AbstractOdeBasedCellCycleModel Class Reference
#include <AbstractOdeBasedCellCycleModel.hpp>
Public Member Functions | |
| AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance()->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >()) | |
| virtual | ~AbstractOdeBasedCellCycleModel () |
| virtual void | UpdateCellCyclePhase () |
| double | GetOdeStopTime () |
| void | SetBirthTime (double birthTime) |
| std::vector< double > | GetProteinConcentrations () const |
| void | SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations) |
| virtual void | ResetForDivision () |
| void | SetFinishedRunningOdes (bool finishedRunningOdes) |
| void | SetDivideTime (double divideTime) |
| void | SetG2PhaseStartTime (double g2PhaseStartTime) |
| virtual void | OutputCellCycleModelParameters (out_stream &rParamsFile) |
Protected Attributes | |
| double | mDivideTime |
| bool | mFinishedRunningOdes |
| double | mG2PhaseStartTime |
Private Member Functions | |
| template<class Archive> | |
| void | serialize (Archive &archive, const unsigned int version) |
Friends | |
| class | boost::serialization::access |
Detailed Description
This class contains all the things common to standard cell cycle ODE models for intracellular protein concentrations (along the lines of Tyson & Novak), such as solving the ODEs until a stopping condition is met.Definition at line 47 of file AbstractOdeBasedCellCycleModel.hpp.
Constructor & Destructor Documentation
| AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel | ( | double | lastTime = SimulationTime::Instance()->GetTime(), |
|
| boost::shared_ptr< AbstractCellCycleModelOdeSolver > | pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() | |||
| ) |
Creates an AbstractOdeBasedCellCycleModel, calls SetBirthTime on the AbstractCellCycleModel to make sure that can be set 'back in time' for cells which did not divide at the current time.
- Parameters:
-
lastTime The birth time of the cell / last time model was evaluated (defaults to the current SimulationTime) pOdeSolver An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)
Definition at line 36 of file AbstractOdeBasedCellCycleModel.cpp.
References AbstractCellCycleModel::SetBirthTime().
| AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel | ( | ) | [virtual] |
Destructor.
Definition at line 46 of file AbstractOdeBasedCellCycleModel.cpp.
Member Function Documentation
| void AbstractOdeBasedCellCycleModel::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 AbstractCellCycleModel.
Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.
Definition at line 60 of file AbstractOdeBasedCellCycleModel.hpp.
References mDivideTime, mFinishedRunningOdes, and mG2PhaseStartTime.
| void AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase | ( | ) | [virtual] |
Default UpdateCellCyclePhase() method for an ODE-based cell-cycle model. This method calls SolveOdeToTime() for G1 phase and adds time for the other phases.
Can be overridden if they should do something more subtle.
Implements AbstractCellCycleModel.
Reimplemented in AbstractWntOdeBasedCellCycleModel.
Definition at line 71 of file AbstractOdeBasedCellCycleModel.cpp.
References EXCEPTION, AbstractCellCycleModel::GetAge(), AbstractCellCycleModel::GetG2Duration(), AbstractCellCycleModel::GetMDuration(), AbstractParameterisedSystem< VECTOR >::GetNumberOfStateVariables(), GetOdeStopTime(), AbstractCellCycleModel::GetSDuration(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCurrentCellCyclePhase, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, mG2PhaseStartTime, CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SolveOdeToTime().
Referenced by AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase().
| double AbstractOdeBasedCellCycleModel::GetOdeStopTime | ( | ) |
Get the time at which the ODE stopping event occurred. Only called in those subclasses for which stopping events are defined.
- Returns:
- the time at which the ODE system reached its stopping event
Definition at line 152 of file AbstractOdeBasedCellCycleModel.cpp.
References DOUBLE_UNSET, and CellCycleModelOdeHandler::mpOdeSolver.
Referenced by AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase(), and UpdateCellCyclePhase().
| void AbstractOdeBasedCellCycleModel::SetBirthTime | ( | double | birthTime | ) | [virtual] |
This overrides the AbstractCellCycleModel::SetBirthTime(double birthTime) because an ODE based cell-cycle model has more to reset...
- Parameters:
-
birthTime the simulation time when the cell was born
Reimplemented from AbstractCellCycleModel.
Definition at line 50 of file AbstractOdeBasedCellCycleModel.cpp.
References mDivideTime, CellCycleModelOdeHandler::mLastTime, and AbstractCellCycleModel::SetBirthTime().
