COBRE: UID: BIOINFORMATICS CORE FACILITY

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 IBEST生物信息学核心目前包括几个计算集群、独立的应用程序服务器、数据存储系统、软件和人员。 我们的主要生产群集由Dell M1000E盘柜和M605刀片式服务器组成。它总共有512个核心(AMD64)和512 GB的总系统内存(每个核心1 GB)。除了我们的主集群之外，我们还维护了一个基于Intel Xeon的96处理器系统，总系统内存为48 GB(每个处理器512MB)，以及一个基于96处理器的PowerPC G5系统，总系统内存为192 GB(每个处理器2 GB)。我们还维护了一个主要用于测试和开发的集群，该集群由44个Intel Xeon处理器和22 GB系统内存(每个处理器512MB)组成。除了研究集群，我们还有一个由Dell PE2950和PE1950服务器组成的小型集群(Datarig)，专门用于454测序数据的后处理。它是40核Intel Xeon集群，总系统内存为96 GB。集群目前采用1 Gb/S TCP互联互通。 独立的应用程序服务器包括3个Dell M905‘S，每个16核和32 GB系统内存；2个Dell PE6950’S，每个8核和8 GB系统内存；以及2个双处理器Sun SPARC V440‘S。 我们支持超过85TB的总数据存储和备份。我们的LTO-4磁带备份系统能够备份20TB的数据。我们的主要生产集群有30TB的专用存储，454个数据集群有15TB的专用存储，其余的生产和开发集群分担剩余的20TB数据存储。所有用户数据都会定期备份。 核心系统位于爱达荷州大学校园内一个1400平方英尺的房间内，该房间是由UI for This Core专门设计和翻新的。1 Gb光纤和铜缆连接所有设备，UI骨干网提供4 Gb/S传输速率。这个房间有一个专用的80KVa UPS，带有三相电源和四个强制空气处理器，连接到多余的大学冷冻水系统。该设施有一台应急备用柴油发电机。 生物信息核心通过1 Gb/S光纤连接到大学主干，为教研室和实验室提供1 Gb/S组网。此外，爱达荷大学已在短期内将校外数据传输能力扩展到2.8 Gb/S，并将在3年内扩展到10 Gb/S。爱达荷大学的部分资金来自NIH Lariat基础设施拨款1000万美元。这将实现与世界其他地区的大规模、高速数据传输，而不仅仅是大学内部的数据传输。这对协作和系统支持都很重要，因为要使我们的许多大型数据库保持最新，需要不断传输来自NCBI等主要数据库提供商的大量数据。 软件 广泛的软件可用于一般序列分析、系统发育和种群遗传学分析、蛋白质结构建模、表达阵列分析、统计和数学建模。这些计算机上可用的软件包括：通用序列分析程序包(EMBOSS等)、数据库访问(PDB、SCOP、GenBank等)、系统发育推断(PHYLIP、PAUP*、MR Bayes、FastDNAml、GeneTree、MODELTEST、P4、PAML、Seq-Gen、TreeView)、群体遗传学(迁移、波动、重组、LamArc、GeneConv)、序列比对(HMMER、Clustanw、Mafft、肌肉等)、序列组装(Phred/Phrap/Consed、Repeatker)、蛋白质结构可视化(Amber、Charmm、Cn3D、Rasol、3D分子查看器)和统计/数学程序包(Matha、mata、R、R、Mafft、Muscle等S3随机空间)。 这些程序中的大多数是免费供学术使用的，也有一些是商业程序包或由Cobre的学生和人员开发的。后者包括用于多序列比对的新软件(Evalyn)，用于基于改进的邻接法推断系统发育树的快速程序(ClearCut)，用于核糖体RNA基因序列的高通量分析的程序(HITSA)，以及用于总结和图形显示HITSA结果的配套程序(StatGen)，以及用于分析关于细菌群落的TRFLP数据的微生物群落分析(MICA)。此外，还开发了促进数据分析的工具，包括使用RepeatMasker检测基因组中转座子的工具“All-And-All”BLAST，以及用于分布式PAUP和BOOTSTRAP分析的工具。这些软件和数据分析工具中的每一个都可以在任何地方免费提供给研究人员。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The IBEST Bioinformatics Core currently comprises several compute clusters, stand-alone application servers, data storage systems, software, and personnel. Our primary production cluster is made up of Dell M1000E enclosures and M605 blades. It has a total of 512 cores (AMD64) and 512GB of total system memory (1GB per core). In addition to our primary cluster we maintain a 96 processor Intel Xeon based system with 48GB total system memory (512MB per processor) and a 96 processor PowerPC G5 based system with 192GB total system memory (2GB per processor). We also maintain a cluster primarily used for testing and development, which is made up of 44 Intel Xeon processors and 22GB of system memory (512MB per processor). In addition to the research clusters we have a small cluster (datarig) made up of Dell PE2950 and PE1950 servers which dedicated to the post-processing of 454 sequencing data. It is a 40 core Intel Xeon cluster with 96GB of total system memory. The clusters are currently networked with 1Gb/s TCP interconnects. The stand-alone application servers include 3 Dell M905's each with 16 cores and 32GB of system memory, 2 Dell PE6950's each with 8 cores and 8GB of system memory and 2 dual processor Sun SPARC V440's. We support over 85TB of total data storage and backup. Our LTO-4 tape backup system