Knox - A Genetic Design Space Repository

Quickstart

Docker Instructions

1. Install Docker Compose
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

Non-Docker Instructions

1. Install Java 17+
2. Set "JAVA_HOME" Environment Variable Path
3. Install Neo4J Desktop 2
4. Open the Desktop app and click "Create instance"
5. Set Instance name to "knox"
6. Set Neo4j version to 2025.07.1
7. Database user should be neo4j
8. set password to "kn0xkn0x"
9. then click "Create"
10. Click "Start instance"
11. Download and Install Maven
12. Clone this repository
13. Run mvn clean install in the root directory of this repo
14. After successful install, Run mvn spring-boot:run in the root directory of this repo
15. Open Knox web interface at http://localhost:8080

AI Chat / Agent Integration

Setup

1. Get an API-key from OPENAI
2. Place API-key in application.properties file (Non-Docker Setup)
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