The Barcode of Life Data (BOLD) Portal is a web application and database designed to support the access, querying, and dissemination of DNA barcode data. DNA barcodes are standardized genetic markers used for species identification, with each record uniquely linking sequence data to specimen information, images, and provenance. Built on open-source technologies—including Couchbase, FastAPI, Redis, and Python—the application provides a scalable and high-performance infrastructure for managing barcode data. Its database follows the Barcode Core Data Model (BCDM - https://github.com/DNAdiversity/BCDM), ensuring structured and interoperable data representation.
The BOLD Portal is designed for multi-institutional deployment, enabling data mirroring and supporting data sovereignty requirements. It includes critical functionalities for monitoring and managing DNA reference libraries through National and Institutional Dashboards, facilitating real-time oversight of barcode repositories. Additionally, the system hosts published datasets, allowing users to download and integrate them into local analytical pipelines.
Developed with an API-first architecture, the application provides a robust API that enables seamless extensions without modifications to the core codebase. Released under the AGPL license, the BOLD Portal promotes open access, collaboration, and interoperability within the global biodiversity informatics community.
- Docker
- NGINX
- Python: FastAPI and Socketserver Logger
- Redis and File System Cache
- Couchbase
- Barcode Core Data Model
Dependencies:
- Barcode Core Data Model repository
- SSL Certificates
- Maintenance job to clear File System Cache
find /tmp/bold-public-portal/cache -type f -amin +1440 -delete
Requirements:
REPO_DIR="bold-public-portal"
# Spool Up
cd $REPO_DIR
tilt up -f docker/Tiltfile
# Spool Down
cd $REPO_DIR
tilt down -f docker/Tiltfile
# Check Status
# Go to http://localhost:10350/overviewCheck that .env is configured correctly and to production values. The following assumes the ansible playbook is not being used and Couchbase is hosted on a different server.
REPO_DIR="bold-public-portal"
# Spool Up
cd $REPO_DIR
docker build -t fastapi-app -f docker/Dockerfile .
docker build -t socketserver-logging -f docker/Dockerfile.socketserver_logging .
docker compose -f docker-compose-production.yml up -d
# Spool Down
cd $REPO_DIR
docker compose -f docker-compose-production.yml down
# Check Status
docker ps -aAlternatively, if the use of screens are required instead of Docker containers:
systemctl start nginx
systemctl start redis
screen -S fastapi-app
cd $REPO_DIR/src
gunicorn main:app --workers 24 --worker-class uvicorn.workers.UvicornWorker --bind 127.0.0.1:8000
screen -S socketserver-logging
cd $REPO_DIR/src
python socketserver_logging.pySee CYPRESS.md
ansible- Ansible playbooks and deployment
db_data- Local simulated database data
docker- Docker and Tilt components
src- Main source code
cypress- Cypress testing configuration
docs- Additional documentation
ETL- Data (BCDM) extraction, transformation, and loading
services- API services; serve the application data but can also be used independently
static- Assets for application presentation
templates- Jinja2/HTML application layout
tools- Miscellaneous tools for the application
views- Application view controllers
@misc{Ratnasingham2025BOLD5, title={BOLD5: A Comprehensive Suite of Applications to Support the Assembly, Preservation, and Application of DNA Barcode Libraries}, author={Sujeevan Ratnasingham, Jireh Agda, Catherine Wei and Josh Agda, Chris Ho, Sameer Padhye, Shweta Purushe, Spandana Chereddy, Spencer Moncton, Dana Rea, Ejhtiar Islam, Paul Hebert}, institution={Centre for Biodiversity Genomics}, year={2025} }
This project was made possible through the support of:
- Canada Foundation for Innovation Major Science Iniatives Fund (MSIF)
- Genome Canada & Ontario Genomics
- Ontario Ministry of Colleges and Universities
- New Frontiers in Research Fund (NFRF)-Transformation