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

“这项奖励是根据2009年美国复苏和再投资法案（公法111-5）资助的。”提案号：09-59713PI(s): Sharp, Richard Dixon, Emily H.；安娜·y·埃斯特维兹；埃德温·哈考特;机构：圣劳伦斯大学职称：MRI-R2/Acq。项目建议：该项目将获得一台微阵列扫描仪和一台高端计算机服务器，使来自计算机科学系、生物学系、统计学和心理学系的12名教员能够进行研究项目。项目包括图像合成、酵母的比较基因组分析、微生物群落的系统发育分析和细菌基因组的比较分析、基因表达的微阵列分析和鸟类觅食研究。这两种仪器都将是圣劳伦斯大学（SLU）校园内的第一种仪器；微阵列扫描仪是纽约州锡拉丘兹以北的第一个，高端服务器是所有邻近大学中的第一个。微阵列扫描仪的安置消除了利用北卡罗来纳的一个以折扣价为本科生进行研究的教师提供服务的需要。这种目前有用但笨拙的程序阻碍了教师扩大他们研究中使用的微阵列的数量和类型，极大地限制了进展。我们选择了一台高端服务器，而不是一组计算机，因为一台机器固有的编程模型比多台机器更简单。大多数St. Lawrence用户使用的软件工具是并行的，而不是分布式的，因此不会从集群中受益。一台机器的大内存容量对于那些需要生成大型哈希表的研究项目尤其有利，例如用于基因组数据库查询的BLAST算法，以及用于光散射数值模拟的光子映射算法。微阵列扫描仪被安置在一间公用设备室内，靠近学院微生物、生物化学、遗传学和细胞生物学实验室，所有生物学院都可以很容易地使用它。扫描仪和空间将由生物系管理，但可供所有科学学科的教师和学生以及来自纽约州北部地区（克拉克森大学，纽约州立大学波茨坦分校，纽约州立大学广州分校，保罗史密斯学院）的科学家/研究人员使用。生物合作项目负责人监督日常操作、培训、所有用户的日程安排和设备维护（通过制造商的服务合同支持）。该服务器将被安置在SLU信息技术（IT）中央服务器设施中。物理维护由IT的服务器经理和IT进行。维护用户账号，进行培训。一个多学科项目指导委员会监督设备的使用和管理。有了新的微阵列扫描仪，微阵列处理的数量将会增加，与运行这些实验相关的成本也会增加。这些较高的研究费用将由生物系的研究支持基金支付。项目结束后，SLU承担所有日常运营和长期维护的费用。更广泛的影响：该仪器对SLU产生了强烈的影响，并加强了SLU的本科生研究文化。新设备将使这些学科的本科生获得关键科学技术和相关方法的经验。然而，该设备的覆盖范围不仅限于SLU；邻近的克拉克森大学的两个研究项目已经确定，并将成为圣劳伦斯谷联合学院的焦点，圣劳伦斯谷联合学院是圣劳伦斯大学和三所邻近大学之间的教育联盟：克拉克森大学、纽约州立大学、波茨坦州立大学和纽约州立大学广州分校。该联盟的成立是为了扩大教师和学生的教育机会的数量和种类，共享资源，并通过联合行动进行创新。重点是招收来自代表性不足背景的学生。

"This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5)." Proposal #: 09-59713PI(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 UniversityProject 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.