#include <WntCellCycleModel.hpp>
Inheritance diagram for WntCellCycleModel:
Collaboration diagram for WntCellCycleModel:
Public Member Functions | |
| WntCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >()) | |
| AbstractCellCycleModel * | CreateCellCycleModel () |
| void | Initialise () |
| virtual void | OutputCellCycleModelParameters (out_stream &rParamsFile) |
Private Member Functions | |
| template<class Archive > | |
| void | serialize (Archive &archive, const unsigned int version) |
| void | ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel () |
| void | AdjustOdeParameters (double currentTime) |
Friends | |
| class | boost::serialization::access |
Detailed Description
Wnt-dependent cell-cycle model. Needs to operate with a WntConcentration singleton object.
This model has a constant length M phase, runs ODEs to decide when to finish G1 phase then adds time for S and G2 phases. The CellProliferativeType is updated dependent on the concentration of beta-catenin (given by one of the ODEs).
Note that this class uses C++'s default copying semantics, and so doesn't implement a copy constructor or operator=.
Definition at line 60 of file WntCellCycleModel.hpp.
Constructor & Destructor Documentation
| WntCellCycleModel::WntCellCycleModel | ( | 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 37 of file WntCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSolver.
Referenced by CreateCellCycleModel().
Member Function Documentation
| void WntCellCycleModel::AdjustOdeParameters | ( | double | currentTime | ) | [private, virtual] |
Adjust any ODE parameters needed before solving until currentTime.
- Parameters:
-
currentTime the time up to which the system will be solved.
Reimplemented from CellCycleModelOdeHandler.
Definition at line 126 of file WntCellCycleModel.cpp.
References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
| void WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel | ( | ) | [private, virtual] |
Update the cell type according to the current beta catenin level as given by the WntCellCycleOdeSystem.
This method carries out the work for UpdateCellProliferativeType(), but does not check the current time, so can also be called by Initialise().
Implements AbstractWntOdeBasedCellCycleModel.
Definition at line 97 of file WntCellCycleModel.cpp.
References AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by Initialise().
| AbstractCellCycleModel * WntCellCycleModel::CreateCellCycleModel | ( | ) | [virtual] |
Overridden builder method to create new copies of this cell-cycle model.
Implements AbstractCellCycleModel.
Reimplemented in StochasticWntCellCycleModel.
Definition at line 55 of file WntCellCycleModel.cpp.
References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mDimension, AbstractOdeBasedCellCycleModel::mDivideTime, AbstractOdeBasedCellCycleModel::mFinishedRunningOdes, AbstractCellCycleModel::mG2Duration, AbstractOdeBasedCellCycleModel::mG2PhaseStartTime, CellCycleModelOdeHandler::mLastTime, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSolver, CellCycleModelOdeHandler::mpOdeSystem, AbstractCellCycleModel::mSDuration, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), AbstractOdeBasedCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetDimension(), AbstractOdeBasedCellCycleModel::SetDivideTime(), AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes(), AbstractCellCycleModel::SetG2Duration(), AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime(), CellCycleModelOdeHandler::SetLastTime(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), CellCycleModelOdeHandler::SetOdeSystem(), AbstractCellCycleModel::SetSDuration(), CellCycleModelOdeHandler::SetStateVariables(), AbstractCellCycleModel::SetStemCellG1Duration(), AbstractCellCycleModel::SetTransitCellG1Duration(), and WntCellCycleModel().
| void WntCellCycleModel::Initialise | ( | void | ) | [virtual] |
Initialise the cell-cycle model at the start of a simulation.
This overridden method sets up a new WntCellCycleOdeSystem and sets the cell type according to the current beta catenin level.
Reimplemented from AbstractCellCycleModel.
Reimplemented in StochasticWntCellCycleModel.
Definition at line 114 of file WntCellCycleModel.cpp.
References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetStateVariables().
| void WntCellCycleModel::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 AbstractWntOdeBasedCellCycleModel.
Reimplemented in StochasticWntCellCycleModel.
Definition at line 137 of file WntCellCycleModel.cpp.
| void WntCellCycleModel::serialize | ( | Archive & | archive, |
| const unsigned int | version | ||
| ) | [inline, private] |
Archive the cell-cycle model and ODE system.
- Parameters:
-
archive the archive version the archive version
Reimplemented from AbstractWntOdeBasedCellCycleModel.
Reimplemented in StochasticWntCellCycleModel.
Definition at line 72 of file WntCellCycleModel.hpp.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractWntOdeBasedCellCycleModel.
Reimplemented in StochasticWntCellCycleModel.
Definition at line 64 of file WntCellCycleModel.hpp.
The documentation for this class was generated from the following files:
- crypt/src/cell/cycle/WntCellCycleModel.hpp
- crypt/src/cell/cycle/WntCellCycleModel.cpp
