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

Welcome to the Chaste wiki.

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”.

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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 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 to work with a specific tagged development version of Chaste. Presently it does not work with any of the previous release versions. However we will tie this code to the next release of Chaste.

Instructions for Ubuntu 16.04 or similar (Chaste version 3.x)

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


  git clone --depth 1 --branch paper/CellBasedComparison https://chaste.cs.ox.ac.uk/git/chaste.git Chaste
  cd Chaste

Alternatively, if you already have a clone of our Git repository then simply run the command

git pull; git checkout paper/CellBasedComparison

to move your source to the correct revision.

This project can be built with either of the two builders SCons or CMake. (Note that SCons will be deprecated in a later release of Chaste.) At this point you should configure Chaste with CMake or deprecated Scons.

You will also need the source for the CellBasedComparison2017 project. This can be done by checking out the version from the repository by using the command


svn checkout -r 27368 --username anonymous https://chaste.cs.ox.ac.uk/svn/chaste/projects/CellBasedComparison2017 projects/CellBasedComparison2017

in the Chaste directory. Note that username for checking out the project code is ‘anonymous’. When prompted for a password then please give an email address.

Instructions for Ubuntu 18.04 or similar (Chaste version 2017.x)

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


  git clone --depth 1 --branch paper/CellBasedComparison18 https://chaste.cs.ox.ac.uk/git/chaste.git Chaste
  cd Chaste

Alternatively, if you already have a clone of our Git repository then simply run the command

git pull; git checkout paper/CellBasedComparison18

to move your source to the correct revision.

This project can be built with either of the two builders SCons or CMake. (Note that SCons will be deprecated in a later release of Chaste.) At this point you should configure Chaste with CMake or deprecated Scons.

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


svn checkout -r 27524 --username anonymous https://chaste.cs.ox.ac.uk/svn/chaste/projects/CellBasedComparison2017 projects/CellBasedComparison2017

in the Chaste directory. Note that username for checking out the project code is ‘anonymous’. When prompted for a password then please give an email address.

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:

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

AdhesionProliferationShort-range signallingLong-range signalling
CASorting_CA_1_t1000Crypt_CA_08_t100DN_CA_01_t1000Morph_Ca_t100
CPSorting_Potts_1_t1000Crypt_Potts_08_t100DN_Potts_01_t1000Morph_Potts_t100
OSSorting_Node_1_t1000Crypt_Node_08_t100DN_Node_01_t1000Morph_Node_t100
VTSorting_Mesh_1_t1000Crypt_Mesh_08_t100DN_Mesh_01_t1000Morph_Mesh_t100
VMSorting_Vertex_1_t1000Crypt_Vertex_08_t100DN_Vertex_01_t1000Morph_Vertex_t100

Running tests

With SCons you can run tests with,


cd <Chaste path>

## Make and run a test at a time:
scons b=GccOpt ts=projects/CellBasedComparison2017/test/TestCellSortingLiteratePaper.hpp
## etc.

## Make and run all tests on 4 threads:
scons b=GccOpt -j4 projects/CellBasedComparison2017

With CMake you can run tests with,


cd <Chaste path>
cd ../chaste-build  ## Assuming you have configured CMake here.
cmake . ## Unnecessary extra step to pick up project and reconfigure

## 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

NB: the paper was developed with the specific tagged development version of Chaste

paper/CellBasedComparison

. It does not work with release version 3.4 or under, but will work on future releases.

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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