#include <DeltaNotchInteriorSrnModel.hpp>

Inheritance diagram for DeltaNotchInteriorSrnModel:

Collaboration diagram for DeltaNotchInteriorSrnModel:

Public Member Functions
	DeltaNotchInteriorSrnModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual AbstractSrnModel *	CreateSrnModel ()

virtual void	ResetForDivision ()

virtual void	Initialise ()

virtual void	SimulateToCurrentTime ()

void	UpdateDeltaNotch ()

double	GetNotch ()

void	SetNotch (double value)

double	GetDelta ()

void	SetDelta (double value)

double	GetTotalEdgeDelta ()

double	GetTotalEdgeNotch ()

virtual void	OutputSrnModelParameters (out_stream &rParamsFile)

virtual void	AddShrunkEdgeToInterior (AbstractSrnModel *pShrunkEdgeSrn)

Public Member Functions inherited from AbstractOdeSrnModel
	AbstractOdeSrnModel (unsigned stateSize, boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractOdeSrnModel ()

void	SetInitialConditions (std::vector< double > initialConditions)

virtual void	ScaleSrnVariables (const double theta)

Public Member Functions inherited from AbstractSrnModel
	AbstractSrnModel ()

virtual	~AbstractSrnModel ()

virtual void	SetCell (CellPtr pCell)

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetSimulatedToTime (double simulatedToTime)

double	GetSimulatedToTime () const

void	OutputSrnModelInfo (out_stream &rParamsFile)

void	SetEdgeLocalIndex (unsigned index)

unsigned	GetEdgeLocalIndex ()

bool	HasEdgeModel () const

void	SetEdgeModelIndicator (const bool isEdgeModel)

virtual void	AddSrnQuantities (AbstractSrnModel *pOtherSrn, const double scale=1.0)

virtual void	AddShrunkEdgeSrn (AbstractSrnModel *pShrunkEdgeSrn)

virtual void	AddMergedEdgeSrn (AbstractSrnModel *pMergedEdgeSrn)

virtual void	SplitEdgeSrn (const double relativePosition)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Public Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~CellCycleModelOdeHandler ()

AbstractOdeSystem *	GetOdeSystem () const

void	SetOdeSystem (AbstractOdeSystem *pOdeSystem)

const boost::shared_ptr< AbstractCellCycleModelOdeSolver >	GetOdeSolver () const

void	SetLastTime (double lastTime)

double	GetDt ()

void	SetDt (double timeStep)

void	SetStateVariables (const std::vector< double > &rStateVariables)

std::vector< double >	GetProteinConcentrations () const

void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)

Protected Member Functions
	DeltaNotchInteriorSrnModel (const DeltaNotchInteriorSrnModel &rModel)

Protected Member Functions inherited from AbstractOdeSrnModel
void	Initialise (AbstractOdeSystem *pOdeSystem)

	AbstractOdeSrnModel (const AbstractOdeSrnModel &rModel)

Protected Member Functions inherited from AbstractSrnModel
	AbstractSrnModel (const AbstractSrnModel &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 AbstractOdeSrnModel
std::vector< double >	mInitialConditions

unsigned	mStateSize

Protected Attributes inherited from AbstractSrnModel
CellPtr	mpCell

double	mSimulatedToTime

unsigned	mEdgeLocalIndex = UNSIGNED_UNSET

bool	mIsEdgeBasedModel = false

Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr< AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

bool	mFinishedRunningOdes

Detailed Description

A subclass of AbstractOdeSrnModel that includes a Delta-Notch ODE system in the sub-cellular reaction network. This class represents model describing cytoplasmic (interior, nuclear) concentration of Delta Notch. Together with DeltaNotchEdgeSrn, this class can model feedback between cytoplasmic and junctional concentration, and cell-cell communication via edge (junctional) concentrations.

Definition at line 53 of file DeltaNotchInteriorSrnModel.hpp.

Constructor & Destructor Documentation

◆ DeltaNotchInteriorSrnModel() [1/2]

DeltaNotchInteriorSrnModel::DeltaNotchInteriorSrnModel ( const DeltaNotchInteriorSrnModel & rModel )

protected

Protected copy-constructor for use by CreateSrnModel(). The only way for external code to create a copy of a SRN 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 SRN model will have had ResetForDivision() called just before CreateSrnModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Parameters

rModel the SRN model to copy.

Definition at line 57 of file DeltaNotchInteriorSrnModel.cpp.

References AbstractUntemplatedParameterisedSystem::GetNumberOfParameters(), CellCycleModelOdeHandler::GetOdeSystem(), AbstractParameterisedSystem< VECTOR >::GetParameter(), CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), CellCycleModelOdeHandler::SetOdeSystem(), and AbstractParameterisedSystem< VECTOR >::SetParameter().

◆ DeltaNotchInteriorSrnModel() [2/2]

DeltaNotchInteriorSrnModel::DeltaNotchInteriorSrnModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() )

Default constructor calls base class.

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 DeltaNotchInteriorSrnModel.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().