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)

cargo install cantata

Run a test

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.

cantata run path/to/sonata/simulation.json

Setup (dev)

git clone https://github.com/thorstenhater/cantata.git

Run a test

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.