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Knox - A Genetic Design Space Repository

Quickstart

Docker 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

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. Set "OPENAI_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

Screen Shots

Design Spaces are represent as directed graphs

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The Design Space above was created using the following GOLDBAR specification

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