didryo/magi

A webserver from the Raphael Lab for mutation annotation and genome interpretation.

MAGI

This repository contains the code to run a webserver based on the GD3 suite of genomic visualization tools. The server allows you to query a set of genes' mutations in cohorts of tumors, and to see mutations and protein-protein interactions among those genes.

The site consists of two main pages:

1. The index page allows the user to choose his/her query genes and datasets.
2. The view page displays the GD3 visualizations for the given query genes and datasets. The view is an AngularJS app. The Angular controller for the view takes the genes and datasets encoded in the query params, and makes a GET request to the server for a JSON object, and then uses Angular-D3 directives to render the resulting visualizations.

Dependencies

• Node.js and NPM (generally included with Node.js).
• MongoDB. Make sure you can run mongod from your terminal. Some basic debugging tips are:
  1. Make sure that you make a directory to store the database. The default is /data/db, so you'll need to make that directory before running mongod.
  2. Make sure that the mongod, mongo, etc. are in your PATH.

Setup

1. Clone the repository:

    git clone https://<user>@bitbucket.org/raphaellab/magi.git
   

2. Install required dependencies:

    npm install
   

3. Start MongoDB:

    mongod &
   

4. Start the server (default port 8000):

    node server.js
   

5. Load data in the following order:

   • PPIs (hint, hprd, iref, multinet)
   • Cancers
   • Genome
   • Domains
   • Pathways (kegg, pindb)
   • Mutations (pancan-hotnet2 (regenerate_pancan_data.sh), tcga-gastric) -- loadDataset

6. View the website at http://localhost:8000/.