Planarian Shape Regulation During Growth and Degrowth

Supplementary Data for:

Mechanistic Regulation of Planarian Shape During Growth and Degrowth
Jason Ko, Waverly Reginato, and Daniel Lobo
Submitted, 2023

Installation

The source code is located in the src folder and can be directly executed with MATLAB (The Mathworks, Inc.) from that folder. It has been tested with release R2021a. The simulations use ROWMAP to numerically solve the equations. To install it, simply download the file rowmap.m into the src folder.

Growth and degrowth simulations

To run the simulations, execute any of the following commands in the MATLAB command prompt, replacing any variables in ALL_CAPS with real data:

For growth simulation, using manual parameters, run:

manualGrowthSimulation(NEW_SIM_ID)

For growth simulation, using the calibrated parameters by the evolutionary algorithm, run:

evolvedGrowthSimulation(NEW_SIM_ID)

For degrowth simulation, run:

degrowthSimulation(NEW_SIM_ID)

where NEW_SIM_ID is a string identifier for the output directory (e.g. 'sim1').

To run some other parameter set, we recommend the configuration in one of the above files.

Note:

As cached simulation data and video data are created, new subdirectories with the results will be automatically created under the results directory.

Evolutionary algorithm

To run the evolutionary algorithm, execute the following commands in a Bash shell:

JOB_NAME=run1
	
export MATLAB_LOG_DIR=~/$1
mkdir "$MATLAB_LOG_DIR"
 
TMPDIR=$(mktemp -d /tmp/matlab-lobo-XXXX)
trap 'rm -rf "$TMPDIR"' EXIT
 
matlab -nodisplay -r "geneticAlgorithm('$TMPDIR', 36, inf, '$JOB_NAME', 36); exit"

where JOB_NAME can be any identifying string for the search being run.

These are the most important scripts for running the evolutionary algorithm:

• geneticAlgorithm.m
• configureProject.m
• configureSimulation.m
• runSimulation.m

After running the evolutionary algorithm, the results can be plot with:

• plotGA.m

Image processing pipeline

The following scripts implement the automatic image analysis pipeline:

• extractShape.m
• extractShape2.m