Acquisition of the Notre Dame Biocomplexity Computer Cluster

收购圣母大学生物复杂性计算机集群

• 批准号: 0420980
• 负责人: Mark Alber
• 金额: $ 16.02万
• 依托单位: University of Notre Dame
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-08-01 至 2007-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0420980&HistoricalAwards=false
• 关键词: Acquisition; Notre; Dame; Biocomplexity; Computer

A grant has been awarded to the University of Notre Dame under the direction of Dr. Mark Alber for support of establishing a Beowulf type Biocomplexity Cluster to provide computer infrastructure for The Notre Dame Interdisciplinary Center for the Study of Biocomplexity (ICSB) to meet its broad research and educational goals. The Biocomplexity Cluster will be added to the existing BoB cluster (http://bob.nd.edu) at Notre Dame. Its addition to this high performance computing facility will be embedded in the administrative structures of the Science Computation Facilities (SCF) at Notre Dame. Establishment of the Cluster will result in dramatic increase in the range and complexity of the biological computations on Notre Dame campus.The ICSB supports the development of quantitative predictive models of biological processes ranging from subcellular to multicellular and ecological. The unique aspects of the ICSB are its interdisciplinary approach, its pursuit of complex biological systems at all scales simultaneously, and its insistence that modeling and quantitative experiments develop jointly. The Biocomplexity Cluster will help ICSB in supporting a variety of projects, which require a high-end computational environment. These projects: Molecular Dynamics, Multiscale Simulation of Avian Limb Development, Microscale Modeling of Cancellous Bone Damage and Environmental Biocomplexity- cover all interacting scales of Biocomplexity phenomena from molecular to environmental. New collaborations with groups working on Biological Networks and Modeling of Cytoskeleton will also greatly benefit from the Cluster. 25% of the CPU time of the Cluster will be accessible to other researchers in the Colleges of Science and Engineering. During academic year up to 5% of the computer time will be allocated for teaching purposes. The Cluster will also allow students participating in the Summer REU programs on Notre Dame campus to learn and apply high-end computational techniques as a part of their training. Interactive web pages will be developed with separate sections aimed at junior-high and high school students to provide educational materials on Biocomplexity which will utilize the Cluster.The interdisciplinary study of Biocomplexity incorporates quantitative modeling into biology and related disciplines, and thus has broad impact on diverse fields such as Biology, Geology, Environmental Engineering, Life Sciences, Computer Science, and Mathematics. The Biocomplexity Cluster will be used to support interdisciplinary research projects and coursework, helping to train a new generation of students in the integration of interdisciplinary biological experimentation and modeling. Collaboration of ICSB with the newly established Indiana University Biocomplexity Institute at Bloomington and the Indiana University Medical School at Indianapolis, formalized as the Indiana Biocomplexity Consortium, will ensure broad impact through student exchange, development of new educational initiatives, and development of additional collaborative research projects. The Cluster will help the ICSB in achieving one of its major goals of developing new computational techniques and tools of broad utility to bioscientists and distributing these freely to researches within the scientific community.

在Mark阿尔伯博士的指导下，圣母大学获得了一笔赠款，用于支持建立一个Beowulf型生物复杂性集群，为圣母大学生物复杂性研究跨学科中心（ICSB）提供计算机基础设施，以实现其广泛的研究和教育目标。生物复杂性集群将被添加到巴黎圣母院现有的BoB集群（http：bob.nd.edu）。它除了这个高性能计算设施将嵌入在科学计算设施（SCF）在圣母院的行政结构。 ICSB的建立将大大增加圣母大学校园生物计算的范围和复杂性。ICSB支持从亚细胞到多细胞和生态的生物过程的定量预测模型的发展。ICSB的独特之处在于其跨学科的方法，同时追求所有尺度的复杂生物系统，以及坚持建模和定量实验的联合发展。生物复杂性集群将帮助ICSB支持各种需要高端计算环境的项目。这些项目：分子动力学，鸟类肢体发育的多尺度模拟，松质骨损伤和环境生物复杂性的微观建模-涵盖从分子到环境的生物复杂性现象的所有相互作用尺度。与生物网络和细胞骨架建模小组的新合作也将大大受益于集群。集群25%的CPU时间将提供给科学和工程学院的其他研究人员。在学年期间，高达5%的计算机时间将分配用于教学目的。该集群还将允许学生参加圣母大学校园的夏季REU计划，学习和应用高端计算技术作为他们培训的一部分。此外，还将开发面向初中生和高中生的交互式网页，提供利用该集群的生物复杂性的教育材料。生物复杂性的跨学科研究将定量建模融入生物学和相关学科，因此对生物学、地质学、环境工程学、生命科学、计算机科学和数学等不同领域产生广泛影响。生物复杂性集群将用于支持跨学科的研究项目和课程，帮助培养新一代学生整合跨学科生物实验和建模。ICSB与布卢明顿新成立的印第安纳州大学生物复杂性研究所和印第安纳波利斯的印第安纳州大学医学院合作，正式成为印第安纳州生物复杂性联盟，将通过学生交流，开发新的教育计划和开发其他合作研究项目来确保广泛的影响。该小组将帮助ICSB实现其主要目标之一，即开发对生物科学家具有广泛用途的新的计算技术和工具，并将其免费分发给科学界的研究人员。