A Cloud-based GWAS Analysis Pipeline for Clinical Researchers

Paul Heinzlreiter, James Richard Perkins, Óscar Torreño, Johan Karlsson, Juan Antonio Ranea, Andreas Mitterecker, Miguel Blanca, Oswaldo Trelles

2014

Abstract

The cost of obtaining genome-scale biomedical data continues to drop rapidly, with many hospitals and universities being able to produce large amounts of data. Managing and analysing such ever-growing datasets is becoming a crucial issue. Cloud computing presents a good solution to this problem due to its flexibility in obtaining computational resources. However, it is essential to allow end-users with no experience to take advantage of the cloud computing model of elastic resource provisioning. This paper presents a workflow that allows the end-user to perform the core steps of a genome wide association analysis where raw gene- expression data is quality assessed. A number of steps in this process are computationally intensive and vary greatly depending on the size of the study, from a few samples to a few thousand. Therefore cloud computing provides an ideal solution to this problem by enabling scalability due to elastic resource provisioning. The key contributions of this paper are a real world application of cloud computing addressing a critical problem in biomedicine through parallelization of the appropriate parts of the workflow as well as enabling the end-user to concentrate on data analysis and biological interpretation of results by taking care of the computational aspects.

Paper Citation

in Harvard Style

Heinzlreiter P., Perkins J., Torreño Ó., Karlsson J., Ranea J., Mitterecker A., Blanca M. and Trelles O. (2014). A Cloud-based GWAS Analysis Pipeline for Clinical Researchers . In Proceedings of the 4th International Conference on Cloud Computing and Services Science - Volume 1: CLOSER, ISBN 978-989-758-019-2, pages 387-394. DOI: 10.5220/0004802103870394

in Bibtex Style

@conference{closer14,
author={Paul Heinzlreiter and James Richard Perkins and Óscar Torreño and Johan Karlsson and Juan Antonio Ranea and Andreas Mitterecker and Miguel Blanca and Oswaldo Trelles},
title={A Cloud-based GWAS Analysis Pipeline for Clinical Researchers},
booktitle={Proceedings of the 4th International Conference on Cloud Computing and Services Science - Volume 1: CLOSER,},
year={2014},
pages={387-394},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004802103870394},
isbn={978-989-758-019-2},
}

in EndNote Style

TY - CONF
JO - Proceedings of the 4th International Conference on Cloud Computing and Services Science - Volume 1: CLOSER,
TI - A Cloud-based GWAS Analysis Pipeline for Clinical Researchers
SN - 978-989-758-019-2
AU - Heinzlreiter P.
AU - Perkins J.
AU - Torreño Ó.
AU - Karlsson J.
AU - Ranea J.
AU - Mitterecker A.
AU - Blanca M.
AU - Trelles O.
PY - 2014
SP - 387
EP - 394
DO - 10.5220/0004802103870394