Research data supporting "Cell-level model to predict the spatiotemporal dynamics of neurodegenerative disease"

This readme file was generated on 2025-08-19 by Shih-Huan Huang. GENERAL INFORMATION • Title of Dataset: Raw data and plotting scripts for "A cell-level model to predict the spatiotemporal dynamics of neurodegenerative disease" First Author Information Name: Shih-Huan Huang ORCID: 0000-0003-1707-9416 Institution: University of Cambridge Address: Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK Email: [e-mail] Corresponding Author Information Name: Georg Meisl ORCID: 0000-0002-6562-7715 Institution: University of Cambridge Address: Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK Email: [e-mail] SHARING/ACCESS INFORMATION • Licenses/restrictions placed on the data: CC BY 4.0: Creative Commons Attribution • Links to publications that cite or use the data: https://doi.org/10.48550/arXiv.2508.15046 • Links to other publicly accessible locations of the data: https://doi.org/10.48550/arXiv.2508.15046 • Links/relationships to ancillary data sets: None • Was data derived from another source? No. • Recommended citation for this dataset: Huang et al., (2025). Dataset for " A cell-level model to predict the spatiotemporal dynamics of neurodegenerative disease ". Apollo – University of Cambridge Repository. 10.17863/CAM.120852 DATA & FILE OVERVIEW File List: The dataset is organized into folders corresponding to each figure in the manuscript, with Python scripts in the root directory for plotting. • Fig2/ to Fig8/: Folders containing raw data files for Figures 2-8. • SIFig1/: Folder containing raw data for Supplementary Figure 1. • *.py and *.ipynb: Python scripts and a Jupyter Notebook used to analyze the raw data and generate the figures. • README: Instructions for the plotting. • Relationship between files, if important: The Python scripts in the root directory use the data files located in the corresponding FigX folders to generate the manuscript figures. • Additional related data collected that was not included in the current data package: None. • Are there multiple versions of the dataset? No. METHODOLOGICAL INFORMATION Description of methods for collection/generation of data: The data was generated from numerical simulations of the first-principles biophysical model described in our associated manuscript. Please refer to the Methods section of the publication for full details on the model and simulation protocols: https://doi.org/10.48550/arXiv.2508.15046 Methods for processing the data: The data provided is the direct, raw output from the numerical simulations. No post-processing or cleaning steps were applied to the raw data files. The included scripts are for analysis and visualization only. Instrument- or software-specific information needed to interpret the data: The plotting scripts require a Python 3.x environment. The following libraries and their dependencies are required to run the scripts: • numpy • matplotlib • pandas • scipy • jupyter (for running the .ipynb notebook)