Bioinformatics Research Published in Nature.
CIS Ph.D. student, Bryan Kolaczkowski, and UO assistant professor of biology, Joe Thornton, used a small cluster of Apple computers to simulate the evolution of thousands of gene sequences on a hypothetical evolutionary tree. They found that a simple logical method known as maximum parsimony is far more accurate under a wide range of conditions than the more widely used technique known as maximum likelihood, which uses a mathematic model of the evolutionary process. Their work impacts the way evolutionary biologists infer the relationships among species.
Bryan works in the area of Bioinformatics and is co-advised by CIS professor John Conery. The cluster consisted of four dual processor G4s and one dual processor G5. Bryan developed a simulator which offered significant improvements over existing systems, primarily ease of simulating evolutionary heterogeneity. He also developed a database-centered workflow management system to handle the large scale simulations, results collection, and statistical analysis. This software will eventually be integrated into Conery's PIP (pipeline interface program).
For more information, see the University of Oregon news story.