Supercomputing Institute for Digital Simulation and Advanced Computation 2006 Annual Research Report 2006 Annual Research Report of the Supercomputing Institute for Digital Simulation and Advanced Computation Visit us on the Internet: www.msi.umn.edu Supercomputing Institute for Digital Simulation and Advanced Computation University of Minnesota 599 Walter 117 Pleasant Street SE Minneapolis, Minnesota 55455 © 2006 by the Regents of the University of Minnesota. All rights reserved. This report was prepared by Supercomputing Institute researchers and staff. Editor: Tracey A. Bartlett This publication can be made available in alternative formats for people with disabilities. Direct requests to [email protected] or call (612) 625-1818. The University of Minnesota is committed to the policy that all persons shall have equal access to its programs, facilities, and employment without regard to race, color, creed, religion, national ori- gin, sex, age, marital status, disability, public assistance status, veteran status, or sexual orientation. contains a minimum of 10% postconsumer waste Table of Contents Introduction Overview . .2 Digital Technology Center . .2 Supercomputing Institute Resources and Programs Core Resources . .3 Research Laboratories Basic Sciences Computing Laboratory . .5 Computational Genetics Laboratory . .6 Digital Technology Computational Biology Laboratory . .7 Laboratory for Large-Scale Data Analysis . .8 Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory . .9 Scientific Data Management Laboratory . .10 Scientific Development and Visualization Laboratory . .11 Graduate Programs Scientific Computational Graduate Program . .12 Computational Neuroscience Program . .12 Partnerships Computational Life Sciences Program . .13 Grid and BlueGene Computing Block Grant . .14 Laboratory for Computational Science and Engineering . .15 Research Scholarship Program . .16 Undergraduate Internship Program . .17 Researchers and Administration Fellows of the Institute . .18 National Advisory Board . .19 Administrative Staff . .19 Technical Support Staff . .20 Committee and Panel Members . .22 External Support . .24 Events Sponsored Symposia Bioinformatics: Building Bridges . .34 VLab Workshop . .35 Outreach Programs Environmental Science Career Days . .36 2006 Annual Research Report of the Supercomputing Institute i Table of Contents (continued) Ongoing and Recently Completed Research Projects From January 1, 2005 Through March 15, 2006 University of Minnesota–Duluth College of Science and Engineering Department of Chemical Engineering . .39 Department of Chemistry and Biochemistry . .39 Department of Computer Science . .41 Department of Physics . .42 Natural Resources Research Institute . .43 Medical School Department of Anatomy, Microbiology, and Pathology . .44 Department of Biochemistry and Molecular Biology . .44 University of Minnesota–Hormel Institute The Hormel Institute . .47 University of Minnesota–Twin Cities Academic Health Center Cancer Center . .60 Center for Computational Genomics and Bioinformatics . .61 Center for Drug Design . .61 Stem Cell Institute . .62 College of Agricultural, Food, and Environmental Sciences Department of Agronomy and Plant Genetics . .63 Department of Animal Science . .66 Department of Entomology . .67 Department of Horticultural Science . .67 Department of Plant Pathology . .68 Department of Soil, Water, and Climate . .71 College of Agricultural, Food, and Environmental Sciences and College of Human Ecology Department of Food Science and Nutrition . .72 ii 2006 Annual Research Report of the Supercomputing Institute Table of Contents (continued) College of Agricultural, Food, and Environmental Sciences and Institute of Technology Department of Biosystems and Agricultural Engineering . .72 College of Biological Sciences Biotechnology Institute . .73 Department of Ecology, Evolution, and Behavior . .74 Department of Plant Biology . .77 College of Biological Sciences and Medical School Department of Biochemistry, Molecular Biology and Biophysics . .82 Department of Genetics, Cell Biology, and Development . .95 College of Education and Human Development Institute of Child Development . .101 College of Liberal Arts Department of Economics . .101 Department of Geography . .102 Department of Sociology . .103 College of Natural Resources Department of Bio-based Products . .103 College of Pharmacy College of Pharmacy . .104 Department of Experimental and Clinical Pharmacology . .105 Department of Medicinal Chemistry . .107 Department of Pharmaceutics . ..