https://github.com/thorstenhater/cantata
Arbor adaptor for SONATA
https://github.com/thorstenhater/cantata
neuroscience simulation
Last synced: about 1 year ago
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Arbor adaptor for SONATA
- Host: GitHub
- URL: https://github.com/thorstenhater/cantata
- Owner: thorstenhater
- Created: 2024-03-21T13:02:15.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2025-03-26T21:08:42.000Z (about 1 year ago)
- Last Synced: 2025-03-26T22:24:01.539Z (about 1 year ago)
- Topics: neuroscience, simulation
- Language: Rust
- Homepage:
- Size: 2.78 MB
- Stars: 1
- Watchers: 1
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: Readme.md
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README
# Cantata
Translate SONATA simulations into Arbor simulation bundles.
## Dependencies
We require a recent version of Rust (1.80), Python (3.10 or later), and HDF5
(development, i.e. headers and libraries). Acquiring some examples in SONATA
will be helpful; you can do so here
https://github.com/AllenInstitute/sonata
or here
https://github.com/AllenInstitute/bmtk
## Setup (stable)
``` sh
cargo install cantata
```
Run a test
``` sh
cantata build path/to/sonata/simulation.json out-dir
cd out-dir
python3 main.py
```
This will perform the translation and create a working simulation in the output
directory `out-dir`. Running the simulation will generate the requested outputs
(spikes and traces) in `out-dir/out`. You may want/need to tweak the simulation.
There is a convenience wrapper that does all of the above and will construct and
execute the simulation in `simulation.sim`.
```sh
cantata run path/to/sonata/simulation.json
```
## Setup (dev)
``` sh
git clone https://github.com/thorstenhater/cantata.git
```
Run a test
``` sh
cd cantata
cargo run -- build path/to/sonata/simulation.json out-dir
cd out-dir
python3 main.py
```
This will perform the translation and create a working simulation in the output
directory `out-dir`. Running the simulation will generate the requested outputs
(spikes and traces) in `out-dir/out`. You may want/need to tweak the simulation.