Chaste  Release::2018.1
TysonNovakCellCycleModel.cpp
1 /*
2 
3 Copyright (c) 2005-2018, University of Oxford.
4 All rights reserved.
5 
6 University of Oxford means the Chancellor, Masters and Scholars of the
7 University of Oxford, having an administrative office at Wellington
8 Square, Oxford OX1 2JD, UK.
9 
10 This file is part of Chaste.
11 
12 Redistribution and use in source and binary forms, with or without
13 modification, are permitted provided that the following conditions are met:
14  * Redistributions of source code must retain the above copyright notice,
15  this list of conditions and the following disclaimer.
16  * Redistributions in binary form must reproduce the above copyright notice,
17  this list of conditions and the following disclaimer in the documentation
18  and/or other materials provided with the distribution.
19  * Neither the name of the University of Oxford nor the names of its
20  contributors may be used to endorse or promote products derived from this
21  software without specific prior written permission.
22 
23 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33 
34 */
35 
36 #include "TysonNovakCellCycleModel.hpp"
37 #include "StemCellProliferativeType.hpp"
38 #include "TransitCellProliferativeType.hpp"
39 
40 TysonNovakCellCycleModel::TysonNovakCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
41  : AbstractOdeBasedCellCycleModel(SimulationTime::Instance()->GetTime(), pOdeSolver)
42 {
43  if (!mpOdeSolver)
44  {
45 #ifdef CHASTE_CVODE
47  mpOdeSolver->Initialise();
48  // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so
49  mpOdeSolver->CheckForStoppingEvents();
50  mpOdeSolver->SetMaxSteps(10000);
51  mpOdeSolver->SetTolerances(1e-6, 1e-8);
52 #else
54  mpOdeSolver->SetSizeOfOdeSystem(6);
55  mpOdeSolver->Initialise();
56  SetDt(0.1/90.0);
57 #endif //CHASTE_CVODE
58  }
59 }
60 
63 {
64  /*
65  * Initialize only those member variables defined in this class.
66  * Create the new cell-cycle model's ODE system and use the current
67  * values of the state variables in mpOdeSystem as an initial condition.
68  *
69  * The member variable mDivideTime is initialized in the
70  * AbstractOdeBasedCellCycleModel constructor.
71  *
72  * The member variables mBirthTime, mReadyToDivide and mDimension
73  * are initialized in the AbstractCellCycleModel constructor.
74  *
75  * Note that the cell proliferative type is (re)set as soon as
76  * InitialiseDaughterCell() is called on the new cell-cycle model.
77  */
78  assert(rModel.GetOdeSystem());
81 }
82 
84 {
85  assert(mpOdeSystem == nullptr);
88 
90 }
91 
93 {
95 
96  assert(mpOdeSystem != nullptr);
97 
110 #ifdef CHASTE_CVODE
112 #else
114 #endif //CHASTE_CVODE
115 }
116 
118 {
119  if (mpCell->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
120  {
121  /*
122  * This method is usually called within a CellBasedSimulation, after the CellPopulation
123  * has called CellPropertyRegistry::TakeOwnership(). This means that were we to call
124  * CellPropertyRegistry::Instance() here when setting the CellProliferativeType, we
125  * would be creating a new CellPropertyRegistry. In this case the cell proliferative
126  * type counts, as returned by AbstractCellPopulation::GetCellProliferativeTypeCount(),
127  * would be incorrect. We must therefore access the CellProliferativeType via the cell's
128  * CellPropertyCollection.
129  */
130  boost::shared_ptr<AbstractCellProperty> p_transit_type =
131  mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<TransitCellProliferativeType>();
132  mpCell->SetCellProliferativeType(p_transit_type);
133  }
134 }
135 
137 {
138  return new TysonNovakCellCycleModel(*this);
139 }
140 
142 {
143  return 1.25;
144 }
145 
147 {
148  return 1.25;
149 }
150 
152 {
153  return false;
154 }
155 
157 {
158  // No new parameters to output, so just call method on direct parent class
160 }
161 
162 // Serialization for Boost >= 1.36
165 #include "CellCycleModelOdeSolverExportWrapper.hpp"
166 EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(TysonNovakCellCycleModel)
void SetStateVariables(const std::vector< double > &rStateVariables)
void SetOdeSystem(AbstractOdeSystem *pOdeSystem)
boost::shared_ptr< AbstractCellCycleModelOdeSolver > mpOdeSolver
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)
AbstractCellCycleModel * CreateCellCycleModel()
void SetStateVariables(const VECTOR &rStateVariables)
static boost::shared_ptr< CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER > > Instance()
TysonNovakCellCycleModel(const TysonNovakCellCycleModel &rModel)
AbstractOdeSystem * GetOdeSystem() const
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)
#define CHASTE_CLASS_EXPORT(T)