VenomKB

Web app version of VenomKB - a knowledge base for aggregating and identifying therapeutic uses of animal venoms and venom compounds.

Current version: 2.0.1-alpha

Installation

> git clone https://github.com/jdromano2/venomkb
> cd venomkb
> npm install

API

VenomKB's API is currently a Mongoose.js interface to a MongoDB database. Although the API currently only supports reading the database contents, future additions to VenomKB will require write access, so the API code should connect to the database via an account that has both read and write access.

MongoDB setup

We are working on creating a fully automated pipeline for bootstrapping the VenomKB database. When this is released, it will be part of the venomkb python package that accompanies the website (see venomkb/).

In the meantime, you can prepare a rough approximation by downloading the data from VenomKB and putting it into a MongoDB database named venomkb_format. This should contain the following collections: dbindexitems, genomes, proteins, and species. Once you have the database, you can connect the code to it by modifying the values in a file named .env, which contains secure configuration details (a sample file with example values can be seen at .env-example).

Configuring VenomKB

VenomKB's configuration is handled largely by setting environment variables. You should make the following environment variables visible to the shell used to start the application server and the API:

• NODE_ENV: Should be one of production or development, depending on whether intend to run the application locally, or deploy on the internet.
• MONGO_IP: Only used when process.env.NODE_ENV == 'production'. Should be set to the host address for the MongoDB database containing venomkb_format. This is the host used by the API to retrieve data.
• MONGO_PW: The password for the user venomkb on the MongoDB database at the IP/hostname above.

Running the app

To test the app in developer mode:

npm start

This spins up local webservers for both the web application (on port 3000) and the API (on port 3001) simultaneously.

To build the app for production:

npm build

This runs Webpack on the web application, which minifies and optimizes the code base, and gathers assets and dependencies and puts them into a structure that can be better deployed over the internet. The application will be deposited into the index/dist/ directory.

Note: The code for the API is already self-contained, and is not touched by the build command.

Reserved Files

Folder contains .eslintrc, .eslintignore and .babelrc files in addition to .gitignore. These files are to provide linting instructions, ignore files for linting, and ensure babel uses ES2015 and React transforms respectively.

Features

(These are technical details regarding how we implement the website. For details about the features of the website itself, see About > Feature map on the website.)

• ES6 support via Babel
• Redux dev tools to help you keep track of the app's state
• Routing using Express and React Router
• Hot module replacement support so you can change modules or react components without having to reload the browser
• Webpack production config so you can build the app and make it ready for production
• Sass support, just import your styles wherever you need them (and to add Bootstrap support)
• eslint to keep your js readable

Contact

VenomKB is maintained by members of the Tatonetti Lab at Columbia University.

For more information, you can contact one of the developers by email:

• Joseph D. Romano: jdr2160@cumc.columbia.edu
• Marine Saint Mezard: marine.saint-mezard@ensta-paristech.fr