Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <AbstractWntOdeBasedCellCycleModel.hpp>
Protected Member Functions | |
double | GetWntLevel () const |
void | UpdateCellCyclePhase () |
AbstractWntOdeBasedCellCycleModel (const AbstractWntOdeBasedCellCycleModel &rModel) | |
Protected Member Functions inherited from AbstractOdeBasedPhaseBasedCellCycleModel | |
AbstractOdeBasedPhaseBasedCellCycleModel (const AbstractOdeBasedPhaseBasedCellCycleModel &rModel) | |
Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel | |
AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel) | |
Protected Member Functions inherited from AbstractCellCycleModel | |
AbstractCellCycleModel (const AbstractCellCycleModel &rModel) | |
Protected Member Functions inherited from CellCycleModelOdeHandler | |
CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler) | |
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 AbstractOdeBasedPhaseBasedCellCycleModel | |
double | mDivideTime |
double | mG2PhaseStartTime |
Protected Attributes inherited from AbstractPhaseBasedCellCycleModel | |
CellCyclePhase | mCurrentCellCyclePhase |
double | mG1Duration |
double | mMinimumGapDuration |
double | mStemCellG1Duration |
double | mTransitCellG1Duration |
double | mSDuration |
double | mG2Duration |
double | mMDuration |
Protected Attributes inherited from AbstractCellCycleModel | |
CellPtr | mpCell |
double | mBirthTime |
bool | mReadyToDivide |
unsigned | mDimension |
Protected Attributes inherited from CellCycleModelOdeHandler | |
double | mDt |
AbstractOdeSystem * | mpOdeSystem |
boost::shared_ptr< AbstractCellCycleModelOdeSolver > | mpOdeSolver |
double | mLastTime |
bool | mFinishedRunningOdes |
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.
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protected |
Protected copy-constructor for use by CreateCellCycleModel. The only way for external code to create a copy of a cell cycle model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.
This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent cell cycle model will have had ResetForDivision() called just before CreateCellCycleModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().
rModel | the cell cycle model to copy. |
Definition at line 47 of file AbstractWntOdeBasedCellCycleModel.cpp.
AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel | ( | boost::shared_ptr< AbstractCellCycleModelOdeSolver > | pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() | ) |
Default constructor.
pOdeSolver | An 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.
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virtual |
Destructor.
Definition at line 43 of file AbstractWntOdeBasedCellCycleModel.cpp.
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virtual |
Overridden CanCellTerminallyDifferentiate() method.
Reimplemented from AbstractCellCycleModel.
Definition at line 141 of file AbstractWntOdeBasedCellCycleModel.cpp.
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pure virtual |
Change cell type to reflect current levels of beta-catenin.
As this method is pure virtual, it must be overridden in subclasses.
Implemented in AbstractVanLeeuwen2009WntSwatCellCycleModel, and WntCellCycleModel.
Referenced by UpdateCellProliferativeType().
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virtual |
Overridden GetAverageStemCellCycleTime() method.
Reimplemented from AbstractPhaseBasedCellCycleModel.
Definition at line 136 of file AbstractWntOdeBasedCellCycleModel.cpp.
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virtual |
Overridden GetAverageTransitCellCycleTime() method.
Reimplemented from AbstractPhaseBasedCellCycleModel.
Definition at line 131 of file AbstractWntOdeBasedCellCycleModel.cpp.
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protected |
Definition at line 65 of file AbstractWntOdeBasedCellCycleModel.cpp.
References WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::Instance(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, and NEVER_REACHED.
Referenced by VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::VanLeeuwen2009WntSwatCellCycleModelHypothesisOne(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo(), WntCellCycleModel::WntCellCycleModel(), AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(), WntCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), and WntCellCycleModel::Initialise().
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virtual |
Overridden OutputCellCycleModelParameters() method.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.
Reimplemented in AbstractVanLeeuwen2009WntSwatCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.
Definition at line 146 of file AbstractWntOdeBasedCellCycleModel.cpp.
References AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters().
Referenced by AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters(), and WntCellCycleModel::OutputCellCycleModelParameters().
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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 AbstractOdeBasedPhaseBasedCellCycleModel.
Reimplemented in StochasticWntCellCycleModel.
Definition at line 97 of file AbstractWntOdeBasedCellCycleModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), CellCycleModelOdeHandler::mpOdeSystem, AbstractOdeBasedPhaseBasedCellCycleModel::ResetForDivision(), and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by StochasticWntCellCycleModel::ResetForDivision().
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inlineprivate |
Archive the cell-cycle model, never used directly - boost uses this.
archive | the archive |
version | the current version of this class |
Definition at line 71 of file AbstractWntOdeBasedCellCycleModel.hpp.
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protectedvirtual |
Call base class UpdateCellCyclePhase, then UpdateCellProliferativeType.
Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.
Definition at line 113 of file AbstractWntOdeBasedCellCycleModel.cpp.
References AbstractOdeBasedPhaseBasedCellCycleModel::GetOdeStopTime(), SimulationTime::Instance(), CellCycleModelOdeHandler::mLastTime, AbstractOdeBasedPhaseBasedCellCycleModel::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 124 of file AbstractWntOdeBasedCellCycleModel.cpp.
References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractCellCycleModel::mpCell, and CellCycleModelOdeHandler::mpOdeSystem.
Referenced by UpdateCellCyclePhase().
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friend |
Needed for serialization.
Definition at line 63 of file AbstractWntOdeBasedCellCycleModel.hpp.