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Master Defense - Rory Carmichael

Start: 4/5/2013 at 2:00PM
End: 4/5/2013 at 4:00PM
Location: 275 Fitzpatrick Hall, EE conference room
Attendees: The Master Thesis presentation is open to student and faculty to attend.
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Rory Carmichael, a Computer Science and Engineering graduate student, will be presenting and defending his Master Thesis on April 5th, 2:00 - 4:00 pm in 275 Fitzpatrick, the EE conference room.

His advisor Dr. Scott Emrich along with his committee members Dr. Patricia Clark and Dr. Douglas Thain will be in attendance.

"Scaling Collaborative Bioinformatics" 

Though many common bioinformatics problems are amenable to parallelization and large datasets are becoming the norm for biological inquiry, biologists do not generally have the skillset to effectively automate, parallelize, and scale their workflows.  This document describes contributions to bioinformatics ranging from collaborative frameworks to the automation of common workflows to the development of novel algorithms.  We begin by describing Biocompute, a web portal that overcomes challenges in user interface design and resource sharing to facilitate collaborations between systems programmers, bioinformatics software developers, and biologists.  Next, we highlight several parallel workflow implementations developed to serve th needs of the University of Notre Dame's biologists. These leverage insights from both biology and distributed systems to achieve their goals.  In imlementing them we encountered and solved several practical challenges on the path to scaling up.  We close with the introduction of a bioinformatics algorithm to detect loci-specific selective pressure favoring codon rarity in ortholog groups that span Archaea, Prokaryota, and Eukaryota.