DOCKER.md

Blue Brain BioExplorer PostgreSQL Database with Docker

Use Docker to run Blue Brain BioExplorer PostgreSQL Database as a service and avoid painful tooling setup.

Prerequisites

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Head over to Docker and install Docker for your own platform.

Setup

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First build the image (it's necessary to do this step if you want to run BioExplorer):

docker build -t bioexplorer-db .

Usage

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If you want to run Blue Brain BioExplorer PostgreSQL Database, use the following command to run the database instance:

# Runs Blue Brain BioExplorer Database on port 5432
docker run -d -p 5432:5432 bioexplorer-db

And run the Blue Brain BioExplorer with the following command:

# Runs the Blue Brain BioExplorer as a service with the HTTP interface bound to port 5000
docker run -ti --rm -p 5000:5000 bioexplorer --http-server :5000 --plugin "BioExplorer --db-name=bioexplorer --db-password=bioexplorer --db-user=postgres --db-host=<ip address> --db-port=5432" --plugin MediaMaker

Replace <ip address> with the IP address of the host where the database docker container is running.

Populating the database with open datasets

A full circuit dataset is available in the Model of Rat Non-barrel Somatosensory Cortex Anatomy publication. A Python Notebook has been included with basic examples of how to explore the dataset.

A vasculature dataset is available from the Blue Brain NGV portal. An example Python Notebook is available to import the VTK dataset into the database. The vasculature Python Notebook can then be used to visualize the vasculature.

NOTE If you are having trouble exiting the process after you run the container (with the above command), use docker stop <container-id> to stop the container. docker ps will give you the current running process.