On July 5th, I successfully defended my doctoral dissertation entitled "Leveraging Large-Scale Distributed Systems for Massive Biological Datasets". After the successful defense, I began my position as a Senior Software Engineer at St. Jude Children's Research Hospital in Memphis, TN on July 22.
Along with Dinesh Rajan of the Cooperative Computing Lab at the University of Notre Dame, we have refined our work on MAKER into an elastic application called E-MAKER. This application has been included as a case study in a paper that Dinesh will present at CCGRID 2013. This paper discusses characteristics of elastic applications and guidelines for developing elastic applications. Additionally we present a model of the execution of E-MAKER and suggest methods to utilize such models to maximize resource performance.
My work on the MAKER genome annotation platform that was presented at ICCABS '12 has been accepted for publication in BMC Genomics as part of a special issue from the conference. The extended paper includes using MAKER on Amazon's EC2 cloud computing framework. Additionally we have supplied our code modifications back to the University of Utah and our work will be incorporated into the main development line for release in the future.
After spending the summer of 2011 at an internship where I did work on rapid genotyping of bacterial genome samples, I returned to the University of Notre Dame for my 3rd year of Ph.D. studies. The work that I had done prior on the MAKER platform was polished and submitted to ICCABS 2012 and was accepted for publication. In addition to this I have been working on my Ph.D.
My research recently has focused on the MAKER annotation tool. As part of my work, I have adapted it for use with the Work Queue distributed computing framework. We are now capable of running MAKER annotations on distributed heterogeneous systems.
I presented a paper entitled "Taming Complex Bioinformatics Workflows with Weaver, Makeflow and Starch" at the 5th Workshop of Workflows in Support of Large-scale Science at Supercomputing 2010 in New Orleans, LA. Further details on the paper and the text can be found on my Research page.
Andrew completed the Ph.D. in Computer Science and Engineering at the University of Notre Dame in July 2013 as a member of the Notre Dame Bioinformatics Laboratory. He is now employed as a Senior Software Engineer in the Computational Biology department at St. Jude Children's Research Hospital.