abcair / KNIndex

A comprehensive database of k-nucleotide physicochemical property values.

KNIndex

A comprehensive database of k-nucleotide physicochemical property values.

Introduction

We deposited all physicochemical property values, as well as the corresponding literatures, into a MySQL database. We implemented the backend system using JavaScript with node.js script engine and the Express framework. The frontend was implemented using JavaScript with the Vue framework. We developed the project on Windows10 platform, using the code editor Visual Studio Code.

Development

If you want to run these codes in the development environment, you should install Node.js (https://nodejs.org/en/download) and MySQL (https://www.mysql.com/downloads/) first on your machine.

After your Node.js environment and MySQL are ready, find out the location of the source code of KNIndex that you unpack and enter this directory in command line program. Then execute the command npm install to install all the dependencies of the project.

Add data to MySQL database

Firstly, you should create a database. Then, add data to the database by loading SQL file propertydb.sql.

Start backend

Enter the server directory in the other command line program. To start backend, users need a file to configure MySQL database information, namely data.base.conf.js. Users can add the file according to data.base.conf.js.example we provided. Then execute the command node index.js.

Start web server

Type and excute the command npm run serve in the first command line program. After a while, KNIndex will start in your default browser.

Please note

• If there are errors after executing the command node index.js when you start backend, please consider executing the SQL statement (ALTER USER 'root'@'localhost' IDENTIFIED WITH mysql_native_password BY 'your password';) to modify the encryption method for MySQL and make sure your MySQL service is enabled.
• If you want to reconfigure the Vue, please see Configuration Reference.
• If you have changed the listening port of backend, please reconfigure devServer.proxy option in vue.config.js accordingly. Otherwise there will be an error: Failed to load resource: the server responded with a status of 500 (Internal Server Error).

Production

If you want to deploy the project to your own server when there are no problems in the development environment, you would need to excute npm run build in the root directory to get the dist folder firstly. And then configure the running environment on the server.

Steps for production

1. Install Node.js and MySQL on the server.
2. Create a database and add data to the database by loading SQL file propertydb.sql.
3. Create a new directory (e.g. knindex) on the server.
4. Upload the dist folder, server folder and package.json file to knindex directory.
5. Execute the command npm install to install all the dependencies in the knindex directory.
6. Install and configure Nginx.
7. You can install PM2 to manager your node process.
8. Type and execute the command pm2 start index.js in the server folder to start the project.

Please note

• If the program does not start properly, please running commands pm2 list and pm2 show 0 (where 0 represents the process id) to view error messages.

Citation

Wen-Ya Zhang, Junhai Xu, Jun Wang, Yuan-Ke Zhou, Wei Chen, Pu-Feng Du, KNIndex: a comprehensive database of physicochemical properties for k-tuple nucleotides, Briefings in Bioinformatics, Volume 22, Issue 4, July 2021, bbaa284, https://doi.org/10.1093/bib/bbaa284.