#include <DeltaNotchEdgeSrnModel.hpp>

Inheritance diagram for DeltaNotchEdgeSrnModel:

Collaboration diagram for DeltaNotchEdgeSrnModel:

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

virtual AbstractSrnModel *	CreateSrnModel ()

virtual void	Initialise ()

virtual void	InitialiseDaughterCell ()

virtual void	SimulateToCurrentTime ()

void	UpdateDeltaNotch ()

double	GetNotch ()

void	SetNotch (double value)

double	GetDelta ()

void	SetDelta (double value)

double	GetNeighbouringDelta () const

double	GetInteriorDelta () const

double	GetInteriorNotch () const

virtual void	OutputSrnModelParameters (out_stream &rParamsFile)

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 AbstractOdeSrnModel
	AbstractOdeSrnModel (unsigned stateSize, boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractOdeSrnModel ()

virtual void	ResetForDivision ()

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)

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	AddShrunkEdgeToInterior (AbstractSrnModel *pShrunkEdgeSrn)

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
	DeltaNotchEdgeSrnModel (const DeltaNotchEdgeSrnModel &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 SRN model represents a membrane/ cortex of a single junction of a cell. This class of models can be used together with DeltaNotchInteriorSrn models. The ODE model used here is an attempt to use previous work (see DeltaNotchSrnModel class) for more detailed description of Delta-Notch interactions involving edge quantities (this or neighbour edge information) and potentially coupling with cytoplasmic concentrations (DeltaNotchInteriorSrn class).

Definition at line 55 of file DeltaNotchEdgeSrnModel.hpp.

Constructor & Destructor Documentation

◆ DeltaNotchEdgeSrnModel() [1/2]

DeltaNotchEdgeSrnModel::DeltaNotchEdgeSrnModel ( const DeltaNotchEdgeSrnModel & 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 56 of file DeltaNotchEdgeSrnModel.cpp.

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

◆ DeltaNotchEdgeSrnModel() [2/2]

DeltaNotchEdgeSrnModel::DeltaNotchEdgeSrnModel ( 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 38 of file DeltaNotchEdgeSrnModel.cpp.

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

Member Function Documentation

◆ AddMergedEdgeSrn()

void DeltaNotchEdgeSrnModel::AddMergedEdgeSrn ( AbstractSrnModel * pMergedEdgeSrn )

virtual

Here we add Delta/Notch when junctions merge via common vertex deletion Override the method declared in AbstractSrnModel class

Parameters

pMergedEdgeSrn Pointer to an SRN

Reimplemented from AbstractSrnModel.

Definition at line 200 of file DeltaNotchEdgeSrnModel.cpp.

References AddSrnQuantities().

◆ AddShrunkEdgeSrn()

void DeltaNotchEdgeSrnModel::AddShrunkEdgeSrn ( AbstractSrnModel * pShrunkEdgeSrn )

virtual

Here we assume that when a neighbouring junctions shrinks, 25% of its Delta/Notch concentration is added to this edge Override the method declared in AbstractSrnModel class

Parameters

pShrunkEdgeSrn Pointer to an SRN

Reimplemented from AbstractSrnModel.

Definition at line 191 of file DeltaNotchEdgeSrnModel.cpp.

References AddSrnQuantities().

◆ AddSrnQuantities()

void DeltaNotchEdgeSrnModel::AddSrnQuantities	(	AbstractSrnModel *	pOtherSrn,
		const double	scale = `1.0`
	)

virtual

Adds Delta/Notch from the input SRN model to this model. Override the method declared in AbstractSrnModel class

Parameters

pOtherSrn	Pointer to an SRN
scale	scale factor

Reimplemented from AbstractSrnModel.

Definition at line 179 of file DeltaNotchEdgeSrnModel.cpp.

References GetDelta(), GetNotch(), SetDelta(), and SetNotch().

Referenced by AddMergedEdgeSrn(), and AddShrunkEdgeSrn().

◆ CreateSrnModel()

AbstractSrnModel * DeltaNotchEdgeSrnModel::CreateSrnModel ( )

virtual

Overridden builder method to create new copies of this SRN model.

Returns: a copy of the current SRN model.

Implements AbstractSrnModel.

Definition at line 82 of file DeltaNotchEdgeSrnModel.cpp.

◆ GetDelta()

double DeltaNotchEdgeSrnModel::GetDelta ( )

Returns: the current Delta level in this edge.

Definition at line 142 of file DeltaNotchEdgeSrnModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

Referenced by AddSrnQuantities().

◆ GetInteriorDelta()

double DeltaNotchEdgeSrnModel::GetInteriorDelta ( ) const

The value of interior Delta is stored as parameters in this model, which is retrieved by this method

Returns: the level of Delta in cell interior

Definition at line 161 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractParameterisedSystem< VECTOR >::GetParameter(), and CellCycleModelOdeHandler::mpOdeSystem.

◆ GetInteriorNotch()

double DeltaNotchEdgeSrnModel::GetInteriorNotch ( ) const

The value of interior Notch is stored as parameters in this model, which is retrieved by this method

Returns: the level of Notch in cell interior

Definition at line 167 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractParameterisedSystem< VECTOR >::GetParameter(), and CellCycleModelOdeHandler::mpOdeSystem.

