AbstractOdeBasedCellCycleModel Class Reference

#include <AbstractOdeBasedCellCycleModel.hpp>

Inheritance diagram for AbstractOdeBasedCellCycleModel:

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List of all members.

Public Member Functions

 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)
virtual void ResetForDivision ()
void SetFinishedRunningOdes (bool finishedRunningOdes)
void SetDivideTime (double divideTime)
void SetG2PhaseStartTime (double g2PhaseStartTime)

Protected Attributes

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

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

Definition at line 36 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::SetBirthTime().

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel (  )  [virtual]

Destructor.

Definition at line 46 of file AbstractOdeBasedCellCycleModel.cpp.

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 Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 60 of file AbstractOdeBasedCellCycleModel.hpp.

References mDivideTime, mFinishedRunningOdes, and mG2PhaseStartTime.

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.

Reimplemented in AbstractWntOdeBasedCellCycleModel.

Definition at line 71 of file AbstractOdeBasedCellCycleModel.cpp.

References EXCEPTION, AbstractCellCycleModel::GetAge(), AbstractCellCycleModel::GetG2Duration(), AbstractCellCycleModel::GetMDuration(), AbstractParameterisedSystem< VECTOR >::GetNumberOfStateVariables(), GetOdeStopTime(), AbstractCellCycleModel::GetSDuration(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCurrentCellCyclePhase, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, mG2PhaseStartTime, CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SolveOdeToTime().

Referenced by AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase().

double AbstractOdeBasedCellCycleModel::GetOdeStopTime (  ) 

Get the time at which the ODE stopping event occurred. Only called in those subclasses for which stopping events are defined.

Returns:
the time at which the ODE system reached its stopping event

Definition at line 152 of file AbstractOdeBasedCellCycleModel.cpp.

References DOUBLE_UNSET, and CellCycleModelOdeHandler::mpOdeSolver.

Referenced by AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase(), and 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 50 of file AbstractOdeBasedCellCycleModel.cpp.

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

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), and TysonNovakCellCycleModel::CreateCellCycleModel().

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 57 of file AbstractOdeBasedCellCycleModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::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 63 of file AbstractOdeBasedCellCycleModel.cpp.

References CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::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 Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractWntOdeBasedCellCycleModel, and StochasticWntCellCycleModel.

Definition at line 141 of file AbstractOdeBasedCellCycleModel.cpp.

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

Referenced by AbstractWntOdeBasedCellCycleModel::ResetForDivision(), TysonNovakCellCycleModel::ResetForDivision(), and Alarcon2004OxygenBasedCellCycleModel::ResetForDivision().

void AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes ( bool  finishedRunningOdes  ) 

Set mFinishedRunningOdes. Used in CreateCellCycleModel().

Parameters:
finishedRunningOdes the new value of mFinishedRunningOdes

Definition at line 162 of file AbstractOdeBasedCellCycleModel.cpp.

References mFinishedRunningOdes.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetDivideTime ( double  divideTime  ) 

Set mDivideTime.

Parameters:
divideTime the new value of mDivideTime

Definition at line 167 of file AbstractOdeBasedCellCycleModel.cpp.

References mDivideTime.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime ( double  g2PhaseStartTime  ) 

Set mG2PhaseStartTime. Used in CreateCellCycleModel().

Parameters:
g2PhaseStartTime the new value of mG2PhaseStartTime

Definition at line 172 of file AbstractOdeBasedCellCycleModel.cpp.

References mG2PhaseStartTime.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractCellCycleModel.

Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 52 of file AbstractOdeBasedCellCycleModel.hpp.

Member Data Documentation

double AbstractOdeBasedCellCycleModel::mDivideTime [protected]

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

Definition at line 72 of file AbstractOdeBasedCellCycleModel.hpp.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), ResetForDivision(), serialize(), SetBirthTime(), SetDivideTime(), and UpdateCellCyclePhase().

bool AbstractOdeBasedCellCycleModel::mFinishedRunningOdes [protected]

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

Definition at line 75 of file AbstractOdeBasedCellCycleModel.hpp.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), ResetForDivision(), serialize(), SetFinishedRunningOdes(), and UpdateCellCyclePhase().

double AbstractOdeBasedCellCycleModel::mG2PhaseStartTime [protected]

The start time for the G2 phase.

Definition at line 78 of file AbstractOdeBasedCellCycleModel.hpp.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), serialize(), SetG2PhaseStartTime(), and UpdateCellCyclePhase().

The documentation for this class was generated from the following files:
Generated on Mon Nov 1 12:35:50 2010 for Chaste by  doxygen 1.5.5