This software was developed using the user project template of Chaste. See the User Projects guide on the Chaste wiki for more information.
The software runs vertex model simulations based on the models presented in the following publications/preprints:
- Boocock et al Nature Physics (2021) doi: 10.1038/s41567-020-01037-7
- Boocock et al bioRxiv (2023) doi: 10.1101/2023.03.24.534111
The code can be used to reproduce the simulation results presented in Boocock et al (2023).
Before installation of this user project you will first need to download and install a version of Chaste. Simulations in Boocock et al (2023) were performed using Chaste 2019.1 and Chaste 2021.1 (recommended).
There are various ways of obtaining Chaste. One method is to clone from the Chaste github repository and change branch to a specific release:
git clone https://github.com/Chaste/Chaste.git
cd Chaste
git checkout release_2021.1
You then need to follow instructions to install dependencies and for first time configuration and build.
Once you have a working installation of Chaste, clone the erk_waves repository to the user projects directory and compile following the instructions in the User Projects guide. When running setup.py you only need to select yes for the cell_based component. To speed up simulations change "CMAKE_BUILD_TYPE" from "Debug" to "Release".
cd Chaste/projects
git clone https://github.com/DBoocock/erk_waves.git
cd erk_waves
python setup_project.py
cd path/to/chaste_build # e.g. cd ~/home/chaste_build
ccmake path/to/Chaste # e.g. ccmake ~/home/Chaste
make TestERKWaveWithSelfPropulsionNoAlignment
The "python" directory within the cloned repository contains a Python script for specifying combinations of parameter values and launching parralel simulations. Copy or move this directory to a convenient location and modify "batch_erk_propulsion_no_alignment.py" to point to the location of the compiled C++ executable in your build (default "~/chaste_build/projects/erk_waves/test/TestERKWaveWithSelfPropulsionNoAlignment").
To run:
python batch_erk_propulsion_no_alignment.py
Simulation output will be saved to a location specified by the system environment variable "CHASTE_TEST_OUTPUT" which you may set as desired. The output directory includes a file "params.txt" documenting parameter values as well as a csv file "results_from_time_xxxx/cell_data.dat" containing simulation data (the data to save is specified in the ErkPropulsionWriterNoAlignment class). Within each row of "cell_data.dat" the first column gives the simulation timepoint, then columns repeat in blocks of 8 containing the following information for each cell:
location_index # Redundant with cell_id
cell_id # Unique cell identifier
x, y # Cell centroid location
erk # ERK level
A0 # Target area
A # Cell area
theta # Angle of self-propulsion
Simulations can be visualized using ParaView: open ParaView and simply import the pvd file from the location "results_from_time_xxxx/results.pvd" (consult the Chaste Tutorials for further information).
The analysis of simulation output published in Boocock et al (2023) was performed using a suite of Python scripts and modules that are available with data using the following download link (850MB download).