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.gitFrom 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