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ToxicoDB is a database of curated toxicogenomics datasets that provides convenient data summary and visualization to mine these complex data. Users can find drug and gene annotations, visualize differential gene expression and enriched pathways within datasets for drug of interest.

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bhklab/ToxicoDB-web

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ToxicoDB Web Application

Setup Instructions

Note: Yarn must be installed on the machine!

  • Clone the repo
git clone git@github.com:bhklab/ToxicoDB.git
cd ToxicoDB
  • In the project directory, install all server dependencies npm i
  • Create .env using .env.example as a reference to access the database
  • Start the server by running npm start or npm run devstart(development mode) command
  • Start the client (development mode) by running yarn start
  • Open http://localhost:3000 to view it in the browser.

Dependencies

  • React
  • React-Router
  • Express
  • Knex
  • Body-parser

Dev Dependenices

  • Nodemon
  • Eslint

Build Instructions

cd client && yarn build

Builds the app for production to the build folder. It correctly bundles React in production mode and optimizes the build for the best performance.

Servers

Migrations

  • knex migrate:make (migration_name) - To create a new migration file.
  • knex migrate:latest - To run the lastest migrations and create corresponding tables.

Seeds (Seeding Files)

  • Create manually a file (touch file_name).
  • Run knex seed:run to run the seeding file(s) in order to seed the table(s) in the database.

About

ToxicoDB is a database of curated toxicogenomics datasets that provides convenient data summary and visualization to mine these complex data. Users can find drug and gene annotations, visualize differential gene expression and enriched pathways within datasets for drug of interest.

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