COBRE: UID: BIOINFORMATICS CORE FACILITY

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目及 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 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 M1000 E盘柜和M605刀片式服务器组成。它总共有512个核心（AMD 64）和512 GB的总系统内存（每个核心1GB）。除了我们的主群集外，我们还维护一个基于96处理器的英特尔至强系统，总系统内存为48 GB（每个处理器512 MB），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个英特尔至强处理器和22 GB系统内存（每个处理器512 MB）组成。除了研究集群外，我们还有一个由Dell PE 2950和PE 1950服务器组成的小型集群（datarig），专门用于454个测序数据的后处理。它是一个40核Intel Xeon群集，总系统内存为96 GB。这些群集目前通过1Gb/s TCP互连进行联网。 独立应用程序服务器包括3台Dell M905，每台配备16个内核和32 GB系统内存; 2台Dell PE 6950，每台配备8个内核和8 GB系统内存;以及2台双处理器Sun PEGV 440。 我们支持超过85 TB的总数据存储和备份。我们的LTO-4磁带备份系统能够备份20 TB的数据。我们的主生产集群有30 TB的专用存储，454 datarig有15 TB的专用存储，其余的生产和开发集群分担了剩余的20 TB数据存储。所有用户数据都定期备份。 核心系统位于爱达荷州大学校园内的一个1400平方英尺的房间内，该房间由UI专门为此核心设计和翻新。1GB的光纤和铜线连接所有设备，UI骨干网提供4GB/s的传输速率。这个房间有一个专用的80 KVa UPS，三相电源和四个强制空气处理器连接到冗余的大学冷冻水系统。该设施有一个紧急备用柴油发电机。 生物信息学核心通过1Gb/s光纤连接到大学主干网，并为教师办公室和实验室提供1Gb/s网络。此外，爱达荷州大学部分通过1000万美元的NIH基础设施赠款资助，已在短期内将校外数据传输容量扩大到2.8Gb/s，并将在3年内扩大到10 Gb/s。这将实现与世界其他地区的大规模高速数据传输，而不仅仅是在大学内部。这对于协作和系统支持都很重要，因为保持我们许多庞大的数据库最新需要不断传输来自主要数据库提供商（如NCBI）的大量数据。 软件 广泛的软件可用于一般序列分析、系统发育和群体遗传学分析、蛋白质结构建模、表达阵列分析、统计学和数学建模。这些计算机上可用的软件包括：通用序列分析软件包（GSSSS等），数据库访问（PDB、SCOP、GenBank等），系统发育推断（PHYLIP、PAUP*、MrBayes、fastDNAml、GeneTree、MODELTEST、P4、PAML、Seq-Gen、TreeView）、群体遗传学（Migrate、Fluctuate、Recombine、Lamarc、GeneConv）、序列比对（HMMER、ClustalW、mafft、muscle等），序列组装（Phred/Phrap/Consed，RepeatMasker），蛋白质结构可视化（Amber，Charmm，Cn 3D，Rasmol，3D Molecular Viewer）和统计/数学软件包（Mathematica，MatLab，R，S3 Stochastic Spatial）。 这些程序中的大多数是免费的学术使用，而其他的是商业软件包或已开发的COBRE的学生和人员。后者包括用于多序列比对的新软件（EVALIGN），（ClearCut），用于推断基于修改的相邻连接方法的系统发育树，用于核糖体RNA基因序列的高通量分析的程序（HiTSA），以及总结和图形显示来自HiTSA的结果的伴随程序（StatGen），和微生物群落分析（云母），用于分析关于细菌群落的TRFLP数据。此外，已经开发了促进数据分析的工具，包括“全对全”BLAST，一种使用RepeatMasker检测基因组中转座因子的工具，以及用于分布式PAUP和自举分析的工具。这些软件和数据分析工具中的每一个都可以免费提供给任何地方的研究人员。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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.