TysonNovakCellCycleModel.cpp

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*/

#include "TysonNovakCellCycleModel.hpp"
#include "StemCellProliferativeType.hpp"
#include "TransitCellProliferativeType.hpp"

TysonNovakCellCycleModel::TysonNovakCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : AbstractOdeBasedCellCycleModel(SimulationTime::Instance()->GetTime(), pOdeSolver)
{
    if (!mpOdeSolver)
    {
#ifdef CHASTE_CVODE
        mpOdeSolver = CellCycleModelOdeSolver<TysonNovakCellCycleModel, CvodeAdaptor>::Instance();
        mpOdeSolver->Initialise();
        // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so
        mpOdeSolver->CheckForStoppingEvents();
        mpOdeSolver->SetMaxSteps(10000);
        mpOdeSolver->SetTolerances(1e-6, 1e-8);
#else
        mpOdeSolver = CellCycleModelOdeSolver<TysonNovakCellCycleModel, BackwardEulerIvpOdeSolver>::Instance();
        mpOdeSolver->SetSizeOfOdeSystem(6);
        mpOdeSolver->Initialise();
        SetDt(0.1/90.0);
#endif //CHASTE_CVODE
    }
}

void TysonNovakCellCycleModel::Initialise()
{
    assert(mpOdeSystem == NULL);
    mpOdeSystem = new TysonNovak2001OdeSystem;
    mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());

    AbstractCellCycleModel::Initialise();
}

void TysonNovakCellCycleModel::ResetForDivision()
{
    AbstractOdeBasedCellCycleModel::ResetForDivision();

    assert(mpOdeSystem != NULL);

#ifdef CHASTE_CVODE
    mpOdeSystem->rGetStateVariables()[5] = 0.5*mpOdeSystem->rGetStateVariables()[5];
#else
    mpOdeSystem->SetStateVariables(mpOdeSystem->GetInitialConditions());
#endif //CHASTE_CVODE
}

void TysonNovakCellCycleModel::InitialiseDaughterCell()
{
    if (mpCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
    {
        /*
         * This method is usually called within a CellBasedSimulation, after the CellPopulation
         * has called CellPropertyRegistry::TakeOwnership(). This means that were we to call
         * CellPropertyRegistry::Instance() here when setting the CellProliferativeType, we
         * would be creating a new CellPropertyRegistry. In this case the cell proliferative
         * type counts, as returned by AbstractCellPopulation::GetCellProliferativeTypeCount(),
         * would be incorrect. We must therefore access the CellProliferativeType via the cell's
         * CellPropertyCollection.
         */
        boost::shared_ptr<AbstractCellProperty> p_transit_type =
            mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<TransitCellProliferativeType>();
        mpCell->SetCellProliferativeType(p_transit_type);
    }
}

AbstractCellCycleModel* TysonNovakCellCycleModel::CreateCellCycleModel()
{
    // Create a new cell-cycle model
    TysonNovakCellCycleModel* p_model = new TysonNovakCellCycleModel(mpOdeSolver);

    /*
     * Set each member variable of the new cell-cycle model that inherits
     * its value from the parent.
     *
     * Note 1: some of the new cell-cycle model's member variables (namely
     * mBirthTime, mCurrentCellCyclePhase, mReadyToDivide, mDt, mpOdeSolver)
     * will already have been correctly initialized in its constructor.
     *
     * Note 2: one or more of the new cell-cycle model's member variables
     * may be set/overwritten as soon as InitialiseDaughterCell() is called on
     * the new cell-cycle model.
     *
     * Note 3: the member variable mDimension remains unset, since this cell-cycle
     * model does not need to know the spatial dimension, so if we were to call
     * SetDimension() on the new cell-cycle model an exception would be triggered;
     * hence we do not set this member variable.
     */
    p_model->SetBirthTime(mBirthTime);
    p_model->SetMinimumGapDuration(mMinimumGapDuration);
    p_model->SetStemCellG1Duration(mStemCellG1Duration);
    p_model->SetTransitCellG1Duration(mTransitCellG1Duration);
    p_model->SetSDuration(mSDuration);
    p_model->SetG2Duration(mG2Duration);
    p_model->SetMDuration(mMDuration);
    p_model->SetDivideTime(mDivideTime);
    p_model->SetFinishedRunningOdes(mFinishedRunningOdes);
    p_model->SetG2PhaseStartTime(mG2PhaseStartTime);
    p_model->SetLastTime(mLastTime);

    /*
     * Create the new cell-cycle model's ODE system and use the current values
     * of the state variables in mpOdeSystem as an initial condition.
     */
    assert(mpOdeSystem);
    p_model->SetOdeSystem(new TysonNovak2001OdeSystem);
    p_model->SetStateVariables(mpOdeSystem->rGetStateVariables());

    return p_model;
}

double TysonNovakCellCycleModel::GetSDuration()
{
    return 0.0;
}

double TysonNovakCellCycleModel::GetG2Duration()
{
    return 0.0;
}

double TysonNovakCellCycleModel::GetMDuration()
{
    return 0.0;
}

double TysonNovakCellCycleModel::GetAverageTransitCellCycleTime()
{
    return 1.25;
}

double TysonNovakCellCycleModel::GetAverageStemCellCycleTime()
{
    return 1.25;
}

bool TysonNovakCellCycleModel::CanCellTerminallyDifferentiate()
{
    return false;
}

void TysonNovakCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output, so just call method on direct parent class
    AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(TysonNovakCellCycleModel)
#include "CellCycleModelOdeSolverExportWrapper.hpp"
EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(TysonNovakCellCycleModel)