Code and data for: Investigating local negative feedback of Rac activity

This archive contains all code, data, and simulation results associated with the manuscript "Investigating local negative feedback of Rac activity by mathematical models and cell motility simulations" by Jupiter Algorta, Jason P. Town, Orion D. Weiner, and Leah Edelstein-Keshet.
The project investigates the role of a local Rac inhibitor in neutrophil-like HL-60 cells using mathematical models and cell motility simulations. We simulate three models of Rac activity: the classical Wave-Pinning (WP) model, the Wave-Pinning with Inhibitor (WPI) model, and the WPI-PIP3 model, which introduces an intermediate signaling component. The models are validated against experimental data from optogenetic stimulation protocols and cell tracking experiments.

Contents:

• Jupyter notebooks that reproduce all figures and simulations from the main text and supplementary information.

• Data folders including experimental single-cell tracks, aligned fluorescence data, and model inputs.

• Full simulation results for back, side, reversal, gradient, and time stimulation protocols.

• Figures used in the manuscript and supplementary materials.

• Supplemental movies showing representative simulation behaviour.

• README documentation explaining folder structure and use.

Software Requirements:
Python packages used include: numpy, scipy, matplotlib, seaborn, pandas, scikit-image, jupyter.

License: Creative Commons Attribution 4.0 International.

Related identifiers:

• GitLab Repository (Updated version): https://gitlab.com/jupiteralgorta/rac-local-feedback 

• Preprint: https://doi.org/10.1101/2025.05.05.651928v1 (bioRxiv)

Version: v1.0

Authors:
Jupiter Algorta
Jason P. Town
Orion D. Weiner
Leah Edelstein-Keshet

Contact: jupitera@math.ubc.ca