MRI-R2: Acquisition of High Performance Computer and Microarray Scanner for Interdisciplinary Research in Computer Science and Biology at St. Lawrence University

Saint Lawrence University, Canton NY

Investigators

Abstract

"This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5)." Proposal #: 09-59713 PI(s): Sharp, Richard Dixon, Emily H.; Estevez, Ana Y.; Harcourt, Edwin; Olendzenski, Lorraine, C. Institution: Saint Lawrence University Title: MRI-R2/Acq.: High Performance Computer and Microarray Scanner for Interdisciplinary Research in Computer Science and Biology at St. Lawrence University Project Proposed: This project, acquiring a microarray scanner and a high-end compute-server, enables the research programs of twelve faculty members from the departments of Computer Science, Biology, Statistics, and Psychology. Projects include image synthesis, comparative genome analysis in yeast, phylogenetic analysis of microbial communities and comparative analysis of bacterial genomes, microarray analysis of gene expression, and bird foraging studies. Both of these instruments will be the first of their kind on the St. Lawrence University (SLU) campus; the microarray scanner is the first in New York State north of Syracuse and the high-end server, the first in any neighboring universities. The placement of a microarray scanner eliminates the need to utilize one in North Carolina that provides services at a discounted rate for faculty conducting research with undergraduate students. This currently useful but unwieldy procedure prevents faculty from expanding the number and types of microarrays used in their research, significantly limiting progress. A single high-end server has been chosen, as opposed to a cluster of computers, due to the simpler programming model inherent in one machine versus many. Most of the St. Lawrence users employ software tools that are parallel, but not distributed, and hence would not benefit from a cluster. The large memory size in one machine is especially beneficial for those research projects that generate large hash tables, such as the BLAST algorithm for genome database querying, and photon-mapping algorithms used in numerical simulations of light scatter. The microarray scanner is housed in a common-use equipment room close to faculty microbiology, biochemistry, genetics and cell biology labs where it will be easily accessible to all biology faculty. The scanner and space will be managed by the Department of Biology, but available for use by faculty and students in all science disciplines, as well as scientists/researchers from the broader North Country Region of New York State (Clarkson University, SUNY-Potsdam, SUNY-Canton, Paul Smith's College). The biology co-PIs oversee day-to-day operations, training, scheduling of all users, and equipment maintenance (via a service contract support from manufacturers). The server will be housed in the SLU Information Technology (IT) Central Server Facility. Physical maintenance is conducted by IT's server manager and IT. User accounts are maintained, and training is conducted. A multidisciplinary Project Steering Committee oversees the use and management of the equipment. With the new microarray scanner on site, the volume of microarray processing will increase, as will the costs associated with running these experiments. These higher research costs will be covered through research support funds from the Biology Department. At the completion of the project period, SLU assumes all costs for the day-to-day operation and long-term maintenance. Broader Impacts: This instrumentation strongly impacts SLU and strengthens SLU's undergraduate research culture. The new equipment will allow undergraduates in these disciplines to gain experience with key scientific technologies and relevant methodologies. However, the reach of the equipment is not limited to SLU alone; two research projects from neighboring Clarkson University have been identified, and will be a focal point for The Associated Colleges of the St. Lawrence Valley, an educational consortium between St. Lawrence University and three neighboring universities: Clarkson University, State University of New York, (SUNY) Potsdam, and SUNY Canton. This consortium was created to expand the number and variety of educational opportunities for faculty and students, to share resources, and to innovate through joint action. Emphasis is placed on the recruitment of students from underrepresented backgrounds.