Home // International Journal On Advances in Networks and Services, volume 5, numbers 3 and 4, 2012 // View article

NGS workflow Optimization using a Hybrid Cloud Infrastructure

Authors:
Lorenzo Mossucca
Olivier Terzo
Klodiana Goga
Andrea Acquaviva
Francesco Abate
Rosalba Provenzano

Keywords: grid computing; cloud computing; virtual; next generation sequencing; hybrid architecture.

Abstract:
E-science applications involve great deal of data, to satisfy these processing requests, distributed computing paradigms, such as cluster, Grid, Virtual Grid, Cloud Computing, and Hybrid System are growing exponentially. Existing computing infrastructures, software system design, and use cases have to take into account the enormity in volume of requests, size of data and computing load. In Bioinformatics field, such as in Next Generation Sequencing technology, in order to have more accurate analysis, it increases the amount of data to process. A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, produces millions of short sequence fragments in a single run. These fragments can be used to measure levels of gene expression and to identify novel splice variants of genes. The proposed solution allows to make the system scalable and flexible reducing elaboration time. The first aspect covers reverse engineering of a fast splice junction mapper for RNA-Seq reads called TopHat in order to make parallelizable tasks and the second aspect concerns the development of hybrid architecture integrating a Grid and a Virtual Grid Environment.

Pages: 324 to 332

Copyright: Copyright (c) to authors, 2012. Used with permission.

Publication date: December 31, 2012

Published in: journal

ISSN: 1942-2644