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https://github.com/helveg/deschepper-etal-2022-source
Documents in preparation of the very first paper De Schepper et al. 2020
https://github.com/helveg/deschepper-etal-2022-source
Last synced: 9 days ago
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Documents in preparation of the very first paper De Schepper et al. 2020
- Host: GitHub
- URL: https://github.com/helveg/deschepper-etal-2022-source
- Owner: Helveg
- Created: 2020-05-22T08:53:39.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-11-29T18:09:37.000Z (about 1 year ago)
- Last Synced: 2024-11-10T15:51:06.618Z (2 months ago)
- Language: Python
- Size: 50.2 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Reconstruction and simulation of an entire column of the cerebellar cortex
Required steps to reproduce De Schepper et al. 2022
## Installing the full software environment
This step is not always required, to simply reproduce the plots from the available datasets, this can be skipped.
```
pip install -r requirements.txt --only-binary=":all:"
```
If you're planning to use MPI, also install `mpi4py`:
```
pip install mpi4py
```
## Usage
1. Plot all figures
```
python plot
```
2. Plot specific figures
```
python plot figure1 figure2
```
The figure names correspond to the filenames without the suffix
3. Build the static image files
```
python build [format]
```
The default format is EPS.
## Obtaining the data
You can obtain an already reconstructed version of the network model at https://doi.org/10.5281/zenodo.7230288 and save it as `/networks/balanced.hdf5`. Otherwise you can reconstruct it yourself by downloading the [morphologies](https://doi.org/10.5281/zenodo.7230455) as `morphologies.hdf5` running:
```
bsb -v=4 -c=configs/balanced.json compile
```
To replicate the figures, you require certain result files in exact locations inside of the `results` folder. These files are available as datasets on Zenodo, here is a list of URLs for each plot:
* `feedforward_jitter`: https://doi.org/10.5281/zenodo.7230239 (place in: `results/single_impulse/sensory_burst`)
* `feedforward`: https://doi.org/10.5281/zenodo.7230798, https://doi.org/10.5281/zenodo.7230830, https://doi.org/10.5281/zenodo.7230836 (place in: `results/clamp`)
* `goc_nspos`, `goc_sync*`: https://doi.org/10.5281/zenodo.7231068 (place in: `results`)
* `goc_nsync`, `goc_sync*`: https://doi.org/10.5281/zenodo.7231161 (place in: `results`)
* `goc_oscillations`: https://doi.org/10.5281/zenodo.7231187 (place in: `results/oscillations`)
* `grc_activation_overlap`: Calcium signal datasets too large to be uploaded (1.44TB). Please reproduce using `sensory_burst_calcium_dense.json`.
## Reproduce the results
In order to reproduce the results for yourself, install `bsb==3.10.3` and use the `balanced.hdf5` network to simulate the configuration files you can find in the `configs` folder. Place the result files for each config as dictated by this config-to-location list: