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knox

(★ 15)

Full stack application for creating, combining, and storing combinatorial genetic design spaces.

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- api_data.js
- api_data.json
- api_project.js
- api_project.json
- index.html
- main.js
- KnoxV1.jpg
- WebImage1.jpg
- WebImage2.jpg
.clang-format
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LICENSE
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# CDN으로 사용하기

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jsDelivr는 공개 GitHub 리포지토리를 별도 설정 없이 CDN으로 즉시 서빙합니다. 버전과 파일을 고르면 웹페이지에 바로 붙일 수 있는 링크와 예시 코드가 만들어집니다.

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명령어 용어집

이 문서에서 사용된 명령어를 모아봤습니다. 낯선 명령어가 있다면 펼쳐서 확인해보세요.

🔍

`mvn`

설명 보기 ▼

Apache Maven: Java 기반 프로젝트를 빌드하고 관리.
더 많은 정보: <https://manned.org/mvn>.

mvn compile

프로젝트 컴파일:

mvn package

컴파일된 코드를 `jar`와 같은 배포 가능한 형식으로 패키지:

mvn package {{[-D|--define]}} skipTests

유닛 테스트를 건너뛰고 컴파일 및 패키지:

// repository documentation

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<p align="center">
  <img src="images/KnoxV1.jpg" alt="Logo" width="600"/>
</p>

## Quickstart

### KnoxApp (Knox + Microservices) Instructions
1) Go to https://github.com/CIDARLAB/KnoxApp

### Docker Instructions
1) Install [Docker Desktop](https://www.docker.com/products/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+](https://www.oracle.com/java/technologies/javase/jdk17-archive-downloads.html)
2) Set "JAVA_HOME" Environment Variable Path
3) Install [Neo4J Desktop 2](http://neo4j.com/download)
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](https://maven.apache.org/download.cgi) and [Install](https://maven.apache.org/install.html) 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

### Microservices
- Install [KnoxAI](https://github.com/CIDARLAB/knoxAI) for Machine Learning
- Install [SeqCompiler](https://github.com/CIDARLAB/ctRSD-simulator-API) for ctRSD circuits

## AI Chat / Agent Integration

### Setup
1) Get an API-key from [OPENAI](https://platform.openai.com/api-keys)
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

<p align="center">
  Design Spaces are represent as directed graphs
</p>

<p align="center">
  <img src="images/WebImage1.jpg" alt="Logo" width="900"/>
</p>

<p align="center">
  The Design Space above was created using the following GOLDBAR specification
</p>

<p align="center">
  <img src="images/WebImage2.jpg" alt="Logo" width="900"/>
</p>