#include <SingleOdeWntCellCycleModel.hpp>
Inheritance diagram for SingleOdeWntCellCycleModel:
Collaboration diagram for SingleOdeWntCellCycleModel:
Public Member Functions | |
| SingleOdeWntCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >()) | |
| void | Initialise () |
| void | UpdateCellCyclePhase () |
| AbstractCellCycleModel * | CreateCellCycleModel () |
| double | GetBetaCateninConcentration () |
| void | SetBetaCateninDivisionThreshold (double betaCateninDivisionThreshold) |
| double | GetBetaCateninDivisionThreshold () |
| virtual void | OutputCellCycleModelParameters (out_stream &rParamsFile) |
Private Member Functions | |
| template<class Archive > | |
| void | serialize (Archive &archive, const unsigned int version) |
| void | ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel () |
| virtual void | AdjustOdeParameters (double currentTime) |
Private Attributes | |
| double | mBetaCateninDivisionThreshold |
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).
Definition at line 58 of file SingleOdeWntCellCycleModel.hpp.
Constructor & Destructor Documentation
| SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel | ( | 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 39 of file SingleOdeWntCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().
Referenced by CreateCellCycleModel().
Member Function Documentation
| void SingleOdeWntCellCycleModel::AdjustOdeParameters | ( | double | currentTime | ) | [private, virtual] |
Adjust any ODE parameters needed before solving until currentTime. Defaults to do nothing.
- Parameters:
-
currentTime the time up to which the system will be solved.
Reimplemented from CellCycleModelOdeHandler.
Definition at line 130 of file SingleOdeWntCellCycleModel.cpp.
References SimpleWntCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
| void SingleOdeWntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel | ( | ) | [private] |
Called by ::Initialise() and ::UpdateCellProliferativeType() only. Updates the mpCell::mCellProliferativeType to match mpOdeSystem's beta-catenin levels
This carries out the work for ::UpdateCellProliferativeType(); But does not check the current time so it can be used by the initialise method.
Definition at line 139 of file SingleOdeWntCellCycleModel.cpp.
References GetBetaCateninConcentration(), GetBetaCateninDivisionThreshold(), AbstractCellCycleModel::mpCell, and CellCycleModelOdeHandler::mpOdeSystem.
Referenced by Initialise(), and UpdateCellCyclePhase().
| AbstractCellCycleModel * SingleOdeWntCellCycleModel::CreateCellCycleModel | ( | ) | [virtual] |
Overridden builder method to create new copies of this cell-cycle model.
Reimplemented from SimpleWntCellCycleModel.
Definition at line 58 of file SingleOdeWntCellCycleModel.cpp.
References SimpleWntCellCycleModel::GetWntLevel(), mBetaCateninDivisionThreshold, AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mG2Duration, CellCycleModelOdeHandler::mLastTime, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSolver, CellCycleModelOdeHandler::mpOdeSystem, AbstractCellCycleModel::mSDuration, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, SimpleWntCellCycleModel::mUseCellProliferativeTypeDependentG1Duration, SimpleWntCellCycleModel::mWntLabelledThreshold, SimpleWntCellCycleModel::mWntStemThreshold, SimpleWntCellCycleModel::mWntTransitThreshold, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), SetBetaCateninDivisionThreshold(), AbstractCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetDimension(), AbstractCellCycleModel::SetG2Duration(), CellCycleModelOdeHandler::SetLastTime(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), CellCycleModelOdeHandler::SetOdeSystem(), AbstractCellCycleModel::SetSDuration(), CellCycleModelOdeHandler::SetStateVariables(), AbstractCellCycleModel::SetStemCellG1Duration(), AbstractCellCycleModel::SetTransitCellG1Duration(), SimpleWntCellCycleModel::SetUseCellProliferativeTypeDependentG1Duration(), SimpleWntCellCycleModel::SetWntLabelledThreshold(), SimpleWntCellCycleModel::SetWntStemThreshold(), SimpleWntCellCycleModel::SetWntTransitThreshold(), and SingleOdeWntCellCycleModel().
| double SingleOdeWntCellCycleModel::GetBetaCateninConcentration | ( | ) |
Return the total beta-catenin concentration
Definition at line 153 of file SingleOdeWntCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel().
| double SingleOdeWntCellCycleModel::GetBetaCateninDivisionThreshold | ( | ) |
Get mBetaCateninDivisionThreshold.
Definition at line 163 of file SingleOdeWntCellCycleModel.cpp.
References mBetaCateninDivisionThreshold.
Referenced by ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel().
| void SingleOdeWntCellCycleModel::Initialise | ( | void | ) | [virtual] |
Initialise the cell-cycle model at the start of a simulation.
This overridden method sets up a new WntCellCycleOdeSystem, sets the cell type according to the current beta catenin level and sets a random G2 duration.
Reimplemented from AbstractSimpleCellCycleModel.
Definition at line 110 of file SingleOdeWntCellCycleModel.cpp.
References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), SimpleWntCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, CellCycleModelOdeHandler::SetLastTime(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().
| void SingleOdeWntCellCycleModel::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 SimpleWntCellCycleModel.
Definition at line 168 of file SingleOdeWntCellCycleModel.cpp.
| void SingleOdeWntCellCycleModel::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 CellCycleModelOdeHandler.
Definition at line 71 of file SingleOdeWntCellCycleModel.hpp.
References mBetaCateninDivisionThreshold.
| void SingleOdeWntCellCycleModel::SetBetaCateninDivisionThreshold | ( | double | betaCateninDivisionThreshold | ) |
Set mBetaCateninDivisionThreshold.
- Parameters:
-
betaCateninDivisionThreshold to be set
Definition at line 158 of file SingleOdeWntCellCycleModel.cpp.
References mBetaCateninDivisionThreshold.
Referenced by CreateCellCycleModel().
| void SingleOdeWntCellCycleModel::UpdateCellCyclePhase | ( | ) | [virtual] |
This specialisation updates the beta-catenin level
Don't call the SimpleWntCellCycleModel - it will overwrite this.
Reimplemented from SimpleWntCellCycleModel.
Definition at line 102 of file SingleOdeWntCellCycleModel.cpp.
References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), SimulationTime::Instance(), and CellCycleModelOdeHandler::SolveOdeToTime().
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from CellCycleModelOdeHandler.
Definition at line 63 of file SingleOdeWntCellCycleModel.hpp.
Member Data Documentation
The cell differentiates when the beta-catenin level drops below this value. Initialised to a Magic Number!
Definition at line 82 of file SingleOdeWntCellCycleModel.hpp.
Referenced by CreateCellCycleModel(), GetBetaCateninDivisionThreshold(), serialize(), and SetBetaCateninDivisionThreshold().
The documentation for this class was generated from the following files:
- crypt/src/cell/cycle/SingleOdeWntCellCycleModel.hpp
- crypt/src/cell/cycle/SingleOdeWntCellCycleModel.cpp
