Cell Based Comparison 2017

This repository contains the code used to produce results in the following paper: Comparing individual-based approaches to modelling the self-organization of multicellular tissues

The authors on this paper are:

• James M. Osborne
• Alexander G. Fletcher
• Joe M. Pitt-Francis
• Philip K. Maini
• David J. Gavaghan

Code to reproduce simulations

The following test files run simulations from the paper:

• TestCellSortingLiteratePaper.hpp
• TestCylindricalCryptLiteratePaper.hpp
• TestDeltaNotchLiteratePaper.hpp
• TestMorphogenMonolayerLiteratePaper.hpp

Continuous testing

This project is regularly compiled, and short versions of each simulation are regularly run every time the main Chaste repository is updated. If you encounter a problem running the code in this project, please open an issue.

The original parameter values are available in a block near the top of each file.

Running these simulations

You must first compile Chaste. Visit our getting started page for full details.

From the projects directory, clone this repository:

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

From your Chaste build directory, configure, compile and run with any configuration you like, for instance:

build$ cmake -DCMAKE_BUILD_TYPE=Release -DChaste_ERROR_ON_WARNING=OFF /path/to/chaste
build$ make -j4 project_CellBasedComparison2017
build$ ctest -j4 -L project_CellBasedComparison2017