Comparing individual-based approaches to modelling the self-organization of multicellular tissues

This section contains pages generated automatically from the source code accompanying the paper “Comparing individual-based approaches to modelling the self-organization of multicellular tissues”, PLOS Comput. Biol., 2017, doi: 10.1371/journal.pcbi.1005387.

Videos#

Adhesion:

Proliferation

Short-range signalling

Long-range signalling

Getting the code and installing dependencies#

Before running these examples you will need to install Chaste’s dependencies. 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 are encouraged to follow the Docker instructions.

To checkout the source code for the specific code revision use the command

git clone https://github.com/Chaste/Chaste.git Chaste
cd Chaste

This project must be built with CMake. At this point you should configure Chaste with CMake.

You will also need the (updated-since-publication) source for the CellBasedComparison2017 project. This can be done by checking out the version from the repository by using the command

cd projects
git clone https://github.com/Chaste/CellBasedComparison2017.git

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 classes which add functionality to the core Chaste code.
2. The test folder contains:
   • TestCellSortingLiteratePaper.hpp - this file can be run to generate the results in Figures 2 and 3.
   • TestCylindricalCryptLiteratePaper.hpp - this file can be run to generate the results in Figures 4, 5 and 6.
   • TestDeltaNotchLiteratePaper.hpp - this file can be run to generate the results in Figures 7 and 8.
   • TestMorphogenMonolayerLiteratePaper.hpp - this file can be run to generate the results in Figures 9, 10 and 11.

Clicking on the images below will take you to the code to run the corresponding simulation.

	Adhesion	Proliferation	Short-range signalling	Long-range signalling
CA
CP
OS
VT
VM

Running tests#

To run the tests, starting from the main Chaste source directory:

mkdir chaste-build && cd chaste-build
cmake ..

## Make and run a test at a time:
make  TestCellSortingLiteratePaperRunner
ctest -R TestCellSortingLiteratePaper
## etc.

## Make and run all tests on 4 threads:
make -j 4 project_CellBasedComparison2017
ctest -j 4 -L project_CellBasedComparison2017

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

Section contents#