New docker image of HN-DREP

HN-DREP: Heterogeneous Network-based Drug Repositioning Evaluation and Prediction database

The HN-DREP database is a platform that is dedicated to evaluating heterogeneous network-based drug repositioning methods and predicting drug-disease associations. It provides an impartial assessment of existing network-driven drug repositioning methods and consolidates predictions from various repositioning methods. This summary represents the current stage of research on heterogeneous network-based drug repositioning methods, which aims to promote the development of drug repositioning.

HN-DREP is available at http://hn-drep.lyhbio.com/.

Reproducing HN-DREP Web Application with Docker: A Step-by-Step Guide

Introduction

Docker is a widely adopted platform for containerization, providing a convenient and reproducible environment for deploying and running applications. In this document, we outline the steps to set up a Docker environment for a Drug Repositioning Platform, facilitating the development and deployment process.

Steps

1. Download Repository Data: Begin by downloading all data (three zip file) from the repository containing the Drug Repositioning Platform codebase. This ensures that the Docker build process has access to all required files and dependencies.

2. Navigate to Dockerfile Directory: Open a terminal or command prompt and navigate to the directory containing the Dockerfile. This file specifies the configuration and dependencies for our Drug Repositioning Platform.

   cd drug

3. Pull Base Image: Start by pulling the required base image from Docker Hub. In this case, we use the PHP 8.1.9 FPM image with the Bullseye distribution.
   docker pull php:8.1.9-fpm-bullseye

4. Build Custom Image: Initiate the image build process using the Dockerfile.
   docker build --no-cache -t cqupt/hn-drep:latest ./

5. Modify Hosts File: Update the hosts file on the host machine to ensure proper domain resolution. For Windows users, this file is typically located at C:\Windows\System32\drivers\etc\hosts. Append the following line to the end of the file:
   127.0.0.1 api

6. Run Container: Execute the Docker run command to launch the containerized application. Replace the directory paths {codedir}with the respective locations of your codebase on the host machine.
   docker run --name drug -itd -p 80:80 -v {codedir}/DrugRepositionUI:/htdocs/DrugRepositionUI:rw -v {codedir}/DrugRepositionApi:/htdocs/DrugRepositionApi:rw cqupt/hn-drep:latest /bin/bash

7. Access via Browser: Open your preferred web browser and navigate to localhost 80 to access the Drug Repositioning Platform.

Conclusion

By following these steps, you can establish a Docker environment tailored for the development and deployment of a Drug Repositioning Platform

Please Cite us:

Yinghong Li, Yinqi Yang, Zhuohao Tong, Yu Wang, Qin Mi, Mingze Bai, Guizhao Liang, Bo Li, Kunxian Shu, A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods, Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae172, https://doi.org/10.1093/bib/bbae172