Neuroagent

LLM agent for interacting with neuroscience tools. Enables ChatGPT-style interactions to query brain regions, morphologies, electrical traces, and scientific literature.

1. Running (Docker Compose)
2. Funding and Acknowledgement

Running (Docker Compose)

The easiest way to run the project is with Docker Compose:

1. Install Docker and Docker Compose
2. Create .env file with required variables:

OPENAI_API_KEY=...
KEYCLOAK_ID=...
KEYCLOAK_SECRET=...
KEYCLOAK_ISSUER=...
NEXTAUTH_SECRET=...

3. Start the services and initialize the database:

docker compose up
docker exec -it neuroagent-backend-1 alembic -x url=postgresql://postgres:pwd@postgres:5432/neuroagent upgrade head
docker exec -it neuroagent-minio-1 mc alias set myminio http://minio:9000 minioadmin minioadmin && docker exec -it neuroagent-minio-1 mc mb myminio/neuroagent

To enable the brain region resolving tool, retrieve your bearer token and make sure to run the following script:

python backend/src/neuroagent/scripts/embed_hierarchies.py $token -e https://staging.openbraininstitute.org/api/entitycore/ -u http://localhost:9000 -b neuroagent -a minioadmin -s minioadmin

which stores a json file in your minio/s3 instance.

4. Access the application at http://localhost:3000

Notes:

• First run will take longer to build frontend and backend images
• To rebuild individual services: docker compose build frontend or docker compose build backend
• Database changes persist in neuroagent_postgres_data volume
• MinIO data persists in neuroagent_minio_data volume
• Redis data persists in neuroagent_redis_data volume
• To reset database: docker volume rm neuroagent_postgres_data
• To stop all services: docker compose down

Running (Frontend and Backend Separately)

See instructions in frontend/README.md and backend/README.md.

Funding and Acknowledgement

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

Copyright © 2024 Blue Brain Project/EPFL
Copyright © 2025 Open Brain Institute