The Nevada INBRE Bioinformatics Core
The NV INBRE Bioinformatics Core was established in 2001 with funding from from Nevada INBRE and NSF EPSCoR (Experimental Program to Stimulate Competitive Research) to meet the growing bioinformatics needs of Nevada researchers. The Core is directed by Dr. Karen Schlauch . The Core administers computer equipment and software, provides bioinformatics IT support and bioinformatics programming, performs data analysis, and offers training and workshops on the methods and tools of analysis.
Next-generation sequencing / Whole-genome sequencing
The Nevada INBRE Bioinformatics Core provides to investigators a comprehensive set of resources, facilities, and analytical tools for the application of next-generation sequencing to biomedical and life science research. The Core performs pre-experiment consultation, sequencing study design, and offers powerful computing resources for sequence processing and analysis. The Core has developed and uses analytical pipelines for de novo sequence assembly, functional annotation, re-sequencing studies, variant identification, and the quantitative analysis of RNA sequences (RNA-seq). In these pipelines, the Open Source analytical tools of each are integrated with sequence data management, format conversion, quality assessment, and quality control, for documentable, reproducible results. All current sequencing platforms are supported: Life Technologies Ion TorrentTM, Illumina®, Pacific Bio® SMRT, and Roche 454 GS-FLX sequencing technologies.
The NevadaBioinformatics Core provides biostatistical tools for university investigators to fulfill their clinical, genomic, proteomic and other research including experimental design, data quality control protocols, power studies, standard hypothesis tests to examine differences in cohort measures or gene expression values, regression, clustering, and other standard statistical methods.
Network analysis is now a standard approach in systems biology to identify putative functional gene groupings, and identifying hub genes, proteins, or metabolites that possibly represent major regulators in a system. The Bioinformatics Core has developed and applied mathematically robust and statistically meaningful methods for network analysis to generate networks from whole-genome datasets in reasonable amounts of computing time.
To provide biomedical and life science researchers access to powerful computational resources and services, the Core maintains a private cloud built with OpenStack for the provision of processing, memory and storage resources, and software environments, configured to research/analytical needs.
The computational power of the cloud combines the resources of one Dell PowerEdge R715, two PowerEdge R515s, one PowerEdge R610, one PowerEdge R420, and two SunFire X2270 servers. Combined, the Bioinformatics Core Cloud spans 120 computational CPU cores with 784 GB of total available memory (RAM). General purpose data storage is managed via the distributed filesystem, GlusterFS. Cloud storage currently spans four Dell R515 servers, providing 48TB of raw storage.
Hardware-accelerated sequence similarity searches (e.g. BLAST, HMM) are performed using a DeCypher® Accelerated Biocomputing Solutions system maintained by the Nevada INBRE Bioinformatics Core. Acceleration level varies by algorithms, from 75-fold to 200-fold speed-ups using the DeCypher® system. The DeCypher® system is powered by two TimeLogic G4.0 model field-programmable gate array (FPGA) accelerator cards controlled using a Dell PowerEdge 2950 server, with two 3.0 GHz Xeon processors and 8 GB of RAM.
Computational Research Grid
The Computational Research Grid is a University-wide resource designed to fulfill the high-performance computing needs of the entire campus. At this time, the Computational Research Grid consisting of multi-core (Opteron) Sun Fire X4100, X4140, X4200, X4600, and V20z nodes from Sun Microsystems. The grid provides a combined 1.8 TB of RAM and 720 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 (http://www.unr.edu/it/research-resources/the-grid).