Proteins to Population:A metacluster for Bioinformatics

从蛋白质到群体：生物信息学元簇

• 批准号: 6501301
• 负责人: Julio Cesar Facelli
• 金额: $ 153.1万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-30 至 2004-09-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6501301
• 关键词: biomedical equipment purchase; computer system design /evaluation; informatics; information retrieval; information systems

DESCRIPTION (provided by applicant): This proposal seeks funding to build a "meta-cluster" to enable the new generation of bioinformatics applications under development at the University of Utah. Meta-clustering moves beyond the concept of a single general purpose computational cluster to specifically tailor resources and computational elements towards problems for which they are optimized. These resources will include a computational "cycle farm", a tightly coupled cluster with fast internode communication for optimitized parallel processing, a visualization cluster a tightly coupled data intensive storage/processing unit and two large storage facilities together forming the meta-cluster.Beyond building such a cluster, a key component of the meta-cluster environment is facilitating and managing access to these resources by individual researchers. Using highly advanced scheduling techniques (Maui/Silver) under development at the Center for High Performance Computing (CHPC) at Utah, each of the separate elements will be seamlessly integrated (from a user's perspective) into what appears to be a single resource. Based on our extensive experience in building and operating clusters of commodity hardware, we have designed the meta-cluster to not only provide the necessary resources for our emerging set of applications but done so in the most cost effective manner. The proposed bio-informatic applications exhibit a large degree of variability, have varied computational, visualization, data and parallel processing needs, and therefore require access to quite heterogeneous resources to perform optimally. These applications range from epidemiological studies of populations to investigations of the mechanics of knees or studies of organ level systems down to detailed atomistic simulations of various biomolecular systems.

描述（由申请人提供）：该提案寻求资金建立一个“元集群”，以支持犹他大学正在开发的新一代生物信息学应用程序。元集群超越了单一通用计算集群的概念，专门针对优化的问题定制资源和计算元素。 这些资源将包括一个计算“循环场”、一个具有快速节点间通信以优化并行处理的紧密耦合集群、一个可视化集群、一个紧密耦合的数据密集型存储/处理单元以及两个大型存储设施，它们一起形成元集群。在这样一个集群中，元集群环境的一个关键组成部分是促进和管理个体研究人员对这些资源的访问。使用犹他州高性能计算中心 (CHPC) 正在开发的高度先进的调度技术（Maui/Silver），每个单独的元素都将（从用户的角度）无缝集成到看似单一的资源中。基于我们在构建和运营商用硬件集群方面的丰富经验，我们设计了元集群，不仅为我们新兴的应用程序集提供必要的资源，而且以最具成本效益的方式提供这些资源。所提出的生物信息学应用程序表现出很大程度的可变性，具有不同的计算、可视化、数据和并行处理需求，因此需要访问相当异构的资源才能最佳地执行。这些应用范围从人群的流行病学研究到膝盖力学的研究或器官水平系统的研究，再到各种生物分子系统的详细原子模拟。

项目成果

Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis.

肌动蛋白丝的变构：分子动力学模拟和粗粒度分析。

• 发表时间: 2005-09-13
• 影响因子: 11.1
• 作者: Chu, Jhih;Voth, Gregory A
• 通讯作者: Voth, Gregory A

Intermolecular shielding from molecular magnetic susceptibility. A new view of intermolecular ring current effects.

分子磁化率的分子间屏蔽。

• 发表时间: 2006-03
• 作者: Facelli; Julio C
• 通讯作者: Julio C

Revisiting the calculation of (13)C chemical shift tensors in cadmium acetate dihydrate with EIM and EIM/cluster methods.

重新审视使​​用 EIM 和 EIM/簇方法计算二水醋酸镉中的 (13)C 化学位移张量。

• 发表时间: 2006-03
• 作者: Orendt; Anita M
• 通讯作者: Anita M

Purification, identification and activity of phomodione, a furandione from an endophytic Phoma species.

磷二酮（一种来自内生茎点霉属的呋喃二酮）的纯化、鉴定和活性。

• 发表时间: 2008-02
• 影响因子: 3.8
• 作者: Hoffman, Angela M;Mayer, Steven G;Strobel, Gary A;Hess, Wilford M;Sovocool, G Wayne;Grange, Andrew H;Harper, James K;Arif, Atta M;Grant, David M;Kelley
• 通讯作者: Kelley

Intermolecular shielding contributions studied by modeling the (13)C chemical-shift tensors of organic single crystals with plane waves.

通过用平面波模拟有机单晶的 (13)C 化学位移张量来研究分子间屏蔽贡献。

• 发表时间: 2009-10-14
• 作者: Johnston, Jessica C;Iuliucci, Robbie J;Facelli, Julio C;Fitzgerald, George;Mueller, Karl T
• 通讯作者: Mueller, Karl T