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CIDARLAB / knox

Full stack application for creating, combining, and storing combinatorial genetic design spaces.
BSD 3-Clause "New" or "Revised" License
11 stars 10 forks source link
combinatorial-algorithms genetic-design graph-algorithms synthetic-biology

readme

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 Neo4J 2) Open the Desktop app and add a new project 3) Within the project, click "Add Graph", then create a local graph using "kn0x" as password 4) Click "Start" 7) Download and Install Maven 8) Clone this repository 9) Run mvn spring-boot:run in the root directory of this repo 10) Open Knox web interface at http://localhost:8080

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