KnoxApp - An AI-Powered tool for Genetic Circuit Generation and Prediction

Quickstart

Instructions

1. Install Docker Desktop
2. Clone this repository
3. run docker-compose up --build in the root directory of this repo
4. Open Knox web interface at http://localhost:8080
5. Open Neo4j web interface at http://localhost:7474
6. Open MLflow web interface at http://localhost:5000
7. Open KnoxAI FASTAPI Docs at http://localhost:8000/docs
8. Open ctRSD-simulator-API FASTAPI Docs at http://localhost:8010/docs

AI Chat / Agent Integration

Setup

1. Get an API-key from OPENAI or CLAUDE
2. Set "OPENAI_API_KEY" or "CLAUDE_API_KEY" Environment Variable with API-key
3. You can then run the application and use the AI features via the AI Chat

Manuscript

Nicholas Roehner, James Roberts, Andrei Lapets, Dany Gould, Vidya Akavoor, Lucy Qin, D. Benjamin Gordon, Christopher Voigt, and Douglas Densmore. GOLDBAR: A Framework for Combinatorial Biological Design. ACS Synthetic Biology Article ASAP (2024).

DOI: https://pubs.acs.org/doi/full/10.1021/acssynbio.4c00296

Webpage

https://www.cidarlab.org/knox