Fitting of a Rac-Inhibitor-PIP3 Model to Spatial and Temporal Dynamics in Neutrophil-like Cells

This archive contains code and data used to jointly fit a mechanistic model of Rac activation and inhibition to both time-series and spatial Rac activity data in neutrophil-like HL-60 cells. The model incorporates Rac self-amplification, negative feedback via a putative inhibitor, and upstream regulation by PIP3.
Temporal data are drawn from fold-change measurements in latrunculin-treated cells, while spatial data are based on Rac distributions in response to varied optogenetic protocols (front, side, global, reversal).
Optimization is performed using differential evolution on a coupled PDE-ODE system implemented in Python.

Software Requirements:
Python packages used include: numpy, scipy, matplotlib, multiprocessing, logging, os, datetime.

License: Creative Commons Attribution 4.0 International.

Related identifiers:
GitLab Repository: 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