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Bioinformatics Facilities

Dell Server

The Center for Bioinformatics at the University of Nevada, Reno was established in 2001 with funding from Nevada INBRE and NSF EPSCoR (Experimental Program to Stimulate Competitive Research) to meet the growing bioinformatics and molecular modeling needs of Nevada researchers. The Center is directed by Dr. Karen Schlauch. The Center administers computer equipment and software, provide bioinformatics IT support and bioinformatics programming support, give workshops, and assist in a number of data analysis applications.

Next-generation or whole-genome sequencing

The Nevada Bioinformatics Center offers pre-experimental consultation and design, de novo sequence assembly, reference alignment, functional annotation, variant identification, and quantitative RNA-seq pipelines.

These major platforms are supported: Life Technologies Ion Torrent™, SOLiD, Illumina®, and Roche 454 GS-FLX technologies. Quality control is carried out using FASTQC and Quake error correction software. De novo assembly of genomic and transcriptomic sequences are performed using the Velvet/Oases, MIRA, and Roche Newbler software programs.

Alignment to known reference genomes (e.g., RNA-seq) is performed using the Bowtie- TopHat-Cufflinks pipeline. Resequencing is completed with SAMtools and GATK. Comparative expression analysis is carried out on the quantities on the fragment-per-kilobase-per-million-reads (FPKM) via Cufflinks, Cuffdiff, and custom-prepared software based on each individual experiment.

The Nevada Bioinformatics Center works closely with the University of Nevada, Reno IT group to assess and comply with all HIPAA compliancy regulations for the generation and storage of human genomic data.

Additional Software Supported

The Center for Bioinformatics also supplies an EST LIMS system that stores and processes EST data files. The estLIMS© system is designed to track projects, principal investigators, and samples, as well as supply researchers with an automated EST analysis pipeline. The system runs on a Dell Precision 490 quad-core Xeon server housed at the Center.

The Center also supplies the licenses for the commercial software packages SYBYL and Accelrys for any academic user in Nevada to perform molecular modeling and the analysis of three-dimensional protein structures. There are also two SGI workstations (a Fuel and an Octane2) with a stereoscopic graphic capability designated for the use of molecular modeling. Additionally, the Center for Bioinformatics maintains nine Linux servers configured for miscellaneous use, including web services, source code control, and custom application servers. The Center for Bioinformatics houses nine Linux workstations made available for all Nevada academic researchers to use either remotely or at the facility. The Center also supports dChip, free software for academic users for the analysis of microarray data and SNP genotyping data. SAS, JMP, and MatLab are statistical analysis tools that are available through university-wide licenses. The statistical programming language R (Open Source) is installed and available on a number of the Center's workstations, as well as on the university computational research grid. R packages from BioConductor (also Open Source) are installed and available on multiple workstations. AraCyc and MapMan are two pathway analysis software packages, free for academic users, which are supported by the Center.

Computational Resources

Resources provided by the Center for Bioinformatics include a DeCypher® Accelerated Biocomputing Solutions system for accelerated bioinformatics algorithms. The system is run on a Dell PowerEdge 2950 server, with two 3.0 GHz Xeon processors, 8GB of DIMM RAM and 4 15K RPM hard drives. The DeCypher® system makes use of a hardware accelerator card that optimizes a set of bioinformatics search and analysis algorithms, and delivers the computational power of at least 75 processor cores.

De novo assembly of next-generation sequencing data and related high-memory tasks are run on an Oracle SunFire X2200 with 8 Xeon processors and 96 GB of SDRAM.

For data storage, the Center houses two Sun X4500 Servers, which provides 24 TB of redundant data storage for Center users. Software resources available to these systems include standard daemons, compilers, utilities and productivity software. Available database systems include MySQL and PostgreSQL.

Computational Research Grid

The Research Grid is a University-wide resource designed to fulfill the high-performance computing needs of the entire campus. At this time, the grid consists of dual-core, multiple-processor (Opteron) X4100, X4200, and X4600 nodes from Sun Microsystems, and dual-processor, dual-core Opteron nodes from PSSC Labs. The grid provides a combined 1.9 TB of RAM and 818 processor cores. A Sun Fire X4500 server provides 24 TB of storage. The grid nodes run the latest version of the Rocks Linux distribution, an operating system specifically designed for clusters of this type. The grid uses the Sun Grid Engine scheduling software to manage jobs and queues.

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University of Nevada, Reno

University of Nevada, Reno
1664 N. Virginia Street
Reno,  NV  89557-

(775) 784-1110
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