stimulating_modular_cultures/README.md

Stimulating Modular Cultures

Data repository

This repository contains experimental data, processed analysis results, and rendered movies to accompany the paper. The subfolders contain compressed zip files, that can be downloaded separately. See below for where individual parts should be placed.

Citable reference:

@misc{yamamoto_modular_2022,
  title = {Modular Architecture Facilitates Noise-Driven Control of Synchrony in Neuronal Networks},
  author = {Yamamoto, Hideaki and Spitzner, F. Paul and Takemuro, Taiki and Buend{\'i}a, Victor and Morante, Carla and Konno, Tomohiro and Sato, Shigeo and {Hirano-Iwata}, Ayumi and Priesemann, Viola and Mu{\~n}oz, Miguel A. and Zierenberg, Johannes and Soriano, Jordi},
  year = {2022},
  eprint = {2205.10563},
  eprinttype = {arxiv},
  primaryclass = {q-bio},
  institution = {{arXiv}},
  doi = {10.48550/arXiv.2205.10563},
  url = {http://arxiv.org/abs/2205.10563},
  archiveprefix = {arXiv},
}

The source code is available via GitHub: https://github.com/Priesemann-Group/stimulating_modular_cultures

To enable plot scripts using the downloaded data (this repo), extract the zip files and place the /dat/ folder inside the base directory of the GitHub repository.

You can use the following one-liner to extract all zip files, if you cloned the full data repo:

cd repo_dir
find ./dat/ -name "*.zip" | while read filename; do unzip -o -d "`dirname "$filename"`" "$filename"; done;

The following structure is assumed by the analysis code (and, for the ./dat/ folder, will be created with above command):

stimulating_modular_cultures (code repo)/
├── ana/paper_plots.py
├── ...
└── dat/
    ├── experiments/
    │   ├── processed/ (extracted zip)
    │   └── raw/       (extracted zip)
    │       └── 1b/realization_id (e.g. 210315_A)
    └── simulations/
        ├── lif/
        │   ├── processed/ (extracted zip)
        │   └── raw/       (not provided)
        └── meso/
            ├── processed/ (extracted zip)
            └── raw/       (not provided)
...