File	Date	Author	Commit
Documentation	2013-01-28	Sébastien Boisvert	[7099d2] added some documentation
client	2013-01-24	Sébastien Boisvert	[420946] support custom sample list
server	2013-01-27	Sébastien Boisvert	[7b5cca] simplified the workflow
AUTHORS	2013-01-09	Sébastien Boisvert	[14d891] worked out the authors file
LICENSE	2013-01-15	Sébastien Boisvert	[7d0a4c] added 2013 for the copyright in the license
README	2013-01-14	Sébastien Boisvert	[fa0789] Updated the demo address
gpl-3.0.txt	2013-01-05	Sébastien Boisvert	[3feb63] fixed permissions for basic files

Read Me

Ray Cloud Browser: interactively skim processed genomics data with energy

Codename: Shagohod
Product manager: Sébastien Boisvert
License: GNU General Public License, version 3
Estimated Time of Arrival: 2013 Q1
Funding: Canadian Institute of Health Research
     S.B. is recipient of a doctoral award from the Canadian Institutes of Health Research (200910GSD-226209-172830). 

## Demo:

http://boisvert.info/Ray-Cloud-Browser

## Motivation

One of the problems with genomics is that you need to deliver large data
to end users before delivering a user experience for visualization.
But most end users are not ready for these large data and in some way it
does not make sense to move large data around.

Ray Cloud Browser is a genome graph browser in the cloud. The purpose is
to visualize genome assemblies and the main claim is that it will help 
researchers understanding a growing array of problems (like assembly algorithms).

The basic design is the same that is found in the Ray assembler -- message passing and
granularity are the two pillars of Ray technologies.
Although currently limited to assembly graph visualization, the Ray technologies
and ideas put forward are reusable freely, through products like RayPlatform, Ray Cloud Browser and
Ray.

For applications of the technology:

Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil.
Ray Meta: scalable de novo metagenome assembly and profiling.
Genome Biology (BioMed Central Ltd).
13:R122, Published: 22 December 2012
http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122

Sébastien Boisvert, François Laviolette, and Jacques Corbeil.
Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
Journal of Computational Biology (Mary Ann Liebert, Inc. publishers).
November 2010, 17(11): 1519-1533.
http://dx.doi.org/doi:10.1089/cmb.2009.0238


## Compatibility and requirements

These products can output a file in the Ray Cloud Browser format:

- Ray assembler http://denovoassembler.sourceforge.net/
- ABySS http://www.bcgsc.ca/platform/bioinfo/software/abyss/

For deployment, a web server is needed and clients must have a modern
web browser supporting HTML5.


## Official website

	https://github.com/sebhtml/Ray-Cloud-Browser


## Legal notice:

All the code is licensed under the GNU General Public License, version 3, see LICENSE.

The client is a fork of the force-graph project (author: Sébastien Boisvert, license: GPLv3).
  => https://github.com/sebhtml/force-graph

Ray Cloud Browser does not bundle any external library.


## How it works

It is a client-server application. The client runs in a browser with Javascript and HTML5.
The server is in C++ and runs with Apache or any web server with CGI support.

The server is in C++ 1998.
The messaging is done with HTTP (rfc 2616).
The client is in HTML5 and Javascript.

see client/README and server/README for more detail.