author
[email protected]

cfOmics Website Demo Code

This repository contains the code of the cfOmics website. It is the same as what's behind the online website, apart from some deployment-related parts.

cfOmics is published in Nucleic Acids Research with DOI: https://doi.org/10.1093/nar/gkad777. If our database has helped you on your research, please cite:

Mingyang Li, Tianxiu Zhou, Mingfei Han, Hongke Wang, Pengfei Bao, Yuhuan Tao, Xiaoqing Chen, Guansheng Wu, Tianyou Liu, Xiaojuan Wang, Qian Lu, Yunping Zhu, Zhi John Lu, cfOmics: a cell-free multi-Omics database for diseases, Nucleic Acids Research, 2023;, gkad777, https://doi.org/10.1093/nar/gkad777

Structure

cfOmics is a comprehensive database for cell-free multi-omics high-throughput data, which is comprised of five parts:

Part	Description	Folder
React.js frontend	Frontend	/frontend/
Node.js backend	Browsing module and for prompting search options	/backend-node/
Django backend	Analyses and drawing plots	/backend-django/
MySQL database	Data storage and orgnization	N/A
Apache webserver	Proxy for handling network traffic	N/A

As the website need a large amount of data to run properly, you will need to directly connect to our working database to run this project. Also, as the proxy web server is only meant for deployment, it is not implemented here.

Request Environment Files Containing Secrets

Because you will need to directly connect to our online database, to prevent abuse of our database and API, you need to contact [email protected] to get three environment files before running this project. Place the environment files and rename them as follows:

Original File	Path	Rename To
.env-react	/frontend/.env-react	/frontend/.env
.env-node	/backend-node/.env-node	/backend-node/.env
.env-django	/backend-django/app/.env-django	/backend-django/app/.env

How to Start

• Make sure the environment files are ready.

• Install Docker and Docker Compose. You can just install Docker Desktop if it's available for your machine.

• You need to have basic exposure to shell.

• Make sure that ports 3000, 8084 and 8085 are not occupied on your machine.

• Clone this repository. At the root level of this repository (the same level as this file), run

  docker compose build # first-time run only
  docker compose up

  Now you can visit the website at http://localhost:3000. The docker compose build command is only required for the first-time start.

• To stop, press CTRL+C and run

  docker compose down

Warning

DO NOT redistribute the built image!