Dynalab

Molecular dynamics simulation platform. Run protein folding simulations via a web interface.

Organization

• frontend/ - react app for submitting and viewing simulation jobs
• backend/ - fastapi server + worker that handles job queue and talks to aws batch
• upside/ - the actual molecular dynamics engine (c++ with python bindings)

Getting Started

1. Start Local Services

You need postgres and redis running locally. Easiest way:

cd backend
docker compose up -d

2. Backend Setup

cd backend
uv sync

This installs all python dependencies into a local .venv.

You'll need a .env file with your aws creds and other information:

DATABASE_URL=...
REDIS_URL=...
AWS_ACCESS_KEY_ID=...
AWS_SECRET_ACCESS_KEY=...
AWS_REGION=...
S3_OUTPUT_BUCKET=...

3. Frontend Setup

cd frontend
npm install

Local Development

Backend API Server

cd backend
uv run uvicorn main:app --reload

Runs on http://localhost:8000 by default.

Backend Worker

cd backend
uv run python worker.py

This polls redis for new simulation jobs and submits them to AWS batch. Also checks on running jobs and updates their status when they complete.

Frontend

cd frontend
npm run dev

Runs on http://localhost:5173. This is the whole (pretty simple) web ui for submitting simulations and viewing results.

Typical dev workflow

1. docker compose up -d (in backend/)
2. run the api server in one terminal
3. run the worker in another terminal
4. run the frontend in a third terminal
5. go to http://localhost:5173