UserTutorials/CreatingAndUsingANewCellProperty

This tutorial is automatically generated from the file trunk/cell_based/test/tutorial/TestCreatingAndUsingANewCellPropertyTutorial.hpp at revision r12669. Note that the code is given in full at the bottom of the page.

An example showing how to create a new cell property and use it in a cell-based simulation

Introduction

In the cell mutation state tutorial we showed how to create a new cell mutation state class, and how this can be used in a cell-based simulation. As well as mutation states, cells may be given much more general properties, using the cell property class hierarchy. In this tutorial, we show how to create a new cell property class, and how this can be used in a cell-based simulation.

1. Including header files

As in previous cell-based Chaste tutorials, we begin by including the necessary header file and archiving headers.

#include <cxxtest/TestSuite.h>
#include <boost/archive/text_oarchive.hpp>
#include <boost/archive/text_iarchive.hpp>

The next header defines a base class for cell properties. Our new cell property will inherit from this abstract class.

#include "AbstractCellProperty.hpp"

The remaining header files define classes that will be used in the cell population simulation test. We have encountered each of these header files in previous cell-based Chaste tutorials.

#include "HoneycombMeshGenerator.hpp"
#include "WildTypeCellMutationState.hpp"
#include "FixedDurationGenerationBasedCellCycleModel.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "CellBasedSimulation.hpp"

Defining the cell property class

As an example, let us consider a cell property class that is used to label those cells that are "motile". This cell property could then be used when implementing some form of chemotaxis down an imposed chemoattractant gradient, as occurs for example when macrophages migrate within a tumour towards high concentrations of the vascular endothelial growth factor VEGF; for further details, see for example Owen et al., J. Theor. Biol. 226: 377-391 (2004).

Note that usually this code would be separated out into a separate declaration in a .hpp file and definition in a .cpp file.

class MotileCellProperty : public AbstractCellProperty
{
private:

We define a member variable mColour, which can be used by visualization tools to paint cells with this mutation state a distinct colour if required.

    unsigned mColour;

The next block of code allows us to archive (save or load) the cell property object in a cell-based simulation. The code consists of a serialize() method, in which we first archive the cell property using the serialization code defined in the base class AbstractCellProperty, then archive the member variable mColour.

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellProperty>(*this);
        archive & mColour;
    }
public:

The default constructor allows us to specify a value for the member variable mColour, or leave it with a default value.

    MotileCellProperty(unsigned colour=5)
        : AbstractCellProperty(),
          mColour(colour)
    {
    }

We then define a destructor and a get method for the member variable mColour.

    ~MotileCellProperty()
    {}
    unsigned GetColour() const
    {
        return mColour;
    }
};

As mentioned in previous cell-based Chaste tutorials, we need to include the next block of code to be able to archive the cell property object in a cell-based simulation, and to obtain a unique identifier for our new cell property for writing results to file.

#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(MotileCellProperty)
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(MotileCellProperty)

This completes the code for MotileCellProperty. Note that usually this code would be separated out into a separate declaration in a .hpp file and definition in a .cpp file.

The Tests

We now define the test class, which inherits from CxxTest::TestSuite.

class TestCreatingAndUsingANewCellPropertyTutorial : public CxxTest::TestSuite
{
public:

Testing the cell property

We begin by testing that our new cell property is implemented correctly.

    void TestMotileCellProperty() throw(Exception)
    {

We begin by testing that some of the base class methods work correctly. We typically use shared pointers to create and access a cell property like MotileCellProperty, for which it makes sense for all cells that have the same mutation to share a pointer to the same cell property object (although strictly speaking, they are not required to). Observe that in this case we have provided a value for the member variable mColour in the MotileCellProperty constructor.

        boost::shared_ptr<AbstractCellProperty> p_property(new MotileCellProperty(8));

Each cell property has a member variable, mCellCount, which stores the number of cells with this cell property. We can test whether mCellCount is being updated correctly by our cell property, as follows.

        TS_ASSERT_EQUALS(p_property->GetCellCount(), 0u);
        p_property->IncrementCellCount();
        TS_ASSERT_EQUALS(p_property->GetCellCount(), 1u);
        p_property->DecrementCellCount();
        TS_ASSERT_EQUALS(p_property->GetCellCount(), 0u);
        TS_ASSERT_THROWS_THIS(p_property->DecrementCellCount(),
                "Cannot decrement cell count: no cells have this cell property");

We can also test whether our cell property is of a given type, as follows.

