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README.md

Ray Cloud Browser: interactively skim processed genomics data with energy

Product manager: Sébastien Boisvert License: GNU General Public License, version 3 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:

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:

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.