calcium-ORAI1-pH

Jupyter notebook and Python code for modelling and analysis of intracellular calcium fluctuations in cancer cells to investigate store-operated calcium entry for ORAI1α and ORAI1β variants at differing extracellular pH, as published in:

Mélanie Robitaille, Michael H. McCullough, Choon Leng So, Sarah J. Roberts-Thomson, Gregory R. Monteith, ORAI1α and ORAI1β have differential sensitivity to extracellular pH, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 2025, 120010, doi: 10.1016/j.bbamcr.2025.120010.

Overview

This repository contains:

• The Jupyter notebook calcium-ORAI1-pH.ipynb which runs the analysis and model fitting for the calcium signalling data, and generating a subset of the results and figures for our study.

Installation and usage

To run the notebook:

1. Clone the repository.
2. Install the Python environment with conda using the included YAML file.

conda env create -f calcium-ORAI1-pH.yml

1. Download/extract the data (see Data availability).
2. Set the data_path_prefix environment variable in the preamble code block of the notebook. The data_path_prefix must point to where the downloaded data resides (i.e., where the folder ORAI1_2023 is stored).
3. Run all cells in order.

Data availability

Please refer to our published article for information on how to download the data.

References

Please see the companion paper linked above for details of the methods and packages used in this code.

Citing this code

If you use or adapt our code or methods in your research, please cite the companion paper linked above or as shown here in BibTeX format:

@article{robitaille2025orai1,
title = {ORAI1α and ORAI1β have differential sensitivity to extracellular pH},
journal = {Biochimica et Biophysica Acta (BBA) - Molecular Cell Research},
pages = {120010},
year = {2025},
issn = {0167-4889},
doi = {https://doi.org/10.1016/j.bbamcr.2025.120010},
url = {https://www.sciencedirect.com/science/article/pii/S0167488925001156},
author = {Mélanie Robitaille and Michael H. McCullough and Choon Leng So and Sarah J. Roberts-Thomson and Gregory R. Monteith},
}

This repository was archived on Zenodo upon acceptance for publication:

Questions

Please email michael.mccullough@anu.edu.au or create GitHub issue if you have questions about the code.