A Cellular Potts Model (CPM) of Colorectal Cancer

This section contains pages generated automatically from the source code accompanying “Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework” http://dx.doi.org/10.4137/CIN.S19332

The code to run single simulations and was used to produce Figures 2 and 3 can be found here TestPottsCryptLiteratePaper.hpp

The code to run parameter sweeps and was used produce Figure 4 can be found here TestPottsCryptSweepsLiteratePaper.hpp

The code to run include mutations and was used produce Figures 5, 7 and 8 can be found here TestPottsCryptMutantLiteratePaper.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 PottsCrypt2015 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/PottsCrypt2015

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:
  • CellShapeOutputModifier.xpp - Modifier class to output the area, perimeter, and circularity of cells in a simulation.
  • FixedSimpleWntCellCycleModel.xpp - A version of the SimpleWntCellCycleModel class to represent the cell cycle model as described in the paper.
  • MutantBaseTrackerModifier.xpp - Modifier class which tracks the base (and top) of the mutant patch.
  • MutantCellPottsUpdateRule.xpp - The component of the Hamiltonian (represented as a PottsUpdateRule) which models mutant cells as described in the paper.
  1. The test folder contains:

Running tests

You can then run tests and simulations with,


cd <Chaste3.3 path>
scons b=GccOpt ts=projects/PottsCrypt2015/test/TestPottsCryptLiteratePaper.hpp

and


scons b=GccOpt ts=projects/PottsCrypt2015/test/TestPottsCryptSweepLiteratePaper.hpp

and


scons b=GccOpt ts=projects/PottsCrypt2015/test/TestPottsCryptMutantLiteratePaper.hpp

NB: the paper was developed with release version 3.3. It will not work with with release version 3.2 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.

Section contents

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