BioGPS - the Gene Annotation Portal

This file tree contains the source code for the user-facing web application portion of BioGPS. It is written in Python and based primarily on Django.

In order to run a complete installation of BioGPS, several separate components are required:

• BioGPS UI (this project)
• MyGene.info (gene annotation data)
• ElasticSearch
• PostgreSQL

Installation

You can follow this step-by-step instruction to setup a working folder to run BioGPS for development purpose.

The following are the all dependencies needed:

Baseline Required Software

• Python 2.6+
• mercurial (for checking out his repo)
• Java JRE 1.6+ (for JS minification)
• NodeJS 0.2.6+ (for LESS compilation)

Python Packages

Extra Python software is required for a production installation, documented in "requirements.txt" and installed via pip:

pip install -r requirements.txt

Additional Python software for development (optional) is documented in "optional_dev.txt":

pip install -r optional_dev.txt

Javascript dependencies

1. ExtJS v3.3.0

   Download from this link, and then extract full ExtJS package (not just ext-all.js) to src/assets/js/ext/3.3.0 folder (need to "mkdir src/assets/js/ext" first).

2. ExtJS plugin ManagedIFrame

   Download from this link, and then extract two files: miframe.js and miframe-debug.js to src/assets/js/ext/plugins folder.

Credits

Active Developers

• Chunlei Wu
• Cyrus Afrasiabi
• Andrew Su

Past Contributors

• Ian MacLeod
• Marc Leglise
• Camilo Orozco
• James Goodale
• Jason Boyer