Welcome to medna-metadata documentation!
medna-metadata is a data management system for tracking environmental DNA samples from field data collection to bioinformatics analyses.
The Sequencing and Bioinformatics Metadata project is funded through the Maine-eDNA RII Track-1 EPSCoR grant supported by the National Science Foundation award #OIA-1849227. Maine-eDNA is a Maine coast-wide research effort to determine the efficacy of ecosystem monitoring through environmental DNA (eDNA). For more in-depth information related to Maine-eDNA, see the Maine-eDNA home page. The metadata project is directly related to the goals of Theme 3: Macrosystem eDNA Integration, but also involved in Theme 1: Sustainable Fisheries and Theme 2: Harmful and Shifting Species. Our efforts contribute to the Data Management and Data Analysis Pipeline work groups. The Sequencing and Bioinformatics Metadata project is a collaboration between the Coordinated Operating Research Entities (CORE) environmental DNA (eDNA) Laboratory and the Data Management Team to facilitate the development of a web application for the management and tracking of eDNA samples (medna-metadata; GitHub).
Kimble, M., Allers, S., Campbell, K., Chen, C., Jackson, L. M., King, B. L., Silverbrand, S., York, G., & Beard, K. (2022). medna-metadata: An open-source data management system for tracking environmental DNA samples and metadata. Bioinformatics, btac556. https://doi.org/10.1093/bioinformatics/btac556
Check out the Installation section for further information, including how to setup the project.
This project is under active development.
- Clone the Repository
- Docker Setup
- Manual Setup
- Install Requirements
- Create PostgreSQL database with PostGIS Extension
- Create Superuser
- Collect Static
- Test The Deployment
- Create Gunicorn Socket and Service files (e.g., daemonizing!)
- Setup Celery and RabbitMQ
- Collect Static Files
- Configure Nginx
- SSL Certificates with Certbot
- Application Programming Interface (API)