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AbstractWntOdeBasedCellCycleModel Class Referenceabstract

#include <AbstractWntOdeBasedCellCycleModel.hpp>

+ Inheritance diagram for AbstractWntOdeBasedCellCycleModel:
+ Collaboration diagram for AbstractWntOdeBasedCellCycleModel:

Public Member Functions

 AbstractWntOdeBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual ~AbstractWntOdeBasedCellCycleModel ()
 
void ResetForDivision ()
 
void UpdateCellProliferativeType ()
 
virtual void ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ()=0
 
double GetAverageTransitCellCycleTime ()
 
double GetAverageStemCellCycleTime ()
 
virtual 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 ()
 
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)
 
virtual void Initialise ()
 
virtual void InitialiseDaughterCell ()
 
CellPtr GetCell ()
 
void SetDimension (unsigned dimension)
 
unsigned GetDimension ()
 
double GetBirthTime () const
 
double GetAge ()
 
virtual bool ReadyToDivide ()
 
virtual AbstractCellCycleModel * CreateCellCycleModel ()=0
 
CellCyclePhase GetCurrentCellCyclePhase ()
 
virtual double GetG1Duration ()
 
double GetStemCellG1Duration ()
 
double GetTransitCellG1Duration ()
 
double GetSG2MDuration ()
 
virtual double GetSDuration ()
 
virtual double GetG2Duration ()
 
virtual double GetMDuration ()
 
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)
 

Protected Member Functions

double GetWntLevel ()
 
void UpdateCellCyclePhase ()
 
- Protected Member Functions inherited from CellCycleModelOdeHandler
bool SolveOdeToTime (double currentTime)
 
virtual void AdjustOdeParameters (double currentTime)
 

Private Member Functions

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

Friends

class boost::serialization::access
 

Additional Inherited Members

- 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

This class contains all the things common to the Wnt cell cycle ODE based models, the resetting method and updating of cell types etc.

The concrete models all need to operate with a WntConcentration singleton object.

These models have a constant length M phase, run ODEs to decide when to finish G1 phase, then add time for S and G2 phases (in some classes, random periods of time). The CellProliferativeType is updated dependent on the concentration of beta-catenin (given by one of the ODEs).

Definition at line 58 of file AbstractWntOdeBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel ( 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 38 of file AbstractWntOdeBasedCellCycleModel.cpp.

AbstractWntOdeBasedCellCycleModel::~AbstractWntOdeBasedCellCycleModel ( )
virtual

Destructor.

Definition at line 43 of file AbstractWntOdeBasedCellCycleModel.cpp.

Member Function Documentation

bool AbstractWntOdeBasedCellCycleModel::CanCellTerminallyDifferentiate ( )
virtual

Overridden CanCellTerminallyDifferentiate() method.

Returns
whether cell can terminally differentiate

Reimplemented from AbstractCellCycleModel.

Definition at line 123 of file AbstractWntOdeBasedCellCycleModel.cpp.

virtual void AbstractWntOdeBasedCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ( )
pure virtual

This must be implemented by subclasses to change cell type to reflect current levels of beta-catenin.

Implemented in WntCellCycleModel, and AbstractVanLeeuwen2009WntSwatCellCycleModel.

Referenced by UpdateCellProliferativeType().

double AbstractWntOdeBasedCellCycleModel::GetAverageStemCellCycleTime ( )
virtual

Overridden GetAverageStemCellCycleTime() method.

Returns
time

Reimplemented from AbstractCellCycleModel.

Definition at line 118 of file AbstractWntOdeBasedCellCycleModel.cpp.

double AbstractWntOdeBasedCellCycleModel::GetAverageTransitCellCycleTime ( )
virtual

Overridden GetAverageTransitCellCycleTime() method.

Returns
time

Reimplemented from AbstractCellCycleModel.

Definition at line 113 of file AbstractWntOdeBasedCellCycleModel.cpp.

double AbstractWntOdeBasedCellCycleModel::GetWntLevel ( )
protected
Returns
the Wnt level experienced by the cell.

Definition at line 47 of file AbstractWntOdeBasedCellCycleModel.cpp.

References WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::Instance(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, and NEVER_REACHED.

Referenced by AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(), WntCellCycleModel::AdjustOdeParameters(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), and WntCellCycleModel::Initialise().

void AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Outputs cell-cycle model parameters to file.

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from AbstractOdeBasedCellCycleModel.

Reimplemented in StochasticWntCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, WntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.

Definition at line 128 of file AbstractWntOdeBasedCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters().

Referenced by WntCellCycleModel::OutputCellCycleModelParameters(), and AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters().

void AbstractWntOdeBasedCellCycleModel::ResetForDivision ( )
virtual

Resets the Wnt 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 Wnt pathway proteins maintain their current values.

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

Reimplemented from AbstractOdeBasedCellCycleModel.

Reimplemented in StochasticWntCellCycleModel.

Definition at line 79 of file AbstractWntOdeBasedCellCycleModel.cpp.

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

Referenced by StochasticWntCellCycleModel::ResetForDivision().

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

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

Parameters
archivethe archive
versionthe current version of this class

Definition at line 71 of file AbstractWntOdeBasedCellCycleModel.hpp.

void AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase ( )
protectedvirtual

Call base class UpdateCellCyclePhase, then UpdateCellProliferativeType.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 95 of file AbstractWntOdeBasedCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::GetOdeStopTime(), SimulationTime::Instance(), CellCycleModelOdeHandler::mLastTime, AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), and UpdateCellProliferativeType().

void AbstractWntOdeBasedCellCycleModel::UpdateCellProliferativeType ( )

Updates the current cell type to reflect whether the beta-catenin level has dropped low enough to make it stop dividing. This should only be called when the cell-cycle model has been evaluated to the current time, or it may give misleading results.

Definition at line 106 of file AbstractWntOdeBasedCellCycleModel.cpp.

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

Referenced by UpdateCellCyclePhase().

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 63 of file AbstractWntOdeBasedCellCycleModel.hpp.

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