        TS_ASSERT_EQUALS(p_property->IsType<WildTypeCellMutationState>(), false);
        TS_ASSERT_EQUALS(p_property->IsType<MotileCellProperty>(), true);

We can also test that archiving is implemented correctly for our cell property, as follows (further details on how to implement and test archiving can be found on the BoostSerialization? page).

        OutputFileHandler handler("archive", false);
        std::string archive_filename = handler.GetOutputDirectoryFullPath() + "property.arch";
        {
            AbstractCellProperty* const p_const_property = new MotileCellProperty(7);
            p_const_property->IncrementCellCount();
            TS_ASSERT_EQUALS(p_const_property->GetCellCount(), 1u);
            TS_ASSERT_EQUALS(dynamic_cast<MotileCellProperty*>(p_const_property)->GetColour(), 7u);
            std::ofstream ofs(archive_filename.c_str());
            boost::archive::text_oarchive output_arch(ofs);
            output_arch << p_const_property;
            delete p_const_property;
        }
        {
            AbstractCellProperty* p_property;
            std::ifstream ifs(archive_filename.c_str());
            boost::archive::text_iarchive input_arch(ifs);
            input_arch >> p_property;
            TS_ASSERT_EQUALS(p_property->GetCellCount(), 1u);
            MotileCellProperty* p_real_property = dynamic_cast<MotileCellProperty*>(p_property);
            TS_ASSERT(p_real_property != NULL);
            TS_ASSERT_EQUALS(p_real_property->GetColour(), 7u);
            delete p_property;
        }
    }

Using the cell property in a cell-based simulation

We conclude with a brief test demonstrating how MotileCellProperty can be used in a cell-based simulation.

    void TestCellBasedSimulationWithP53GainOfFunctionCellMutationState() throw(Exception)
    {

We begin by setting up the start time, as follows.

        SimulationTime::Instance()->SetStartTime(0.0);

We use the HoneycombMeshGenerator to create a honeycomb mesh covering a circular domain of given radius, as follows.

        HoneycombMeshGenerator generator(10, 10, 0);
        MutableMesh<2,2>* p_mesh = generator.GetCircularMesh(5);

We now create a shared pointer to our new property, as follows.

        boost::shared_ptr<AbstractCellProperty> p_motile(new MotileCellProperty);

Next, we create some cells, as follows.

        boost::shared_ptr<AbstractCellMutationState> p_state(new WildTypeCellMutationState);
        std::vector<CellPtr> cells;
        for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
        {

For each node we create a cell with our cell-cycle model and the wild-type cell mutation state. We then add the property MotileCellProperty to a random selection of the cells, as follows.

            FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
            p_model->SetCellProliferativeType(STEM);
            CellPropertyCollection collection;
            if (RandomNumberGenerator::Instance()->ranf() < 0.5)
            {
                collection.AddProperty(p_motile);
            }
            CellPtr p_cell(new Cell(p_state, p_model, false, collection));

Now, we define a random birth time, chosen from [-T,0], where T = t₁ + t₂, where t₁ is a parameter representing the G₁ duration of a stem cell, and t₂ is the basic S+G₂+M phases duration.

            double birth_time = - RandomNumberGenerator::Instance()->ranf() *
                                    (p_model->GetStemCellG1Duration()
                                        + p_model->GetSG2MDuration());

Finally, we set the birth time and push the cell back into the vector of cells.

            p_cell->SetBirthTime(birth_time);
            cells.push_back(p_cell);
        }

Now that we have defined the mesh and cells, we can define the cell population. The constructor takes in the mesh and the cells vector.

        MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);

We then pass in the cell population into a CellBasedSimulation, and set the output directory and end time.

        CellBasedSimulation<2> simulator(cell_population);
        simulator.SetOutputDirectory("TestCellBasedSimulationWithMotileCellProperty");
        simulator.SetEndTime(10.0);

We create a force law and pass it to the CellBasedSimulation.

        GeneralisedLinearSpringForce<2> linear_force;
        linear_force.SetCutOffLength(3);
        simulator.AddForce(&linear_force);

Test that the Solve() method does not throw any exceptions.

        TS_ASSERT_THROWS_NOTHING(simulator.Solve());

Finally, we call Destroy() on the singleton classes.

