AbstractOdeBasedCellCycleModel Class Reference

#include <AbstractOdeBasedCellCycleModel.hpp>

Inheritance diagram for AbstractOdeBasedCellCycleModel:

Collaboration diagram for AbstractOdeBasedCellCycleModel:

List of all members.

Public Member Functions

AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance()->GetTime())

AbstractOdeBasedCellCycleModel (const AbstractOdeBasedCellCycleModel &rOtherModel)

virtual ~AbstractOdeBasedCellCycleModel ()

virtual void UpdateCellCyclePhase ()

virtual bool SolveOdeToTime (double currentTime)=0

virtual double GetOdeStopTime ()=0

void SetBirthTime (double birthTime)

std::vector< double > GetProteinConcentrations () const

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

virtual void ResetForDivision ()

Protected Attributes

AbstractOdeSystem * mpOdeSystem

double mLastTime

double mDivideTime

bool mFinishedRunningOdes

double mG2PhaseStartTime

Private Member Functions

template<class Archive>

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

Friends

class boost::serialization::access

Detailed Description

This class contains all the things common to standard cell cycle ODE models for intracellular protein concentrations (along the lines of Tyson & Novak), such as solving the ODEs until a stopping condition is met.

Definition at line 47 of file AbstractOdeBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel ( double lastTime = SimulationTime::Instance()->GetTime() )

Creates an AbstractOdeBasedCellCycleModel, calls SetBirthTime on the AbstractCellCycleModel to make sure that can be set 'back in time' for cells which did not divide at the current time.

Parameters:

lastTime

The birth time of the cell / last time model was evaluated (defaults to the current SimulationTime)

Definition at line 31 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::SetBirthTime().

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel ( const AbstractOdeBasedCellCycleModel & rOtherModel )

Copy constructor.

This is needed because we store and manage a pointer to an ODE system. Note that this class doesn't actually copy the ODE system, because each subclass will use a different type. Hence subclasses *must* copy their own ODE system in their copy constructor.

Parameters:

rOtherModel

the cell cycle model being copied.

Definition at line 42 of file AbstractOdeBasedCellCycleModel.cpp.

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel ( ) [virtual]

This destructor deletes the mpOdeSystem.

Definition at line 53 of file AbstractOdeBasedCellCycleModel.cpp.

References mpOdeSystem.

Member Function Documentation

template<class Archive>

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

Archive the cell cycle model and member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel, IngeWntSwatCellCycleModel, StochasticWntCellCycleModel, TysonNovakCellCycleModel, and WntCellCycleModel.

Definition at line 60 of file AbstractOdeBasedCellCycleModel.hpp.

References mDivideTime, mFinishedRunningOdes, mG2PhaseStartTime, mLastTime, mpOdeSystem, and AbstractOdeSystem::rGetStateVariables().

void AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase ( ) [virtual]

Default UpdateCellCyclePhase() method for an ODE-based cell cycle model. This method calls SolveOdeToTime() for G1 phase and adds time for the other phases.

Can be overridden if they should do something more subtle.

Implements AbstractCellCycleModel.

Definition at line 86 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::GetAge(), AbstractCellCycleModel::GetG2Duration(), AbstractCellCycleModel::GetMDuration(), AbstractOdeSystem::GetNumberOfStateVariables(), GetOdeStopTime(), AbstractCellCycleModel::GetSDuration(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCurrentCellCyclePhase, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, mG2PhaseStartTime, mLastTime, mpOdeSystem, AbstractOdeSystem::rGetStateVariables(), and SolveOdeToTime().

virtual bool AbstractOdeBasedCellCycleModel::SolveOdeToTime ( double currentTime ) [pure virtual]

This method must be implemented by each subclass - solves the ODEs to a given time.

Parameters:

currentTime

the current time

Returns:: Whether a stopping event occurred.

Implemented in IngeWntSwatCellCycleModel, TysonNovakCellCycleModel, and WntCellCycleModel.

Referenced by UpdateCellCyclePhase().

virtual double AbstractOdeBasedCellCycleModel::GetOdeStopTime ( ) [pure virtual]

This method must be implemented by each subclass

When the ODEs have reached a stopping event it returns the time at which the ODEs stopped running so a delay can be added in for S-G2-M phases if necessary.

Returns:: The time at which the ODE reached its stopping event.

Implemented in AbstractWntOdeBasedCellCycleModel, and TysonNovakCellCycleModel.

Referenced by UpdateCellCyclePhase().

void AbstractOdeBasedCellCycleModel::SetBirthTime ( double birthTime ) [virtual]

This overrides the AbstractCellCycleModel::SetBirthTime(double birthTime) because an ODE based cell cycle model has more to reset...

Parameters:

birthTime

the simulation time when the cell was born

Reimplemented from AbstractCellCycleModel.

Definition at line 62 of file AbstractOdeBasedCellCycleModel.cpp.

References mDivideTime, mLastTime, and AbstractCellCycleModel::SetBirthTime().

std::vector< double > AbstractOdeBasedCellCycleModel::GetProteinConcentrations ( ) const

Returns the protein concentrations at the current time (useful for tests)

NB: Will copy the vector - you can't use this to modify the concentrations.

Definition at line 70 of file AbstractOdeBasedCellCycleModel.cpp.

References mpOdeSystem, and AbstractOdeSystem::rGetStateVariables().

