wiki:PaperTutorials/CellBasedComparison2017

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".

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.

Adhesion Proliferation Short-range signalling Long-range signalling
CA source:projects/CellBasedComparison2017/figures/Sorting_CA_1_t1000.png source:projects/CellBasedComparison2017/figures/Crypt_CA_08_t100.png source:projects/CellBasedComparison2017/figures/DN_CA_01_t1000.png source:projects/CellBasedComparison2017/figures/Morph_Ca_t100.png
CP source:projects/CellBasedComparison2017/figures/Sorting_Potts_1_t1000.png source:projects/CellBasedComparison2017/figures/Crypt_Potts_08_t100.png source:projects/CellBasedComparison2017/figures/DN_Potts_01_t1000.png source:projects/CellBasedComparison2017/figures/Morph_Potts_t100.png
OS source:projects/CellBasedComparison2017/figures/Sorting_Node_1_t1000.png source:projects/CellBasedComparison2017/figures/Crypt_Node_08_t100.png source:projects/CellBasedComparison2017/figures/DN_Node_01_t1000.png source:projects/CellBasedComparison2017/figures/Morph_Node_t100.png
VT source:projects/CellBasedComparison2017/figures/Sorting_Mesh_1_t1000.png source:projects/CellBasedComparison2017/figures/Crypt_Mesh_08_t100.png source:projects/CellBasedComparison2017/figures/DN_Mesh_01_t1000.png source:projects/CellBasedComparison2017/figures/Morph_Mesh_t100.png
VM source:projects/CellBasedComparison2017/figures/Sorting_Vertex_1_t1000.png source:projects/CellBasedComparison2017/figures/Crypt_Vertex_08_t100.png source:projects/CellBasedComparison2017/figures/DN_Vertex_01_t1000.png source:projects/CellBasedComparison2017/figures/Morph_Vertex_t100.png

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

Last modified 3 years ago Last modified on Nov 27, 2018, 2:16:50 PM