Documentation for Release 2024.2

Running Delta Notch Simulations

This tutorial is automatically generated from TestRunningDeltaNotchSimulationsTutorial.hpp at revision 409e06cb314b. Note that the code is given in full at the bottom of the page.

An example showing how to run Delta/Notch simulations

Introduction

In this tutorial we show how Chaste can be used to simulate a growing cell monolayer culture into which a simple model of Delta/Notch signalling is incorporated. This model was developed by Collier et al. (“Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling”, J. Theor. Biol. 183:429-446) and comprises two ODEs to describe the evolution in concentrations of Delta and Notch in each cell. The ODE for Notch includes a reaction term that depends on the mean Delta concentration among neighbouring cells. Thus in this simulation each cell needs to be able to access information about its neighbours. We use the CellData class to facilitate this, and introduce a subclass of OffLatticeSimulation called DeltaNotchOffLatticeSimulation to handle the updating of CellData at each time step as cell neighbours change.

The test

As in previous tutorials, we begin by including the necessary header files. We have encountered these files already. Recall that often, either CheckpointArchiveTypes.hpp or CellBasedSimulationArchiver.hpp must be included the first Chaste header.

#include <cxxtest/TestSuite.h>
#include "CheckpointArchiveTypes.hpp"
#include "AbstractCellBasedTestSuite.hpp"
#include "HoneycombMeshGenerator.hpp"
#include "HoneycombVertexMeshGenerator.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "OffLatticeSimulation.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "NagaiHondaForce.hpp"
#include "SimpleTargetAreaModifier.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "DifferentiatedCellProliferativeType.hpp"
#include "WildTypeCellMutationState.hpp"
#include "CellAgesWriter.hpp"
#include "CellIdWriter.hpp"
#include "CellProliferativePhasesWriter.hpp"
#include "CellVolumesWriter.hpp"
#include "CellMutationStatesCountWriter.hpp"
#include "CellProliferativePhasesCountWriter.hpp"
#include "CellProliferativeTypesCountWriter.hpp"
#include "SmartPointers.hpp"
#include "PetscSetupAndFinalize.hpp"
#include "UniformG1GenerationalCellCycleModel.hpp"

The next header file defines a simple subcellular reaction network model that includes the functionality for solving each cell’s Delta/Notch signalling ODE system at each time step, using information about neighbouring cells through the CellData class.

#include "DeltaNotchSrnModel.hpp"

The next header defines the simulation class modifier corresponding to the Delta-Notch SRN model. This modifier leads to the CellData cell property being updated at each timestep to deal with Delta-Notch signalling.

#include "DeltaNotchTrackingModifier.hpp"

Having included all the necessary header files, we proceed by defining the test class.

class TestRunningDeltaNotchSimulationsTutorial : public AbstractCellBasedTestSuite
{
public:

Test 1: a vertex-based monolayer with Delta/Notch signalling

In the first test, we demonstrate how to simulate a monolayer that incorporates Delta/Notch signalling, using a vertex-based approach.

    void TestVertexBasedMonolayerWithDeltaNotch()
    {

We include the next line because vertex simulations cannot be run in parallel

        EXIT_IF_PARALLEL;

First we create a regular vertex mesh.

        HoneycombVertexMeshGenerator generator(5, 5);
        boost::shared_ptr<MutableVertexMesh<2,2> > p_mesh = generator.GetMesh();

We then create some cells, each with a cell-cycle model, UniformG1GenerationalCellCycleModel and a subcellular reaction network model DeltaNotchSrnModel, which incorporates a Delta/Notch ODE system, here we use the hard coded initial conditions of 1.0 and 1.0. In this example we choose to make each cell differentiated, so that no cell division occurs.

        std::vector<CellPtr> cells;
        MAKE_PTR(WildTypeCellMutationState, p_state);
        MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);

        for (unsigned elem_index=0; elem_index<p_mesh->GetNumElements(); elem_index++)
        {
            UniformG1GenerationalCellCycleModel* p_cc_model = new UniformG1GenerationalCellCycleModel();
            p_cc_model->SetDimension(2);

We choose to initialise the concentrations to random levels in each cell.

            std::vector<double> initial_conditions;
            initial_conditions.push_back(RandomNumberGenerator::Instance()->ranf());
            initial_conditions.push_back(RandomNumberGenerator::Instance()->ranf());
            DeltaNotchSrnModel* p_srn_model = new DeltaNotchSrnModel();
            p_srn_model->SetInitialConditions(initial_conditions);

            CellPtr p_cell(new Cell(p_state, p_cc_model, p_srn_model));
            p_cell->SetCellProliferativeType(p_diff_type);
            double birth_time = -RandomNumberGenerator::Instance()->ranf()*12.0;
            p_cell->SetBirthTime(birth_time);
            cells.push_back(p_cell);
        }

Using the vertex mesh and cells, we create a cell-based population object, and specify which results to output to file.