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

Sets the protein concentrations and time when the model was last evaluated - should only be called by tests

Parameters:

	lastTime	the SimulationTime at which the protein concentrations apply
	proteinConcentrations	a standard vector of doubles of protein concentrations

Definition at line 77 of file AbstractOdeBasedCellCycleModel.cpp.

References mLastTime, mpOdeSystem, AbstractOdeSystem::rGetStateVariables(), and AbstractOdeSystem::SetStateVariables().

void AbstractOdeBasedCellCycleModel::ResetForDivision ( ) [virtual]

For a naturally cycling model this does not need to be overridden in the subclasses. But most models should override this function and then call AbstractOdeBasedCellCycleModel::ResetForDivision() from inside their version.

Reimplemented from AbstractCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, and TysonNovakCellCycleModel.

Definition at line 158 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mBirthTime, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, mLastTime, and AbstractCellCycleModel::ResetForDivision().

Referenced by TysonNovakCellCycleModel::ResetForDivision(), and AbstractWntOdeBasedCellCycleModel::ResetForDivision().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel, IngeWntSwatCellCycleModel, StochasticWntCellCycleModel, TysonNovakCellCycleModel, and WntCellCycleModel.

Definition at line 52 of file AbstractOdeBasedCellCycleModel.hpp.

Member Data Documentation

AbstractOdeSystem* AbstractOdeBasedCellCycleModel::mpOdeSystem [protected]

The system of ODEs for the cell cycle model.

Definition at line 74 of file AbstractOdeBasedCellCycleModel.hpp.

Referenced by WntCellCycleModel::ChangeCellTypeDueToCurrentBetaCateninLevel(), IngeWntSwatCellCycleModel::ChangeCellTypeDueToCurrentBetaCateninLevel(), IngeWntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel(), IngeWntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel(), IngeWntSwatCellCycleModel::GetNuclearBetaCateninLevel(), GetProteinConcentrations(), IngeWntSwatCellCycleModel::IngeWntSwatCellCycleModel(), WntCellCycleModel::Initialise(), IngeWntSwatCellCycleModel::Initialise(), TysonNovakCellCycleModel::ResetForDivision(), AbstractWntOdeBasedCellCycleModel::ResetForDivision(), WntCellCycleModel::serialize(), IngeWntSwatCellCycleModel::serialize(), serialize(), SetProteinConcentrationsForTestsOnly(), WntCellCycleModel::SolveOdeToTime(), TysonNovakCellCycleModel::SolveOdeToTime(), IngeWntSwatCellCycleModel::SolveOdeToTime(), TysonNovakCellCycleModel::TysonNovakCellCycleModel(), UpdateCellCyclePhase(), AbstractWntOdeBasedCellCycleModel::UpdateCellType(), WntCellCycleModel::WntCellCycleModel(), and ~AbstractOdeBasedCellCycleModel().

double AbstractOdeBasedCellCycleModel::mLastTime [protected]

The last time the cell cycle ODEs were evaluated.

Definition at line 77 of file AbstractOdeBasedCellCycleModel.hpp.

Referenced by ResetForDivision(), serialize(), SetBirthTime(), SetProteinConcentrationsForTestsOnly(), WntCellCycleModel::SolveOdeToTime(), TysonNovakCellCycleModel::SolveOdeToTime(), IngeWntSwatCellCycleModel::SolveOdeToTime(), UpdateCellCyclePhase(), and AbstractWntOdeBasedCellCycleModel::UpdateCellType().

double AbstractOdeBasedCellCycleModel::mDivideTime [protected]

The time at which the cell should divide - Set this to DBL_MAX in constructor.

Definition at line 80 of file AbstractOdeBasedCellCycleModel.hpp.

Referenced by ResetForDivision(), serialize(), SetBirthTime(), and UpdateCellCyclePhase().

bool AbstractOdeBasedCellCycleModel::mFinishedRunningOdes [protected]

Whether the cell cycle model is currently in a delay (not solving ODEs).

Definition at line 83 of file AbstractOdeBasedCellCycleModel.hpp.

Referenced by ResetForDivision(), serialize(), and UpdateCellCyclePhase().

double AbstractOdeBasedCellCycleModel::mG2PhaseStartTime [protected]

The start time for the G2 phase

Definition at line 86 of file AbstractOdeBasedCellCycleModel.hpp.

Referenced by serialize(), and UpdateCellCyclePhase().

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

/tmp/release_1.1/cancer/src/tissue/cell/cycle/AbstractOdeBasedCellCycleModel.hpp
/tmp/release_1.1/cancer/src/tissue/cell/cycle/AbstractOdeBasedCellCycleModel.cpp


Public Member Functions
	AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance()->GetTime())
	AbstractOdeBasedCellCycleModel (const AbstractOdeBasedCellCycleModel &rOtherModel)
virtual	~AbstractOdeBasedCellCycleModel ()
virtual void	UpdateCellCyclePhase ()
virtual bool	SolveOdeToTime (double currentTime)=0
virtual double	GetOdeStopTime ()=0
void	SetBirthTime (double birthTime)
std::vector< double >	GetProteinConcentrations () const
void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
virtual void	ResetForDivision ()
Protected Attributes
AbstractOdeSystem *	mpOdeSystem
double	mLastTime
double	mDivideTime
bool	mFinishedRunningOdes
double	mG2PhaseStartTime
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access