There are several aspects to the way the Bioregistry web application is deployed listed in this section.
The bioregistry.io domain is registered with Namecheap and costs about $33 per year. It is managed
and supported by the Gyori Lab for Computaional Biomedicine at Northeastern University.
The Bioregistry source code is licensed under the MIT License and is hosted openly on GitHub at https://github.com/biopragmatics/bioregistry. These are the software and operating system specifications for the currently running instance of the Bioregistry:
The Bioregistry is hosted on an Amazon Elastic Compute Cloud (EC2) via a load balancing service to stay secure and highly available. It is managed and supported by the Gyori Lab for Computational Biomedicine at Northeastern University.
These are the hardware and operating system specifications for the currently running instance of the Bioregistry:
A Docker image is automatically built weekly following the update workflow on GitHub Actions and pushed to the biopragmatics/bioregistry DockerHub repository. This image is built with the Python 3.9 alpine base image, which significantly reduces non-essential components. The final compressed image weights less than 40 MB of disk space and runs inside Docker with about 65 MB of memory at baseline. This could easily fit on a dedicated t4g.nano instance on AWS that costs about $37/year on-demand or around $20/year reserved.
The Bioregistry's EC2 instance runs the following script on a cron job that stops the current running instance, pulls the latest image from this DockerHub repository and starts it back up. The whole process only takes a few seconds.
#!/bin/bash
# /data/services/restart_bioregistry.sh
# Store the container's hash
BIOREGISTRY_CONTAINER_ID=$(docker ps --filter "name=bioregistry" -aq)
# Stop and remove the old container, taking advantage of the fact that it's named specifically
if [ -n "BIOREGISTRY_CONTAINER_ID" ]; then
docker stop $BIOREGISTRY_CONTAINER_ID
docker rm $BIOREGISTRY_CONTAINER_ID
fi
# Pull the latest
docker pull biopragmatics/bioregistry:latest
# Run the start script, remove -d to run interactively
docker run -id --name bioregistry -p 8766:8766 biopragmatics/bioregistry:latestThis script can be put on the EC2 instance and run via SSH with:
#!/bin/bash
ssh -i ~/.ssh/<credentials>.pem <user>@<address> 'sh /data/services/restart_bioregistry.sh'
The SSL/TLS certificate for bioregistry.io so it can be served with HTTPS is managed through
the AWS Certificate Manager.
The Bioregistry is funded by the Chan Zuckerberg Initiative (CZI) Open Science Grant 2023-329850 which stipulates unlimited no-cost extensions. We have allocated part of this grant to ensure that the domain registration, hosting, and hardware will be funded in the medium- and long term under a conservative cost estimate of around $100-200/year.
The Bioregistry implements the Open Code, Open Data, Open Infrastructure (O3) Guidelines as a means to enable and encourage community contribution and maintenance in the medium- and long term. All code is permissively licensed with the MIT License and all data is under the Creative Commons Zero (CCO) license, meaning anyone can reuse the data as they see fit.
The Bioregistry can be mirrored following these instructions.
The Bioregistry can be deployed using custom content by following these instructions.
Stakeholders in the Bioregistry have been interested in questions including:
These questions do not have easy answers and apply to most databases, software, and web applications in the life sciences. As first steps towards addressing those, we have written explicit, public, well-defined contribution guidelines, code of conduct, and project governance.
If you would like to be part of this discussion and/or development of these policies, you can try the following:
Content negotiation was implemented in PR #682 in order to better comply with FAIR-ness evaluations such as th FAIR Enough Evaluation