TysonNovakCellCycleModel Class Reference

#include <TysonNovakCellCycleModel.hpp>

Inheritance diagram for TysonNovakCellCycleModel:

Collaboration diagram for TysonNovakCellCycleModel:

List of all members.

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)

Private Member Functions

template<class Archive>

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

Friends

class TestOdeBasedCellCycleModels

class boost::serialization::access

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 47 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 31 of file TysonNovakCellCycleModel.cpp.

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

Referenced by CreateCellCycleModel().

Member Function Documentation

template<class Archive>

void TysonNovakCellCycleModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the cell-cycle model, never used directly - boost uses this.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 62 of file TysonNovakCellCycleModel.hpp.

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, the CellwiseData and/or other singletons will also have been initialised.

Reimplemented from AbstractCellCycleModel.

Definition at line 52 of file TysonNovakCellCycleModel.cpp.

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

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 61 of file TysonNovakCellCycleModel.cpp.

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

AbstractCellCycleModel * TysonNovakCellCycleModel::CreateCellCycleModel ( ) [virtual]

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

Implements AbstractCellCycleModel.

Definition at line 94 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetSDuration ( ) [virtual]

Get 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 140 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetG2Duration ( ) [virtual]

Get 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 150 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetMDuration ( ) [virtual]

Get 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 160 of file TysonNovakCellCycleModel.cpp.

void TysonNovakCellCycleModel::InitialiseDaughterCell ( ) [virtual]

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

Reimplemented from AbstractCellCycleModel.

Definition at line 86 of file TysonNovakCellCycleModel.cpp.

References AbstractCellCycleModel::mCellProliferativeType.

double TysonNovakCellCycleModel::GetAverageTransitCellCycleTime ( ) [virtual]

Overridden GetAverageTransitCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 170 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetAverageStemCellCycleTime ( ) [virtual]

Overridden GetAverageStemCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 175 of file TysonNovakCellCycleModel.cpp.

bool TysonNovakCellCycleModel::CanCellTerminallyDifferentiate ( ) [virtual]

Overridden CanCellTerminallyDifferentiate() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 181 of file TysonNovakCellCycleModel.cpp.

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 186 of file TysonNovakCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 54 of file TysonNovakCellCycleModel.hpp.

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

cell_based/src/population/cell/cycle/TysonNovakCellCycleModel.hpp
cell_based/src/population/cell/cycle/TysonNovakCellCycleModel.cpp


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)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	TestOdeBasedCellCycleModels
class	boost::serialization::access