferentiate ( )

virtual

Overridden CanCellTerminallyDifferentiate() method.

Returns: whether cell can terminally differentiate

Reimplemented from AbstractCellCycleModel.

Definition at line 199 of file TysonNovakCellCycleModel.cpp.

AbstractCellCycleModel * TysonNovakCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 114 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetAverageStemCellCycleTime ( )

virtual

Overridden GetAverageStemCellCycleTime() method.

Returns: time

Reimplemented from AbstractCellCycleModel.

Definition at line 194 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetAverageTransitCellCycleTime ( )

virtual

Overridden GetAverageTransitCellCycleTime() method.

Returns: time

Reimplemented from AbstractCellCycleModel.

Definition at line 189 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetG2Duration ( )

virtual

Returns: the duration of the cell's G2 phase.

Tyson & Novak pretends it is running ODEs in just G1, but they really represent the whole cell cycle so we set the other phases to zero.

Reimplemented from AbstractCellCycleModel.

Definition at line 169 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetMDuration ( )

virtual

Returns: the duration of the cell's M phase.

Tyson & Novak pretends it is running ODEs in just G1, but they really represent the whole cell cycle so we set the other phases to zero.

Reimplemented from AbstractCellCycleModel.

Definition at line 179 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetSDuration ( )

virtual

Returns: the duration of the cell's S phase.

Tyson & Novak pretends it is running ODEs in just G1, but they really represent the whole cell cycle, so we set the other phases to zero.

Reimplemented from AbstractCellCycleModel.

Definition at line 159 of file TysonNovakCellCycleModel.cpp.

void TysonNovakCellCycleModel::Initialise ( void )

virtual

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

This method will be called precisely once per cell set up in the initial cell population. It is not called on cell division; use ResetForDivision(), CreateCellCycleModel() and InitialiseDaughterCell() for that.

By the time this is called, a CellPopulation will have been set up, so the model can know where its cell is located in space. If relevant to the simulation, any singletons will also have been initialised.

Reimplemented from AbstractCellCycleModel.

Definition at line 61 of file TysonNovakCellCycleModel.cpp.

References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractCellCycleModel::Initialise(), CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetStateVariables().

void TysonNovakCellCycleModel::InitialiseDaughterCell ( )

virtual

If the daughter cell type is stem, change it to transit.

Reimplemented from AbstractCellCycleModel.

Definition at line 95 of file TysonNovakCellCycleModel.cpp.

References AbstractCellCycleModel::mpCell.

void TysonNovakCellCycleModel::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 AbstractOdeBasedCellCycleModel.

Definition at line 204 of file TysonNovakCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters().

void TysonNovakCellCycleModel::ResetForDivision ( )

virtual

Reset cell-cycle model by calling AbstractOdeBasedCellCycleModelWithStoppingEvent::ResetForDivision() and setting initial conditions for protein concentrations.

This model needs the protein concentrations and phase resetting to G0/G1.

In theory, the solution to the Tyson-Novak equations should exhibit stable oscillations, and we only need to halve the mass of the cell each period.

However, the backward Euler solver used to solve the equations currently returns a solution that diverges after long times, so we must reset the initial conditions each period.

When running with CVODE however we can use the halving the mass of the cell method.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 70 of file TysonNovakCellCycleModel.cpp.

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

template<class Archive >