OpenBEL - Web Tools

OpenBEL is an open source and open community project providing BEL (Biological Expression Language) and a set of tools to process/store biological knowledge. As BEL expressions may become very complex, our project aims to develop a web visualization tool for BEL graph to enhance user's comprehension and interaction, using HTML5 and Javascript libraries.

0. Setup

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Environment Ruby >= 2.1.2 Rails >= 4.1.4

After cloning this project follow these steps:

• bundle install (installs all needed gems)
• Configure config/database.yml (details here)
  • example configuration:

  development:
    adapter: mysql2
    encoding: utf8
    database: openbel_webtools
    username: root
    password:
    host: 127.0.0.1
    port: 3306

• rake db:migrate (setup your database)
• rails s (run server)
• access localhost:3000 to see if everything is working
• Enjoy!

1. Graph Structure

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This project make use of JSON Graph Specification Project (http://json-graph-format.info/) to make BEL files graphs available for multi-purpose use.

2. Graph Plugins

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• Cytoscape.js (http://cytoscape.github.io/cytoscape.js/)
• Cytoscape.js Navigator (https://github.com/cytoscape/cytoscape.js-navigator)