There are several aspects to the way the Bioregistry web application is deployed listed in this section.
bioregistry.io domain is registered with Namecheap and costs about $33 per year. It is managed
and supported by the INDRA Lab, a part of the Laboratory of
Systems Pharmacology and Harvard Program in Therapeutic Science
(HiTS) at Harvard Medical School.
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 INDRA Lab, a part of the Laboratory of Systems Pharmacology and Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.
These are the software and operating system specifications for the currently running instance of the Bioregistry:
A Docker image is automatically built on a cron job in the biopragmatics/bioregistry-docker GitHub repository 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 $20/year reserved.
The Bioregistry's EC2 instance runs the following script on a cron job that stops the current running instance, pulls the latest image from this DockerHub repository and starts it back up. The whole process only takes a few seconds.
#!/bin/bash # store the bioregistry id BIOREGISTRY_CONTAINER_ID=$(docker ps --filter "name=bioregistry" -q) # Stop and remove the old container taking advantage # of the fact that it's named specifically docker stop $BIOREGISTRY_CONTAINER_ID docker rm $BIOREGISTRY_CONTAINER_ID # Pull the latest docker pull biopragmatics/bioregistry:latest # Run the start script docker run -id --name bioregistry -p 8766:8766 biopragmatics/bioregistry:latest
This 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.
So far, the Bioregistry (both the data and web application) have been curated and developed within a small team and used by a limited audience. This means we have been able to address issues very quickly. However, this attitude is not scalable to larger audiences, where changes have higher potential for disruption of users' usages. With that being said, there are many things we are looking to discuss with potential stakeholders including (but not limited to):
These questions do not have easy answers and apply to most databases, software, and web applications in the life sciences. If you would like to be part of this discussion, please join us on the OBO Community Slack workspace's #ontotools channel.