        VertexBasedCellPopulation<2> cell_population(*p_mesh, cells);
        cell_population.AddCellPopulationCountWriter<CellMutationStatesCountWriter>();
        cell_population.AddCellPopulationCountWriter<CellProliferativeTypesCountWriter>();
        cell_population.AddCellPopulationCountWriter<CellProliferativePhasesCountWriter>();
        cell_population.AddCellWriter<CellProliferativePhasesWriter>();
        cell_population.AddCellWriter<CellAgesWriter>();
        cell_population.AddCellWriter<CellVolumesWriter>();

We are now in a position to create and configure the cell-based simulation object, pass a force law to it, and run the simulation. We can make the simulation run for longer to see more patterning by increasing the end time.

        OffLatticeSimulation<2> simulator(cell_population);
        simulator.SetOutputDirectory("TestVertexBasedMonolayerWithDeltaNotch");
        simulator.SetSamplingTimestepMultiple(10);
        simulator.SetEndTime(1.0);

Then, we define the modifier class, which automatically updates the values of Delta and Notch within the cells in CellData and passes it to the simulation.

        MAKE_PTR(DeltaNotchTrackingModifier<2>, p_modifier);
        simulator.AddSimulationModifier(p_modifier);

        MAKE_PTR(NagaiHondaForce<2>, p_force);
        simulator.AddForce(p_force);

This modifier assigns target areas to each cell.

        MAKE_PTR(SimpleTargetAreaModifier<2>, p_growth_modifier);
        simulator.AddSimulationModifier(p_growth_modifier);
        simulator.Solve();
    }

To visualize the results, use Paraview. See the Visualizing With Paraview tutorial for more information.

Load the file $CHASTE_TEST_OUTPUT/TestVertexBasedMonolayerWithDeltaNotch/results_from_time_0/results.pvd.

Test 2 - a node-based monolayer with Delta/Notch signalling

In the next test we run a similar simulation as before, but this time with node-based ‘overlapping spheres’ model.

    void TestNodeBasedMonolayerWithDeltaNotch()
    {

We include the next line because HoneycombMeshGenerator, used in this test, is not yet implemented in parallel.

        EXIT_IF_PARALLEL;

Most of the code in this test is the same as in the previous test, except we now create a ’nodes-only mesh’ and NodeBasedCellPopulation.

        HoneycombMeshGenerator generator(5, 5);
        boost::shared_ptr<MutableMesh<2,2> > p_generating_mesh = generator.GetMesh();
        NodesOnlyMesh<2> mesh;

The mechanics cut-off length (second argument) is used in this simulation to determine nearest neighbours for the purpose of the Delta/Notch intercellular signalling model.

        mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);

        std::vector<CellPtr> cells;
        MAKE_PTR(WildTypeCellMutationState, p_state);
        MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
        for (unsigned i=0; i<mesh.GetNumNodes(); i++)
        {
            UniformG1GenerationalCellCycleModel* p_cc_model = new UniformG1GenerationalCellCycleModel();
            p_cc_model->SetDimension(2);

We choose to initialise the concentrations to random levels in each cell.

            std::vector<double> initial_conditions;
            initial_conditions.push_back(RandomNumberGenerator::Instance()->ranf());
            initial_conditions.push_back(RandomNumberGenerator::Instance()->ranf());
            DeltaNotchSrnModel* p_srn_model = new DeltaNotchSrnModel();
            p_srn_model->SetInitialConditions(initial_conditions);

            CellPtr p_cell(new Cell(p_state, p_cc_model, p_srn_model));
            p_cell->SetCellProliferativeType(p_diff_type);
            double birth_time = -RandomNumberGenerator::Instance()->ranf()*12.0;
            p_cell->SetBirthTime(birth_time);
            cells.push_back(p_cell);
        }

        NodeBasedCellPopulation<2> cell_population(mesh, cells);
        cell_population.AddCellPopulationCountWriter<CellProliferativeTypesCountWriter>();
        cell_population.AddCellPopulationCountWriter<CellMutationStatesCountWriter>();
        cell_population.AddCellWriter<CellIdWriter>();
        cell_population.AddCellPopulationCountWriter<CellProliferativePhasesCountWriter>();
        cell_population.AddCellWriter<CellAgesWriter>();

        OffLatticeSimulation<2> simulator(cell_population);
        simulator.SetOutputDirectory("TestNodeBasedMonolayerWithDeltaNotch");
        simulator.SetSamplingTimestepMultiple(10);
        simulator.SetEndTime(5.0);

Again we define the modifier class, which automatically updates the values of Delta and Notch within the cells in CellData and passes it to the simulation.

        MAKE_PTR(DeltaNotchTrackingModifier<2>, p_modifier);
        simulator.AddSimulationModifier(p_modifier);

As we are using a node-based cell population, we use an appropriate force law.

        MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
        p_force->SetCutOffLength(1.5);
        simulator.AddForce(p_force);

        simulator.Solve();
    }
};

To visualize the results, use Paraview. See the Visualizing With Paraview tutorial for more information.

Load the file $CHASTE_TEST_OUTPUT/TestNodeBasedMonolayerWithDeltaNotch/results_from_time_0/results.pvd, and add a spherical glyph.

Note that, for larger simulations, you may need to unclick “Mask Points” (or similar) so as not to limit the number of glyphs displayed by Paraview.

Full code

#include <cxxtest/TestSuite.h>
#include "CheckpointArchiveTypes.hpp"
#include "AbstractCellBasedTestSuite.hpp"
#include "HoneycombMeshGenerator.hpp"
#include "HoneycombVertexMeshGenerator.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "OffLatticeSimulation.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "NagaiHondaForce.hpp"
#include "SimpleTargetAreaModifier.hpp"
#include "GeneralisedLinearSpringForce.hpp"
#include "DifferentiatedCellProliferativeType.hpp"
#include "WildTypeCellMutationState.hpp"
#include "CellAgesWriter.hpp"
#include "CellIdWriter.hpp"
#include "CellProliferativePhasesWriter.hpp"
#include "CellVolumesWriter.hpp"
#include "CellMutationStatesCountWriter.hpp"
#include "CellProliferativePhasesCountWriter.hpp"
#include "CellProliferativeTypesCountWriter.hpp"
#include "SmartPointers.hpp"
#include "PetscSetupAndFinalize.hpp"
#include "UniformG1GenerationalCellCycleModel.hpp"
#include "DeltaNotchSrnModel.hpp"
#include "DeltaNotchTrackingModifier.hpp"

class TestRunningDeltaNotchSimulationsTutorial : public AbstractCellBasedTestSuite
{
public:

    void TestVertexBasedMonolayerWithDeltaNotch()
    {
        EXIT_IF_PARALLEL;

        HoneycombVertexMeshGenerator generator(5, 5);
        boost::shared_ptr<MutableVertexMesh<2,2> > p_mesh = generator.GetMesh();

        std::vector<CellPtr> cells;
        MAKE_PTR(WildTypeCellMutationState, p_state);
        MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);

        for (unsigned elem_index=0; elem_index<p_mesh->GetNumElements(); elem_index++)
        {
            UniformG1GenerationalCellCycleModel* p_cc_model = new UniformG1GenerationalCellCycleModel();
            p_cc_model->SetDimension(2);

            std::vector<double> initial_conditions;
            initial_conditions.push_back(RandomNumberGenerator::Instance()->ranf());
            initial_conditions.push_back(RandomNumberGenerator::Instance()->ranf());
            DeltaNotchSrnModel* p_srn_model = new DeltaNotchSrnModel();
            p_srn_model->SetInitialConditions(initial_conditions);

            CellPtr p_cell(new Cell(p_state, p_cc_model, p_srn_model));
            p_cell->SetCellProliferativeType(p_diff_type);
            double birth_time = -RandomNumberGenerator::Instance()->ranf()*12.0;
            p_cell->SetBirthTime(birth_time);
            cells.push_back(p_cell);
        }

        VertexBasedCellPopulation<2> cell_population(*p_mesh, cells);
        cell_population.AddCellPopulationCountWriter<CellMutationStatesCountWriter>();
        cell_population.AddCellPopulationCountWriter<CellProliferativeTypesCountWriter>();
        cell_population.AddCellPopulationCountWriter<CellProliferativePhasesCountWriter>();
        cell_population.AddCellWriter<CellProliferativePhasesWriter>();
        cell_population.AddCellWriter<CellAgesWriter>();
        cell_population.AddCellWriter<CellVolumesWriter>();

        OffLatticeSimulation<2> simulator(cell_population);
        simulator.SetOutputDirectory("TestVertexBasedMonolayerWithDeltaNotch");
        simulator.SetSamplingTimestepMultiple(10);
        simulator.SetEndTime(1.0);

        MAKE_PTR(DeltaNotchTrackingModifier<2>, p_modifier);
        simulator.AddSimulationModifier(p_modifier);

        MAKE_PTR(NagaiHondaForce<2>, p_force);
        simulator.AddForce(p_force);

        MAKE_PTR(SimpleTargetAreaModifier<2>, p_growth_modifier);
        simulator.AddSimulationModifier(p_growth_modifier);
        simulator.Solve();
    }

    void TestNodeBasedMonolayerWithDeltaNotch()
    {
        EXIT_IF_PARALLEL;

        HoneycombMeshGenerator generator(5, 5);
        boost::shared_ptr<MutableMesh<2,2> > p_generating_mesh = generator.GetMesh();
        NodesOnlyMesh<2> mesh;
        mesh.ConstructNodesWithoutMesh(*p_generating_mesh, 1.5);

        std::vector<CellPtr> cells;
        MAKE_PTR(WildTypeCellMutationState, p_state);
        MAKE_PTR(DifferentiatedCellProliferativeType, p_diff_type);
        for (unsigned i=0; i<mesh.GetNumNodes(); i++)
        {
            UniformG1GenerationalCellCycleModel* p_cc_model = new UniformG1GenerationalCellCycleModel();
            p_cc_model->SetDimension(2);

            std::vector<double> initial_conditions;
            initial_conditions.push_back(RandomNumberGenerator::Instance()->ranf());
            initial_conditions.push_back(RandomNumberGenerator::Instance()->ranf());
            DeltaNotchSrnModel* p_srn_model = new DeltaNotchSrnModel();
            p_srn_model->SetInitialConditions(initial_conditions);

            CellPtr p_cell(new Cell(p_state, p_cc_model, p_srn_model));
            p_cell->SetCellProliferativeType(p_diff_type);
            double birth_time = -RandomNumberGenerator::Instance()->ranf()*12.0;
            p_cell->SetBirthTime(birth_time);
            cells.push_back(p_cell);
        }

        NodeBasedCellPopulation<2> cell_population(mesh, cells);
        cell_population.AddCellPopulationCountWriter<CellProliferativeTypesCountWriter>();
        cell_population.AddCellPopulationCountWriter<CellMutationStatesCountWriter>();
        cell_population.AddCellWriter<CellIdWriter>();
        cell_population.AddCellPopulationCountWriter<CellProliferativePhasesCountWriter>();
        cell_population.AddCellWriter<CellAgesWriter>();

        OffLatticeSimulation<2> simulator(cell_population);
        simulator.SetOutputDirectory("TestNodeBasedMonolayerWithDeltaNotch");
        simulator.SetSamplingTimestepMultiple(10);
        simulator.SetEndTime(5.0);

        MAKE_PTR(DeltaNotchTrackingModifier<2>, p_modifier);
        simulator.AddSimulationModifier(p_modifier);

        MAKE_PTR(GeneralisedLinearSpringForce<2>, p_force);
        p_force->SetCutOffLength(1.5);
        simulator.AddForce(p_force);

        simulator.Solve();
    }
};

Running Delta Notch Simulations

Running Differential Adhesion Simulations

Running Delta Notch Simulations

An example showing how to run Delta/Notch simulations#

Introduction#

The test#

Test 1: a vertex-based monolayer with Delta/Notch signalling#

Test 2 - a node-based monolayer with Delta/Notch signalling#

Full code#

An example showing how to run Delta/Notch simulations

Introduction

The test

Test 1: a vertex-based monolayer with Delta/Notch signalling

Test 2 - a node-based monolayer with Delta/Notch signalling

Full code