is capable of backing up 20TB of data. Our main production cluster has 30TB of dedicated storage, the 454 datarig has 15TB of dedicated storage, and the remaining production and development clusters split the remaining 20TB of data storage. All user data is backed up regularly. The core systems are located on the University of Idaho campus in a 1400 square foot room that has been specifically designed and renovated by UI for this Core. 1GB fiber and copper connect all equipment, and the UI backbone provides 4GB/s transfer rates. This room has a dedicated 80KVa UPS with three phase power and four forced air handlers attached to redundant university chilled water systems. The facility has an emergency backup diesel generator. The bioinformatics core is connected to the university backbone with 1Gb/s fiber and provides 1Gb/s networking to the faculty offices and laboratories. Also, the University of Idaho, funded in part through the $10M NIH Lariat infrastructure grant, has expanded off campus data transmission capacity to 2.8Gb/s in the short term, and will expand to 10Gb/s within 3 years. This will enable large, high-speed data transfer with the rest of the world, rather than just within the university. This is important for both collaborations and for systems support, since keeping our many huge databases up to date requires constant transmission of vast amounts of data from primary database providers such as NCBI. Software A wide array of software is available for general sequence analysis, phylogenetic and population genetics analyses, protein structure modeling, expression array analysis, statistics and mathematical modeling. The software available on these computers include: General Sequence Analysis Packages (EMBOSS, etc.), Database Access (PDB, SCOP, GenBank, etc.), Phylogenetic Inference (PHYLIP, PAUP*, MrBayes, fastDNAml, GeneTree, MODELTEST, P4, PAML, Seq-Gen, TreeView), Population Genetics (Migrate, Fluctuate, Recombine, Lamarc, GeneConv), Sequence Alignment (HMMER, ClustalW, mafft, muscle, etc.), Sequence Assembly (Phred/Phrap/Consed, RepeatMasker), Protein Structure Visualization (Amber, Charmm, Cn3D, Rasmol, 3D Molecular Viewer), and Statistical/Mathematical Packages (Mathematica, MatLab, R, S3 Stochastic Spatial). Most of these programs are free for academic use, while others are commercial packages or have been developed by COBRE students and personnel. The latter includes new software (EVALYN) for multiple sequence alignments, a fast program (ClearCut) for inferring phylogenetic trees that is based on a modified neighbor joining method, a program for high throughput analysis of ribosomal RNA gene sequences (HiTSA), and a companion program (StatGen) that summarizes and graphically displays the results from HiTSA, and the Microbial Community Analysis (MiCA) for analyzing TRFLP data about bacterial communities. In addition, tools to facilitate data analysis have been developed including an "all-against-all" BLAST, a tool for detecting transposable elements in genomes that uses RepeatMasker, as well as tools for distributed PAUP and bootstrap analysis. Each of these software and data analysis tools is freely available to researchers anywhere.