Bioinformatics

Nevada Center for Bioinformatics

The Nevada Center for Bioinformatics (CFB) (http://bioinformatics.unr.edu) was established in 2001 with funding from NIH BRIN (Biomedical Research Infrastructure Network) and NSF EPSCoR (Experimental Program to Stimulate Competitive Research) to meet the growing bioinformatics and molecular modeling needs of Nevada researchers.

Resources provided by the Nevada 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.

The Center 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.

For data storage capabilities, 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.

Immediately available commercial tools for the analysis of microarray data include GeneSifter and XRAY. 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 also installed and available on several workstations. AraCyc and MapMan are two pathway analysis software packages that are free for academic users, and are supported by the Center. Microsoft Excel is also available on some Center workstations.

The Nevada Center for Bioinformatics at UNR is directed by Dr. Karen Schlauch, and includes two additional full-time employees to manage and administer computer equipment and software, provide bioinformatics IT support and bioinformatics programming support, give workshops, and assist in a number of data analysis applications.

University of Nevada 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 518 GB of RAM and 386 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.