http://GeneSpot.org

Development Branches :: http://genespot.org/branches

This software tool for systems biology provides a way to view TCGA data from a gene-centric point-of-view. It includes a number of interactive visualizations, and allows the user to save their current exploration. This application also enables the user to select specific cancers and genes of interest, and load data that is generated from a variety of TCGA analysis.

All software is presented AS IS to the general community. Our priority is to continuously improve the software to serve research in systems biology and computational biology.

Acknowledgements

This project hosts software developed to support the TCGA Genomic Data Analysis Center (GDAC) at the Institute for Systems Biology (ISB) and MD Anderson Cancer Center. Visit our project website at http://cancerregulome.org.

For more information, please contact codefor@systemsbiology.org or info@csacr.org.

Developer Instructions

Operating System Support The example commands in this file are directed at Linux and Mac OS X users. However, it should be expected (unless explicitly noted) that these technologies are supported by the Windows operating system.

Browser Support This web applications adopts the HTML5 standard. Backwards compatibility with some older generation browsers is resolved through use of Google Chrome Frame (http://www.google.com/chromeframe). We will work to ensure that this software supports mobile devices and tablets using HTML5 web browsers. But we will focus our testing efforts on the most commonly-used platforms: iOS and Android. Please submit an issue if there are malfunctions in the system on a particular device.

Build Dependencies

• NodeJS Package Manager (npm) - https://npmjs.org

• Brunch - http://brunch.io/

npm install -g brunch

Web Server Dependencies

• NGINX - http://wiki.nginx.org/Install

npm is the recommended web development server

cd $WEBAPP_ROOT
npm install // creates node_modules includes all web server dependencies
npm start // starts dev web server at http://localhost:3333

Database Dependencies

• MongoDB - http://docs.mongodb.org/manual/installation/

// Using Homebrew for Mac OS
brew update
brew install mongodb

Python Dependencies

• Python 2.7 - http://www.python.org/download/releases/

• Tornado Web

  • http://www.tornadoweb.org/
  • https://github.com/downloads/facebook/tornado/tornado-2.4.1.tar.gz

tar xvzf tornado-2.4.1.tar.gz
cd tornado-2.4
python setup.py build
sudo python setup.py install

It is also possible to add the tornado directory to your PYTHONPATH instead of building with setup.py, since the standard library includes epoll support.

[sudo] easy_install -U tornado

• Google OAUTH2 API - https://developers.google.com/api-client-library/python/start/installation

[sudo] easy_install --upgrade google-api-python-client

• PyMongo - http://api.mongodb.org/python/current/installation.html

[sudo] easy_install -U pymongo 

JavaScript Dependencies

This build packages third-party JavaScript libraries into a single vendor.js file. Developers should download additional libraries into the app_root/vendor directory, and the build system will automatically integrate them (see app_root/_public).

These third-party JavaScript libraries, as well as the build directories (vendor, node_modules, _public) SHOULD NOT be checked-in to individual project repositories.

Required JavaScript Libraries

• Backbone.js -> Data model
• Underscore.js -> Data structure utilities
• d3.js -> Visualizations
• jQuery -> UI, DOM manipulation, effects
• Bootstrap.js -> UI style and structure

Application Configuration

Configuration files SHOULD NOT be checked-in to individual project repositories.

This web application specifies the following configuration files (see examples in app_root/examples):

proxy.json

• Location: app_root/examples
• Provides information to npm dev server
• Configures remote and local proxies to web services

ningx.conf

• Location: nginx_root
• Provides information to NGINX web server
• Configures remote and local proxies to web services

tornado.config

• Location: specified at command-line

cd $WEBAPP_ROOT
python websvcs/tornadoapp.py --config_file=/local/path/to/tornado.config

• Provides information to tornado services running within tornado

Property	Description	Example
web_configs	Directory containing display.json and datamodel.json (see below)	/local/webapps/MyWebApp/configurations
data_path	Directory containing data files to be served (e.g. feature matrices, lookups)	/local/webapps/MyWebApp/data
client_id	OAUTH2 application identifier	1234567890.apps.googleusercontent.com
client_secret	OAUTH2 secret key	blwleldIKudk3B7eBldPPsSc15b8
client_host	OAUTH2 redirect address	http://example.org:3333
authorized_users	Simple mechanism to limit access to the application	["user@example.com","example@gmail.com"]
mongo_uri	Connection string for mongo database used to store sessions	mongodb://localhost:3030
mongo_lookup_uri	Connectionstring database used to store data (e.g. Feature Matrices)	mongodb://hostname:3030

Google OAUTH2 APIs - obtain information and API access keys from https://code.google.com/apis/console/

display.json

• Location: specified in tornado.config (see above)
• Specifies identifying UI elements (e.g. titles, links in the About menu)
• Specifies links to Hangout URL

Example configuration

{
    "title":"TCGA Cancer Regulome :: Example",
    "hangoutUrl":"https://plus.google.com/hangouts/_?gid={app-gid}",
    "aboutLinks":[
        { 
            "label":"TCGA Home",
            "url":"http://cancergenome.nih.gov"
        }
    ]
}

datamodel.json

• Location: specified in tornado.config (see above)
• Specifies data source elements such as files, directories, and data services available to the application
• Includes information such as labels and data types

This file allows the application to dynamically associate data sources to UI views

Example configuration

{
    "data_sets":{
        "label":"Data Sets",
        "mutations":{
            "label":"Mutations",
            "catalog":{
                "Protein_Mutations_Per_Cancer_Type":{
                    "id":"Protein_Mutations_Per_Cancer_Type",
                    "label":"Protein Mutations Per Cancer Type",
                    "service":"lookups/mutations",
                    "description":"This dataset was prepared from TCGA MAF files produced by Firehose",
                    "provenance":"provenance_v7_23nov_2012.txt",
                    "model":"Mutations"
                },
                "mutsig_rankings":{
                    "id":"mutsig_rankings",
                    "label":"MutSig Rankings",
                    "service":"lookups/mutsig_rankings",
                    "description":"This dataset was prepared from TCGA MutSig 2.0 data produced by Firehose"
                },
                "mutsig_top20":{
                    "id":"mutsig_top20",
                    "label":"MutSig Top20",
                    "service":"mutsig_rankings"
                },
                "mutsig_provenance":{
                    "id":"mutsig_provenance",
                    "label":"MutSig Provenance",
                    "service":"data/provenance/mutsig_provenance.json"
                }
            }
        }
    }
}

Initial Dev Setup

1. Clone this repository
2. Install Required Dependencies (see above)
3. Download Third-Party JavaScript libraries and extract into root directory
4. Build Web App npm install npm start
5. Start tornado web services python websvcs/tornadoapp.py --config_file=/local/path/to/tornado.config
6. Open web browser at http://localhost:3333