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，以建立一个“元集群”，使新一代的生物信息学应用程序正在开发中的犹他州大学。元聚类超越了单个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“循环农场”，一个紧密耦合的集群与快速节点间通信优化并行处理，一个可视化集群紧密耦合的数据密集型存储/处理单元和两个大型存储设施一起形成的元集群。除了建立这样一个集群，元集群环境的一个关键组成部分是促进和管理这些资源的访问由个人研究人员。使用犹他州的高性能计算中心（CHPC）正在开发的高度先进的调度技术（Maui/银），每个单独的元素将被无缝地集成（从用户的角度来看）到一个似乎是单一资源的东西中。基于我们在构建和运营商品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完成。所提出的生物信息学应用表现出很大程度的可变性，具有不同的计算，可视化，数据和并行处理的需求，因此需要访问相当异构的资源，以最佳地执行。这些应用范围从人群的流行病学研究到膝盖力学的调查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

7Li NMR chemical shift titration and theoretical DFT calculation studies: solvent and anion effects on second-order complexation of 12-crown-4 and 1-aza-12-crown-4 with lithium cation in several aprotic solvents.

7Li NMR化学位移滴定和理论DFT计算研究：溶剂和阴离子对12-crown-4和1-aza-12-crown-4与锂阳离子在几种非质子溶剂中的二级络合的影响。

• DOI: 10.1002/mrc.2542
• 发表时间: 2010
• 期刊: Magnetic resonance in chemistry : MRC
• 作者: Masiker,MarilynC;Mayne,CharlesL;Boone,BrianJ;Orendt,AnitaM;Eyring,EdwardM
• 通讯作者: Eyring,EdwardM

An improved multistate empirical valence bond model for aqueous proton solvation and transport.

• DOI: 10.1021/jp076658h
• 发表时间: 2008-01
• 期刊: The journal of physical chemistry. B
• 作者: Yujie Wu;Hanning Chen;Feng Wang;F. Paesani;G. Voth

A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties.

• DOI: 10.1063/1.1869417
• 发表时间: 2005-03
• 期刊: The Journal of chemical physics
• 作者: H. Tepper;G. Voth

Solid-state 13C NMR and quantum chemical investigation of metal diene complexes.

金属二烯配合物的固态 13C NMR 和量子化学研究。

• DOI: 10.1002/mrc.1981
• 发表时间: 2007
• 期刊: Magnetic resonance in chemistry : MRC
• 作者: Ma,Zhiru;Facelli,JulioC;Pugmire,RonaldJ;Dunn,BrianC;Turpin,GregoryC;Eyring,EdwardM;Ernst,RichardD
• 通讯作者: Ernst,RichardD

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

使用具有标准力场的并行遗传算法预测柔性分子的晶体结构。

• DOI: 10.1002/jcc.21189
• 发表时间: 2009
• 期刊: Journal of computational chemistry
• 影响因子: 3
• 作者: Kim,Seonah;Orendt,AnitaM;Ferraro,MartaB;Facelli,JulioC
• 通讯作者: Facelli,JulioC