AbstractVanLeeuwen2009WntSwatCellCycleModel Class Reference
#include <AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp>
Public Member Functions | |
| AbstractVanLeeuwen2009WntSwatCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >()) | |
| void | Initialise () |
| double | GetMembraneBoundBetaCateninLevel () |
| double | GetCytoplasmicBetaCateninLevel () |
| double | GetNuclearBetaCateninLevel () |
| virtual void | InitialiseOdeSystem (double wntConcentration, boost::shared_ptr< AbstractCellMutationState > pMutationState)=0 |
| 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.Definition at line 47 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.
Constructor & Destructor Documentation
| AbstractVanLeeuwen2009WntSwatCellCycleModel::AbstractVanLeeuwen2009WntSwatCellCycleModel | ( | 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 31 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
Member Function Documentation
| void AbstractVanLeeuwen2009WntSwatCellCycleModel::serialize | ( | Archive & | archive, | |
| const unsigned int | version | |||
| ) | [inline, private] |
Archive the cell-cycle model, never used directly - boost uses this.
- Parameters:
-
archive the archive version the current version of this class
Reimplemented from AbstractWntOdeBasedCellCycleModel.
Reimplemented in VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.
Definition at line 60 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.
| void AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel | ( | ) | [private, virtual] |
Called by Initialise() and UpdateCellProliferativeType() only. Updates 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.
Implements AbstractWntOdeBasedCellCycleModel.
Definition at line 36 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References AbstractCellCycleModel::mCellProliferativeType, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by Initialise().
| void AbstractVanLeeuwen2009WntSwatCellCycleModel::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 70 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
| void AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise | ( | void | ) | [virtual] |
See AbstractCellCycleModel::Initialise()
In this case we set up a new ODE system for a daughter cell.
Reimplemented from AbstractCellCycleModel.
Definition at line 56 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), InitialiseOdeSystem(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetStateVariables().
| double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel | ( | ) |
- Returns:
- the level of membrane bound beta-catenin. To be used in cell-cell adhesion calculations.
Definition at line 79 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), VertexCryptSimulation2d::WriteBetaCatenin(), and CryptSimulation2d::WriteBetaCatenin().
| double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel | ( | ) |
- Returns:
- the level of cytoplasmic beta-catenin (including ubiquitinated - awaiting degradation)
Definition at line 84 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by VertexCryptSimulation2d::WriteBetaCatenin(), and CryptSimulation2d::WriteBetaCatenin().
| double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel | ( | ) |
- Returns:
- the level of nuclear beta-catenin. To be used in transcription
Definition at line 91 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by VertexCryptSimulation2d::WriteBetaCatenin(), and CryptSimulation2d::WriteBetaCatenin().
| virtual void AbstractVanLeeuwen2009WntSwatCellCycleModel::InitialiseOdeSystem | ( | double | wntConcentration, | |
| boost::shared_ptr< AbstractCellMutationState > | pMutationState | |||
| ) | [pure virtual] |
Pure virtual method to be implemented in concrete classes, which should should allocate the mOdeSystem variable using the appropriate hypothesis (one or two).
- Parameters:
-
wntConcentration Wnt concentration pMutationState Mutation state
Implemented in VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.
Referenced by Initialise().
| void AbstractVanLeeuwen2009WntSwatCellCycleModel::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 VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.
Definition at line 99 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters().
Referenced by VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::OutputCellCycleModelParameters(), and VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::OutputCellCycleModelParameters().
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractWntOdeBasedCellCycleModel.
Reimplemented in VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.
Definition at line 52 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.
The documentation for this class was generated from the following files:
- crypt/src/cell/cycle/AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp
- crypt/src/cell/cycle/AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp
