Distribution of mitotic events in healthy and irradiated crypts

This section contains pages generated automatically from the source code accompanying Dunn et al. (2016) “Combined changes in Wnt signaling response and contact inhibition induce altered proliferation in radiation-treated intestinal crypts” in Mollecular Biology of the Cell http://dx.doi.org/10.1091/mbc.E15-12-0854

The code to simulate crypts and run parameter sweeps, which was used produce Figure 3 (and SI Figures 1.1-1.5), can be found here TestCryptProliferationDistributionLiteratePaper.hpp

The code to simulate crypts initialy comprised of control and gamma cells, and was used produce Figure 6, can be found here TestCryptTakeoverProbabilityLiteratePaper.hpp

Before looking at these, you may wish to look at some of the basic user tutorials for Chaste.

Getting the code and installing dependencies

Before running these examples you will need to install Chaste’s dependencies and the source code for version 3.3. The easiest way to do this is using an Ubuntu machine (or an Ubuntu virtual machine) as discussed on InstallGuides/UbuntuPackage. Note that Chaste is only fully supported on Linux/Unix systems, so users of Windows or Mac OS X may need to follow the virtual machine route. For manual installation of each dependency, on any version of Linux, see DeveloperInstallGuide.

NB: the paper was developed with release version 3.3 of Chaste. It does not work with release version 3.2 or under. It may need updating to work on newer revisions of the trunk code.

You will also need the source for the CryptProliferationDistribution project. This can be done by checking out the version from the repository by using the command


svn checkout https://chaste.cs.ox.ac.uk/svn/chaste/projects/CryptProliferationDistribution

in the projects folder of the Chaste directory.

Now the project should be installed, and everything should compile and run correctly. You can now run the tests or simulations, or create your own test suites.

Documentation

There are two folders - src and test.

  1. The src folder contains the following classes:
  • CellRetainerForce.xpp - The force which restrains stem and paneth cells in the base of the crypt.
  • CryptCellCycleModel.xpp - A cell cycle model which combines all 6 models investigated in the paper. Each model is selected by setting member variables.
  • CryptGeometryBoundaryCondition3d.xpp - The 3D gemoetry of the crypt based on measurements from a 6 week old male wild type mouse.
  • DifferentialAdhesionSpringForce.xpp - The force between cells, specifying differntial adhesion between stem and paneth cells.
  • OffLatticeSimulationWithMonoclonalStoppingEvent.xpp - A special simulations class where the simulation stops when the crypt becomes all one type, mutant or healthy.
  • PanethCellProliferativeType.xpp - A marker for paneth cells.
  1. The test folder contains:

Running tests

You can then run tests and simulations with,


cd <Chaste3.3 path>
scons b=GccOpt ts=projects/CryptProliferationDistribution/test/TestCryptProliferationDistributionLiteratePaper.hpp

and


scons b=GccOpt ts=projects/CryptProliferationDistribution/test/TestCryptTakeoverProbilityLiteratePaper.hpp

NB: the paper was developed with release version 3.4. It will not work with with release version 3.3 or under.

For further information on using Chaste, see the extensive guide material. You may also wish to look at some of the basic user tutorials.

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