Cycloop

Cycloop is the repository containing the MATLAB code that supports the findings of the study: 'Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control.'

Repo Contents

• Computational_Analysis
• Illustrative_Platform_Code
• Simulator
• Supplementary_Data_1

System Requirements

Hardware Requirements

Cycloop requires only a standard computer with enough RAM to run the code in the MATLAB environment.

OS Requirements

This package is supported for macOS Catalina and Windows 10. The package has been tested on the following systems:

• macOS Catalina
• Windows 10

Software Dependencies

• MATLAB R2019a
• Additional MATLAB toolboxes (e.g. Signal Processing Toolbox, Image Processing Toolbox, etc.)

Installation Guide

1. Download the repository from https://github.com/dibbelab/Cycloop .
2. Unpack the files.
3. Start MATLAB and navigate to the Cycloop folder.

Demo

See the Instructions for Use section.

Instructions for Use

Simulator

Set the working directory to ./Simulator/.

• Run the script main_code.m to generate the simulations shown in Fig. 3b-e and Fig. 4b-e.
• Run the script make_SFIG2_bd.m to generate the analysis shown in Supplementary Fig. 2b, d.
• Run the script make_SFIG2_ce.m to generate the analysis shown in Supplementary Fig. 2c, e.

Computational Analysis

Non-Cycling Strain

Set the working directory to ./Computational_Analysis/NonCycling/.

• Run the script Main.m to generate the outputs related to the microfluidics experiments shown in Fig. 2, Fig. 3f-t, Supplementary Fig. 3, Supplementary Fig. 5, and Supplementary Fig. 6.
• Run the script make_SuppFig1_abc.m to generate the outputs related to the microfluidics experiment shown in Supplementary Fig. 1a-c.
• Run the script make_SuppFig1_def.m to generate the single-cell traces shown in Supplementary Fig. 1d-f.
• Run the script make_SuppFig4.m to generate the quantitative analysis shown in Supplementary Fig. 4a, c, e, g.

Single-cell traces

To regenerate the single-cell traces, follow these steps:

1. Download the raw images from https://zenodo.org/record/4516319/files/Raw_images%28NonCycling%29.zip .
2. Unpack the raw images in the folder ./Computational_Analysis/NonCycling/Raw_images/.
3. Delete the *.mat files located in the folder ./Computational_Analysis/NonCycling/Cell_traces/.
4. Run the script Main.m.

Cycling Strain

Set the working directory to ./Computational_Analysis/Cycling/.

• Run the script main_script.m to generate the outputs related to the microfluidics experiments shown in Fig. 4f-t, Supplementary Fig. 7 and Supplementary Fig. 8.
• Run the script make_SFIG4.m to generate the quantitative analysis shown in Supplementary Fig. 4b, d, f, h.
• Run the script make_SFIG9.m to generate the correlation analysis shown in Supplementary Fig. 9.

Single-cell traces

To regenerate the single-cell traces, follow these steps:

1. Download the raw images from https://zenodo.org/record/4516319/files/Raw_images%28Cycling%29.zip .
2. Unpack the raw images in the folder ./Computational_Analysis/Cycling/Raw_images/.
3. Delete the *.mat files located in the folder ./Computational_Analysis/Cycling/Cell_traces/.
4. Run the script main_script.m.

Illustrative Code

Illustrative Platform Code

The folder ./Illustrative_Platform_Code contains the illustrative code used to perform the microfluidics control experiments.

License

This code is licensed under the GNU General Public License v3.0.