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ODE-APP

Web Pipeline For Kinetic (ODE-Based) Models.

To start the application (production)

This application makes use of docker and docker compose, so first install them. Learn more about this here.

Run the following commands to start the application:

docker-compose build
docker-compose up

After this open up a browser and go to http://localhost:3000

To run the containers in the background run:

docker-compose up -d

To stop the above containers run:

docker-compose stop

Repository Structure

 |- client              -> Contains the code of the react client
    |- src              -> Source files of the react client
        |- components   -> React components
        |- store        -> global store
 |- server              -> Contains the code of the node server
    |- routes           -> API routes
    |- controllers      -> API controllers
    |- models           -> Sequelize(SQL) models
    |- config           -> Configuration files
    |- python           -> Python scripts to parse SBML files and simulate ODE models
    |- scripts          -> Utility scripts
 |- docker-compose.yml  -> Docker Compose files that runs the application using docker
 |- package.json        -> The main package.json governing the yarn workspaces
 |- README.md           -> The main documentation file. Also this file :)

Development

Follow the instructions below to get the app up and running in development:

  • You need Node, Yarn and Python 3(alongside pip) to run this application. Download them here - Node, Yarn and Python. Further you also need a server of a postgresql database running. Learn more about postgresql here.

  • First you will need to install the dependencies of the project. Do that by running this:

    # inside the repo
yarn # Node and React dependencies
# Python dependencies
pip install python-libsbml
python -m pip install server/python/lib/stimator-0.9.120-py3-none-any.whl

  • Next you have to setup an environment file (.env) with appropriate variables in the /server folder, an example .env would look like this:

    SERVER_PORT = /* Specifiy a port here (Optional) */
DB_HOST = /* Your database host (Optional) */
DB_NAME = /* Your database name */
DB_USER = /* Your database user */
DB_PASSWORD = /* Your database user's password */

  • Then run the following command to start both the React Client and Node Server(concurrently):

    yarn dev

Other Scripts

  • To run the node server individually, use:

    yarn server

    ---OR---

    # In /server
yarn start

  • To sync tables in the database, use:

    # In /server
yarn sync-tables

    With force option (will delete existing tables with the same names):

    # In /server
yarn sync-tables -f

  • To run the react client individually, use:

    yarn client

    ---OR---

    # In /client
yarn start

  • To run tests on the react client, use:

    # In /client
yarn test

  • To build a production react client, use:

    # In /client
yarn build

  • To eject the configuartion and scripts from the react-scripts package, use:

    # In /client
yarn eject