Connecting Biological Detail with Neural Computation: Application to the Cerebellar Granule-Golgi Microcircuit

Andreas Stöckel, Terry Stewart, Chris Eliasmith

The repository contains the code used to produce the data shown in the paper Topics in Cognitive Science (TopiCS) paper "Connecting Biological Detail with Neural Computation: Application to the Cerebellar Granule-Golgi Microcircuit" (to appear later this year).

Running the code

The code to execute and visualise the experiments can be found in the notebooks folder, the model itself is located in the model folder. We recommend that you use the provided Docker file to build a Docker container that can run the code.

Using the Pre-Built Docker Container

To reproduce the results from the paper you can use the provided Docker container to enter a reproducible environment.

Prerequisite
Install Docker or a compatible container manager such as Podman on your system. Please follow the documentation on the Docker homepage our your operating system manual.

Step 1:
Download the file topics2021_cerebellum_docker_astoeckel_tcstewart_celiasmith.tar.bz2 from OSF.

Step 2:
Place the downloaded file in a new directory. Open a command prompt and cd into this directory. Then, execute the following.

# Import the docker container
docker import topics2021_cerebellum_docker_astoeckel_tcstewart_celiasmith.tar.bz2 cerebellum

# Create a `data` directory; this is where the generated files will be stored.
mkdir data

# Execute the docker container.
docker run -p 4567:4567 -v "$PWD/data:/topics2021-cerebellum/notebooks/out:z" -it cerebellum /topics2021-cerebellum/run.sh

This will start a Jupyter lab instance inside the docker container; open the displayed URL (e.g., http://127.0.0.1:4567/lab?token=...) in your browser. Files stored in the notebooks/out folder inside the container will appear in the data folder outside the container. All other changes to the filesystem are not persistent.

Building the Docker container from scratch

Download the file topics2021_cerebellum_source_astoeckel_tcstewart_celiasmith.tar.bz2 from OSF, or, alternatively, clone this GitHub repository.

Unpack the archive and open a command prompt inside the root directory of the archive. Then run the following commands.

# Step 1: Build the docker container
docker build -t cerebellum .

# Step 2: Execute the docker container.
docker run -p 4567:4567 -v "$PWD/data:/topics2021-cerebellum/notebooks/out:z" -it cerebellum

Running the experiments

Open the Jupyter notebook instance and navigate to the notebooks folder. Execute all notebooks in order. Depending on your machine, this will take a quite a few hours.

The results will be placed in the data directory.

Bibliography entry

The article will appear later this year (2021) in the "Best of ICCM" special issue.

License

Copyright (C) 2019-2021 Andreas Stöckel, Terry Stewart

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.