◆ GetNeighbouringDelta()

double DeltaNotchEdgeSrnModel::GetNeighbouringDelta ( ) const

Returns: the current level of Delta in the neighbouring cell's edge.

Definition at line 155 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractParameterisedSystem< VECTOR >::GetParameter(), and CellCycleModelOdeHandler::mpOdeSystem.

◆ GetNotch()

double DeltaNotchEdgeSrnModel::GetNotch ( )

Returns: the current Notch level in this edge.

Definition at line 129 of file DeltaNotchEdgeSrnModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

Referenced by DeltaNotchInteriorSrnModel::AddShrunkEdgeToInterior(), and AddSrnQuantities().

◆ Initialise()

void DeltaNotchEdgeSrnModel::Initialise ( )

virtual

Initialise the SRN model at the start of a simulation.

This overridden method sets up a new Delta-Notch ODE system.

Reimplemented from AbstractOdeSrnModel.

Definition at line 96 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractOdeSrnModel::Initialise().

◆ InitialiseDaughterCell()

void DeltaNotchEdgeSrnModel::InitialiseDaughterCell ( )

virtual

This method is called when a new edge is created (e.g. after cell division or T1 swap)

Reimplemented from AbstractSrnModel.

Definition at line 101 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractSrnModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::SetParameter(), and AbstractParameterisedSystem< VECTOR >::SetStateVariable().

◆ OutputSrnModelParameters()

void DeltaNotchEdgeSrnModel::OutputSrnModelParameters ( out_stream & rParamsFile )

virtual

Output SRN model parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOdeSrnModel.

Definition at line 173 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractOdeSrnModel::OutputSrnModelParameters().

◆ serialize()

template<class Archive >

void DeltaNotchEdgeSrnModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the SRN model and member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 68 of file DeltaNotchEdgeSrnModel.hpp.

◆ SetDelta()

void DeltaNotchEdgeSrnModel::SetDelta ( double value )

Set the Delta level in this edge.

Parameters

value the new Delta level in this edge

Definition at line 149 of file DeltaNotchEdgeSrnModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

Referenced by AddSrnQuantities().

◆ SetNotch()

void DeltaNotchEdgeSrnModel::SetNotch ( double value )

Set the Notch level in this edge.

Parameters

value the new Notch level in this edge

Definition at line 136 of file DeltaNotchEdgeSrnModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

Referenced by AddSrnQuantities().

◆ SimulateToCurrentTime()

void DeltaNotchEdgeSrnModel::SimulateToCurrentTime ( )

virtual

Overridden SimulateToTime() method for custom behaviour. Updates parameters (such as neighbour or interior Delta/Notch) and runs the simulation to current time

Reimplemented from AbstractOdeSrnModel.

Definition at line 87 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractOdeSrnModel::SimulateToCurrentTime(), and UpdateDeltaNotch().

◆ SplitEdgeSrn()

void DeltaNotchEdgeSrnModel::SplitEdgeSrn ( const double relativePosition )

virtual

By default, Edge concentrations are split according to the lengths of two new edges , when an edge is split, relative to the original edge they are created from. Override the method declared in AbstractSrnModel class

Parameters

relativePosition position of the node splitting the two new edges relative to the original edge, used when splitting Edge concentrations

Reimplemented from AbstractSrnModel.

Definition at line 206 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractOdeSrnModel::ScaleSrnVariables().

◆ UpdateDeltaNotch()

void DeltaNotchEdgeSrnModel::UpdateDeltaNotch ( )

Update the levels of Delta and Notch of neighbouring edge sensed by this edge That is, fetch neighbour values from CellEdgeData object, storing the sensed information, into this model

Definition at line 114 of file DeltaNotchEdgeSrnModel.cpp.

References AbstractSrnModel::GetEdgeLocalIndex(), AbstractSrnModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetParameter().

Referenced by SimulateToCurrentTime().

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 60 of file DeltaNotchEdgeSrnModel.hpp.

The documentation for this class was generated from the following files:

cell_based/src/cell/srn/DeltaNotchEdgeSrnModel.hpp
cell_based/src/cell/srn/DeltaNotchEdgeSrnModel.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DeltaNotchEdgeSrnModel() [1/2]

◆ DeltaNotchEdgeSrnModel() [2/2]

Member Function Documentation

◆ AddMergedEdgeSrn()

◆ AddShrunkEdgeSrn()

◆ AddSrnQuantities()

◆ CreateSrnModel()

◆ GetDelta()

◆ GetInteriorDelta()

◆ GetInteriorNotch()

◆ GetNeighbouringDelta()

◆ GetNotch()

◆ Initialise()

◆ InitialiseDaughterCell()

◆ OutputSrnModelParameters()

◆ serialize()

◆ SetDelta()

◆ SetNotch()

◆ SimulateToCurrentTime()

◆ SplitEdgeSrn()

◆ UpdateDeltaNotch()

Friends And Related Symbol Documentation

◆ boost::serialization::access