metadata
title: mRNA Design Studio
emoji: 🧬
colorFrom: green
colorTo: blue
sdk: docker
app_port: 5007
pinned: false
mRNA Design Studio
A browser-based workbench for designing, analyzing, and assembling mRNA sequences. Import sequence data from CSV files or PostgreSQL databases, run codon-usage and structural analyses, score sequences with pluggable models, assemble inserts into plasmid backbones with QC checks, and export results — all from a single reactive UI powered by Panel.
- Import Data — load sequences from CSV/Excel files or PostgreSQL, map columns to the mRNA model, and organize into worklists
- Model Repository — register local Python scoring/generative models or remote API endpoints
- Worklist — inspect, analyze (GC%, CAI, homopolymers, restriction sites), score with loaded models, and export sequences as CSV
- Parts Workshop — browse and compose reusable sequence parts (UTRs, Kozak, CDS, PolyA)
- Assemble Plasmid — pick a backbone and cloning strategy, run QC, and export assembled constructs
- Generate Sequences — create optimized mRNA variants with configurable generation settings
Getting Started
The only prerequisite is a terminal with make and curl (both come pre-installed on macOS; on Windows use Git Bash or WSL). No Python install is required — the setup command handles everything.
git clone <repo-url> && cd mrna_design_studio
make setup # installs uv, Python 3.13, and all dependencies (~1 min)
make run # starts the app at http://localhost:5007
Run make by itself to see every available command:
make help
setup One-time setup: install Python, create venv, install deps
run Start the app
run-debug Start with DEBUG-level logging
kill Stop the app if it's running
restart Kill + restart the app
test Run the test suite
lint Lint with ruff
clean Remove the virtual environment
db-up Start the demo PostgreSQL database (requires Docker)
db-down Stop the demo database
db-status Check database container status
Demo database (optional)
A Docker Compose file is included to spin up a PostgreSQL instance pre-loaded with sample mRNA sequences:
make db-up # start the container
make run # connect using the pre-filled credentials on the Import Data tab
make db-down # stop when done