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| std::vector< double > AbstractOdeBasedCellCycleModel::GetProteinConcentrations | ( | ) | const |
Returns the protein concentrations at the current time (useful for tests)
NB: Will copy the vector - you can't use this to modify the concentrations.
Definition at line 57 of file AbstractOdeBasedCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
| void AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly | ( | double | lastTime, | |
| std::vector< double > | proteinConcentrations | |||
| ) |
Sets the protein concentrations and time when the model was last evaluated - should only be called by tests
- Parameters:
-
lastTime the SimulationTime at which the protein concentrations apply proteinConcentrations a standard vector of doubles of protein concentrations
Definition at line 63 of file AbstractOdeBasedCellCycleModel.cpp.
References CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and AbstractOdeSystem::SetStateVariables().
| void AbstractOdeBasedCellCycleModel::ResetForDivision | ( | ) | [virtual] |
For a naturally cycling model this does not need to be overridden in the subclasses. But most models should override this function and then call AbstractOdeBasedCellCycleModel::ResetForDivision() from inside their version.
Reimplemented from AbstractCellCycleModel.
Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractWntOdeBasedCellCycleModel, and StochasticWntCellCycleModel.
Definition at line 141 of file AbstractOdeBasedCellCycleModel.cpp.
References AbstractCellCycleModel::mBirthTime, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, CellCycleModelOdeHandler::mLastTime, and AbstractCellCycleModel::ResetForDivision().
Referenced by AbstractWntOdeBasedCellCycleModel::ResetForDivision(), TysonNovakCellCycleModel::ResetForDivision(), and Alarcon2004OxygenBasedCellCycleModel::ResetForDivision().
| void AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes | ( | bool | finishedRunningOdes | ) |
Set mFinishedRunningOdes. Used in CreateCellCycleModel().
- Parameters:
-
finishedRunningOdes the new value of mFinishedRunningOdes
Definition at line 162 of file AbstractOdeBasedCellCycleModel.cpp.
References mFinishedRunningOdes.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractOdeBasedCellCycleModel::SetDivideTime | ( | double | divideTime | ) |
Set mDivideTime.
- Parameters:
-
divideTime the new value of mDivideTime
Definition at line 167 of file AbstractOdeBasedCellCycleModel.cpp.
References mDivideTime.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime | ( | double | g2PhaseStartTime | ) |
Set mG2PhaseStartTime. Used in CreateCellCycleModel().
- Parameters:
-
g2PhaseStartTime the new value of mG2PhaseStartTime
Definition at line 172 of file AbstractOdeBasedCellCycleModel.cpp.
References mG2PhaseStartTime.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters | ( | out_stream & | rParamsFile | ) | [virtual] |
Outputs cell cycle model parameters to file.
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Implements AbstractCellCycleModel.
Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.
Definition at line 177 of file AbstractOdeBasedCellCycleModel.cpp.
References AbstractCellCycleModel::OutputCellCycleModelParameters().
Referenced by AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters(), TysonNovakCellCycleModel::OutputCellCycleModelParameters(), and Alarcon2004OxygenBasedCellCycleModel::OutputCellCycleModelParameters().
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractCellCycleModel.
Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.
Definition at line 52 of file AbstractOdeBasedCellCycleModel.hpp.
Member Data Documentation
double AbstractOdeBasedCellCycleModel::mDivideTime [protected] |
The time at which the cell should divide - Set this to DBL_MAX in constructor.
Definition at line 72 of file AbstractOdeBasedCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), ResetForDivision(), serialize(), SetBirthTime(), SetDivideTime(), and UpdateCellCyclePhase().
bool AbstractOdeBasedCellCycleModel::mFinishedRunningOdes [protected] |
Whether the cell-cycle model is currently in a delay (not solving ODEs).
Definition at line 75 of file AbstractOdeBasedCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), ResetForDivision(), serialize(), SetFinishedRunningOdes(), and UpdateCellCyclePhase().
double AbstractOdeBasedCellCycleModel::mG2PhaseStartTime [protected] |
The start time for the G2 phase.
Definition at line 78 of file AbstractOdeBasedCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), serialize(), SetG2PhaseStartTime(), and UpdateCellCyclePhase().
The documentation for this class was generated from the following files:
- cell_based/src/population/cell/cycle/AbstractOdeBasedCellCycleModel.hpp
- cell_based/src/population/cell/cycle/AbstractOdeBasedCellCycleModel.cpp
