CiC: EAGER: Inferring Pattern and Processes of Genome Evolution Through Cloud Computing

University Of Florida, Gainesville FL

Investigators

Abstract

The University of Florida is awarded a grant to implement and evaluate the latest methods for identifying the evolutionary history of gene duplications and losses on the Microsoft Azure cloud computing platform, and will use these methods to reconstruct the history of whole genome duplications in plants. One of the greatest challenges in evolutionary biology is to identify genetic mechanisms responsible for adaptive changes and species diversification. The availability of large-scale genomic data sets from many diverse species provides unprecedented opportunities to identify such important genetic changes. Gene duplication plays a key role in gaining new gene functions and, consequently, adaptive innovations. However, in order to link gene duplications with adaptive changes, it is necessary to determine when in evolutionary history the duplications took place. Recently developed model-based methods enable scientists to map the locations of gene duplications and loss events within a species phylogeny. However, these methods are computationally intensive, and consequently, have only been implemented for small data sets. Cloud computing through the Microsoft Azure platform offers the ideal system in which to extend the implementations of these methods to incorporate full genomic data sets from many organisms and to keep pace with the rapid accumulation of new genome sequences. Education and training in computational biology are a major component of this project. Not only will this work motivate new research into modeling gene evolution and enable enormous analyses to identify potential genomic innovations, it also will provide unique opportunities for cross-disciplinary training for a post-doc and graduate student. Furthermore, educational resources on the uses of cloud computing for large-scale bioinformatics analyses will be developed for the classroom and internet, and a workshop on cloud computing for evolutionary analyses will be held in conjunction with a conference of evolutionary biologists.