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. Main Script Details
   • Simulations
   • Bifurcation Diagrams
   • MatCont Analysis
   • PyDSTool Analysis
   • Illustrations
5. Helper Scripts
6. Codes and Data Not Included
7. Citation
8. Contact Information

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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.

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Main Scripts

• ./codes/nnamm_simulations.m: Runs the main simulations.
• ./codes/bd_draw_alpha.m: Draws bifurcation diagrams.
• ./codes/matcont_analysis.m: Performs MatCont analyses.
• ./codes/pydstool_analysis.py: Performs PyDSTool analyses.
• ./codes/illustrations_basic.mlx: An interactive MATLAB Notebook for handling data and creating figures.

Refer to Main Script Details for more information.

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Data

• Post-processed neuronal connectome for simulations:
  ./data/connectomes/HCP-average_laus18-3_sc.csv

• Post-processed astrocytic connectome for simulations:
  ./data/connectomes/ICBM152A09C_laus18-3_mid-fs-311558V_weights.csv

• Labels for post-processed connectomes:
  ./data/connectomes/hierarchy.laus18-3.lobes.xls

• Raw connectomes and their labels:
  ./data/connectomes/raw/

• Post-processed whole-brain mean data after running calibration simulations:
  ./data/analyses/activity/papaya-r0/activity.whole-brain.mean.xls

• Post-processed whole-brain mean data after running main simulations:
  ./data/analyses/activity/papaya-r1/activity.whole-brain.mean.xls

• Post-processed limit cycle curves data from PyDSTool analyses:
  ./data/bifurcation-diagrams/alpha/C_Pyr_to_Pyr-7.5.lcc.mat

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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 31).
• Outputs are saved relative to proj_dir (see line 22).
• Does not check available RAM or disk memory before running. Guidance for configuration is provided (see line 43).

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 7).

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 16) 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 27).
• Outputs are saved in the same directory as the input files with consistent naming.

PyDSTool Analysis

./codes/pydstool_analysis.py

• Continues limit cycles using PyDSTool (see link in Codes and Data Not Included).
• Uses outputs from ./codes/bd_draw_alpha.m as inputs (see line 159).
• Outputs are saved in the same directory as the input files with consistent naming.

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.

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Helper Scripts

• ./codes/nnamm/
• ./codes/functions/
• ./codes/util/

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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

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Citation

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

Ali et al., 2024, "Dialogue mechanisms between astrocytic and neuronal networks: a whole-brain modelling approach", PLOS Computational Biology, DOI: 10.1371/journal.pcbi.1012683

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Contact Information

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