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README: Network of Neuron-Astrocyte Mass Models (NNAMM) Simulations

This README file assists in understanding the codes and data accompanying the manuscript titled "Dialogue mechanisms between astrocytic and neuronal networks: a whole-brain modelling approach".

Table of Contents

  1. Requirements
  2. Main Scripts
  3. Data
  4. Data Use Terms
  5. Main Script Details
  6. Helper Scripts
  7. Codes and Data Not Included
  8. Citation
  9. Contact Information

Requirements

To run the scripts, the following software and packages are required:

  • MATLAB (tested with version R2022a)
  • MatCont (tested with version 7.3)
  • Python (tested with version 3.6.15)
  • PyDSTool (tested with version 0.91.0)

For detailed methodologies, please refer to the manuscript.

Main Scripts

Refer to Main Script Details for more information.

Data

Data Use Terms

This repository includes a structural connectome derived from the Human Connectome Project (HCP) Young Adult dataset. Users of this data must comply with the HCP Data Use Terms. For more information, see the HCP Young Adult Data Use Terms.

Main Script Details

Simulations

./codes/nnamm_simulations.m

  • Performs network simulations using dependencies located in ./codes/util/, ./codes/functions/, and ./codes/nnamm/. The variable proj_dir (line 12) specifies these dependencies.
  • Utilises post-processed connectomes from ./data/connectomes/ (see line 38).
  • Outputs are saved relative to proj_dir (see line 29).
  • Does not check available RAM or disk memory before running. Guidance for configuration is provided (see line 50).

Bifurcation Diagrams

./codes/bd_draw_alpha.m

  • Quickly draws bifurcation diagrams.
  • Depends on files in ./codes/util/ and ./codes/functions/. Ensure the variable proj_dir (line 6) is correctly specified.
  • Outputs are saved relative to proj_dir (see line 15).

MatCont Analysis

./codes/matcont_analysis.m

  • Continues saddle-node and Hopf branches using MatCont.
  • Dependencies are located in ./codes/util/ and ./codes/functions/. The variable proj_dir (line 9) specifies these dependencies.
  • The MatCont library is not included in ./codes/ and must be provided (see link in Codes and Data Not Included). The variable matcont_bin (line 23) specifies the path to the root directory of the MatCont library (which contains the function init.m).
  • Requires outputs from ./codes/bd_draw_alpha.m as inputs (see line 34).
  • Outputs are saved in the same directory as the input files with consistent naming.

PyDSTool Analysis

./codes/pydstool_analysis.py

Illustrations

./codes/illustrations_basic.mlx
./codes/illustrations_basic.html

  • Guides users in handling data and creating figures (e.g., structural connectomes, simulation outputs, and bifurcation data).
  • Relies on files in ./data/, ./codes/util/, and ./codes/functions/. Configure proj_dir (line 1) for dependencies.

Helper Scripts

Codes and Data Not Included

  • Brain Connectivity Toolbox, 2019-03-03 release, link
  • Connectome Mapper 3, version 3.0.3, link
  • FreeSurfer, version 6.0.0, link
  • MatCont, version 7.3, link
  • MuxViz, version 3.1, link
  • PyDSTool, version 0.91.0, link
  • Scientific Colour Maps, version 7.0.1, link
  • Scilpy Python library, version 1.3.0, link
  • SET, version 1.0, link
  • Tractoflow, version 2.2.1, link

Citation

If you use this code or data in your research, please cite:

Ali et al., 2025, "Dialogue mechanisms between astrocytic and neuronal networks: a whole-brain modelling approach", PLOS Computational Biology, DOI: 10.1371/journal.pcbi.1012683

Contact Information

For questions or issues, contact Obaï Bin Ka'b Ali at [ali.obaibk (at) gmail (dot) com].