        SimulationTime::Destroy();
        RandomNumberGenerator::Destroy();
    }
};

Code

The full code is given below

File name `TestCreatingAndUsingANewCellPropertyTutorial.hpp`

#include <cxxtest/TestSuite.h>

#include <boost/archive/text_oarchive.hpp>
#include <boost/archive/text_iarchive.hpp>

#include "AbstractCellProperty.hpp"
#include "HoneycombMeshGenerator.hpp"
#include "WildTypeCellMutationState.hpp"
#include "FixedDurationGenerationBasedCellCycleModel.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "CellBasedSimulation.hpp"

class MotileCellProperty : public AbstractCellProperty
{
private:

    unsigned mColour;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellProperty>(*this);
        archive & mColour;
    }

public:

    MotileCellProperty(unsigned colour=5)
        : AbstractCellProperty(),
          mColour(colour)
    {
    }

    ~MotileCellProperty()
    {}

    unsigned GetColour() const
    {
        return mColour;
    }
};

#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(MotileCellProperty)
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(MotileCellProperty)

class TestCreatingAndUsingANewCellPropertyTutorial : public CxxTest::TestSuite
{
public:

    void TestMotileCellProperty() throw(Exception)
    {
        boost::shared_ptr<AbstractCellProperty> p_property(new MotileCellProperty(8));

        TS_ASSERT_EQUALS(p_property->GetCellCount(), 0u);
        p_property->IncrementCellCount();
        TS_ASSERT_EQUALS(p_property->GetCellCount(), 1u);
        p_property->DecrementCellCount();
        TS_ASSERT_EQUALS(p_property->GetCellCount(), 0u);
        TS_ASSERT_THROWS_THIS(p_property->DecrementCellCount(),
                "Cannot decrement cell count: no cells have this cell property");

        TS_ASSERT_EQUALS(p_property->IsType<WildTypeCellMutationState>(), false);
        TS_ASSERT_EQUALS(p_property->IsType<MotileCellProperty>(), true);

        OutputFileHandler handler("archive", false);
        std::string archive_filename = handler.GetOutputDirectoryFullPath() + "property.arch";

        {
            AbstractCellProperty* const p_const_property = new MotileCellProperty(7);
            p_const_property->IncrementCellCount();

            TS_ASSERT_EQUALS(p_const_property->GetCellCount(), 1u);
            TS_ASSERT_EQUALS(dynamic_cast<MotileCellProperty*>(p_const_property)->GetColour(), 7u);

            std::ofstream ofs(archive_filename.c_str());
            boost::archive::text_oarchive output_arch(ofs);

            output_arch << p_const_property;

            delete p_const_property;
        }

        {
            AbstractCellProperty* p_property;

            std::ifstream ifs(archive_filename.c_str());
            boost::archive::text_iarchive input_arch(ifs);

            input_arch >> p_property;

            TS_ASSERT_EQUALS(p_property->GetCellCount(), 1u);

            MotileCellProperty* p_real_property = dynamic_cast<MotileCellProperty*>(p_property);
            TS_ASSERT(p_real_property != NULL);
            TS_ASSERT_EQUALS(p_real_property->GetColour(), 7u);

            delete p_property;
        }
    }

    void TestCellBasedSimulationWithP53GainOfFunctionCellMutationState() throw(Exception)
    {
        SimulationTime::Instance()->SetStartTime(0.0);

        HoneycombMeshGenerator generator(10, 10, 0);
        MutableMesh<2,2>* p_mesh = generator.GetCircularMesh(5);

        boost::shared_ptr<AbstractCellProperty> p_motile(new MotileCellProperty);

        boost::shared_ptr<AbstractCellMutationState> p_state(new WildTypeCellMutationState);
        std::vector<CellPtr> cells;
        for (unsigned i=0; i<p_mesh->GetNumNodes(); i++)
        {
            FixedDurationGenerationBasedCellCycleModel* p_model = new FixedDurationGenerationBasedCellCycleModel();
            p_model->SetCellProliferativeType(STEM);

            CellPropertyCollection collection;
            if (RandomNumberGenerator::Instance()->ranf() < 0.5)
            {
                collection.AddProperty(p_motile);
            }

            CellPtr p_cell(new Cell(p_state, p_model, false, collection));

            double birth_time = - RandomNumberGenerator::Instance()->ranf() *
                                    (p_model->GetStemCellG1Duration()
                                        + p_model->GetSG2MDuration());

            p_cell->SetBirthTime(birth_time);
            cells.push_back(p_cell);
        }

        MeshBasedCellPopulation<2> cell_population(*p_mesh, cells);

        CellBasedSimulation<2> simulator(cell_population);
        simulator.SetOutputDirectory("TestCellBasedSimulationWithMotileCellProperty");
        simulator.SetEndTime(10.0);

        GeneralisedLinearSpringForce<2> linear_force;
        linear_force.SetCutOffLength(3);
        simulator.AddForce(&linear_force);

        TS_ASSERT_THROWS_NOTHING(simulator.Solve());

        SimulationTime::Destroy();
        RandomNumberGenerator::Destroy();
    }
};