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ODE-APP

Web Pipeline for visualizing and simulating kinetic(ODE-based) biological models.

Index

  1. Usage
  2. Kinetic Laws
  3. References

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, use:

docker-compose up -d

To stop the above containers run:

docker-compose stop

Repository Structure

 |- client              -> Contains the code of the react client
    |- build            -> Build of the react client
    |- src              -> Source files of the react client
        |- components   -> React components
        |- store        -> Global store
        |- assets       -> Static assets
 |- 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
        |- lib          -> Custom stimator library wheel package
    |- scripts          -> Utility scripts
 |- cypress             -> Contains all the tests for the project
 |- 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

Testing

This project uses cypress for testing.

  • To run tests for the project, use:

    yarn test

  • To open cypress only, use:

    yarn cypress

Other Scripts

  • To run the node server individually, use:

    yarn server:start

    ---OR---

    # In /server
yarn start

  • To build the server for production, use:

    yarn server:build

    ---OR---

    # In /server
yarn build

  • 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:start

    ---OR---

    # In /client
yarn start

  • To build a production react client, use:

    yarn client:build

    ---OR---

    # In /client
yarn build

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

    # In /client
yarn eject