Monadic DNA Explorer

Match your DNA data against an open ended catalogue of DNA traits with private AI-powered analysis

🔗 Repository: github.com/Monadic-DNA/Explorer

Features

• Interactive exploration of GWAS Catalog studies with quality-aware filtering
• Upload and analyze your personal genetic data (23andMe, AncestryDNA, Monadic DNA)
• Private AI analysis powered by Nillion's nilAI - your data is processed in a Trusted Execution Environment
• Save and export your results

Development

Preparing local data

Fetch the latest GWAS Catalog data from https://www.ebi.ac.uk/gwas/api/search/downloads/alternative into the localdata directory. This is "All associations v1.0.2 - with added ontology annotations, GWAS Catalog study accession numbers and genotyping technology" from https://www.ebi.ac.uk/gwas/docs/file-downloads.

Create a new SQLite database at localdata/gwas_catalog.sqlite.

Load the contents of the TSV file into the SQLite database using your favorite method.

Running the Monadic DNA Explorer

The repository includes a Next.js single-page application for exploring studies stored in localdata/gwas_catalog.sqlite.

npm install
npm run dev

The development server defaults to http://localhost:3000. You can override the database location by exporting GWAS_DB_PATH before starting the server.

Production Deployment

Using PostgreSQL in Production

For production deployments, you can use a remote PostgreSQL database instead of the local SQLite database:

1. Set up your PostgreSQL database with the GWAS catalog data
2. Set the POSTGRES_DB environment variable to your PostgreSQL connection string:

export POSTGRES_DB="postgresql://username:password@host:port/database"
# or for production with SSL:
export POSTGRES_DB="postgresql://username:password@host:port/database?sslmode=require"

3. Build and start the application:

npm run build
npm start

Environment Variables

• POSTGRES_DB: PostgreSQL connection string (if set, takes precedence over SQLite)
• GWAS_DB_PATH: Path to SQLite database file (only used if POSTGRES_DB is not set)
• NILLION_API_KEY: (Optional) API key for Nillion's nilAI to enable private AI analysis of results

Database Schema

The application expects a table named gwas_catalog with the standard GWAS Catalog schema. The PostgreSQL version should mirror the SQLite schema structure.

Performance Optimization

For optimal performance with large GWAS datasets, apply the provided database indexes:

# For SQLite
sqlite3 /path/to/gwas_catalog.sqlite < sql/sqlite_indexes.sql

# For PostgreSQL
psql $POSTGRES_DB < sql/postgresql_indexes.sql

These indexes can improve query performance by 10-100x for search operations. See sql/README.md for detailed instructions.

License

Dual License: This software is available under a dual licensing model:

Personal/Non-Commercial Use - MIT License

Free for personal, educational, academic, and non-commercial use under the MIT License. See LICENSE-MIT.md for details.

Commercial Use - Commercial License Required

Commercial use requires obtaining a commercial license. This includes:

• Use in commercial products or services
• Use by for-profit organizations
• Integration into commercial applications
• Revenue-generating activities

Contact us for commercial licensing:

• Email: hello@monadicdna.com
• Website: https://monadicdna.com

See LICENSE for full dual license details and LICENSE-COMMERCIAL.md for commercial license terms.

Citations

Cerezo M, Sollis E, Ji Y, Lewis E, Abid A, Bircan KO, Hall P, Hayhurst J, John S, Mosaku A, Ramachandran S, Foreman A, Ibrahim A, McLaughlin J, Pendlington Z, Stefancsik R, Lambert SA, McMahon A, Morales J, Keane T, Inouye M, Parkinson H, Harris LW. doi.org/10.1093/nar/gkae1070 Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D998–D1005