The HEMU database and analysis platform for Andropogoneae grasses

1 Project Introduction

HEMU is an easy-to-handle, graphical based database and analysis platform for Andropogoneae grasses which enables user to discover genomic data from multiple representative Andropogoneae species within a click.

The name "HEMU" draws its inspiration from the Chinese classic, the Book of Songs, symbolizing robust crops and bountiful harvests. HEMU encompasses massive multi-omics data and is equipped with six sophisticated analysis toolkits, which enables easy utilization of the bioinformatics data and customized performance of comparative analysis from novel perspectives among Andropogoneae species.

The project is currently deployed and available for open research use HERE.

To cite this project: Zhu, Y., Wang, Z., Zhou, Z., Liu, Y., Gao, X., Guo, W., & Shi, J. (2023). HEMU: an integrated comparative genomics database and analysis platform for Andropogoneae grasses. Plant Communications, 100786. https://doi.org/10.1016/j.xplc.2023.100786

2 Deploying the Main HEMU Framework

Currently, the project is deployed on a server running Ubuntu 20.04 LTS.

Step1: create environment and install prerequisites

conda env create -f HEMUdb_new.yaml

Step2: configure MySQL server, creating a database for data storage

CREATE DATABASE hemu_database DEFAULT CHARSET utf8mb4 COLLATE utf8mb4_general_ci;

Step3: configure Redis server, which can be run with docker

docker run --name redis-hemu -p 6379:6379 redis

Step4: Start the server instance using uwsgi, then start the celery task backend

# Start server using uwsgi configurations
uwsgi --ini /path/to/config/hemu_uwsgi.ini

# Start celery worker for handling async tasks
cd /path/to/projectdir/ && nohup celery -A HEMU_Database_Main worker -l info > /path/to/logdir/hemu_celery.log