On-Lattice Agent-based Simulation of Populations of Cells within the Open-Source Chaste Framework"

This section contains pages generated automatically from the source code accompanying Figueredo et al (2013) “On-Lattice Agent-based Simulation of Populations of Cells within the Open-Source Chaste Framework”, Royal Society Interface Focus. doi: 10.1098/rsfs.2012.0081

The code to run single simulations, which was used to produce the figures in the paper, can be found here TestCaWithMultipleMutationStatesLiteratePaper.hpp and here TestCaBasedCellPopulationUsingPdesLiteratePaper.hpp

Before looking at this, 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 3.2. 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.

You will to checkout revision 18673 of the Chaste source code. 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/trunk -r 18673

You will also need the source for the InterfaceFocus2013 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/InterfaceFocus2013

in the projects folder of the Chaste directory. If you dont have a Chaste user account you can use the username “anonymous” and your email for the password.

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 classes necesary to run the simulation. These define the aditional ell cycle models etc. that not in the core chaste code.
  2. The test folder contains:

== Running tests == You can then run tests and simulations with,


cd <Chaste path>
scons b=GccOpt ts=projects/InterfaceFocus2013/test/TestCaWithMultipleMutationStatesLiteratePaper.hpp

and


scons b=GccOpt ts=projects/InterfaceFocus2013/test/TestCaBasedCellPopulationUsingPdesLiteratePaper.hpp

NB: the paper was developed with r18673 version. It may not work with other revisions.

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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