Genomics Resources at UNM

Analytical and Translational Genomics Shared Resource

The Analytical and Translational Genomics (ATG) Shared Resource is the genomics and next-generation sequencing core facility in the UNM Cancer Center. ATG was originally the Keck-UNM Genomics Resource (KUGR), founded in 2000 and focused on microarray technologies. In the last few years ATG has transitioned primarily to next-generation sequencing technologies using the Ion Proton and Ion Torrent PGM platforms. ATG staff include a research technician and an expert data analyst with expertise analyzing genomics data sets with software such as GeneSpring, CLC Bio and R/Bioconductor. ATG also has a fully equipped and upgraded Affymetrix system with two automated fluidics stations and a scanner with autoloader, an Agilent BioAnalyzer, a Nanodrop droplet spectrophotometer, a Qubit fluorometer and Qiagen Qiacube robot for automated sample processing and related equipment for performing genomics, gene expression and microarray experiments. ATG is supported by the State of New Mexico, the UNM Cancer Center, the UNM Clinical Translational Science Center and by user fees.

Bioinformatics Expertise

Bioinformatics support in the UNM Cancer Center is provided by an integrated team including experts in genomics, biostatistics, database management and computational approaches. This team was recently established to address the sophisticated data analysis needs required by next-generation DNA sequencing based assays and approaches. The bioinformatics team currently includes C. Stidley, H. Kang and L. Luo (biostatistics), G. Pickett (genomics) and J. Byars (computation and programming) and the team is led by S.Ness and J. Edwards. The bioinformatics team members are in dedicated space on the ground floor of the CRF building, one floor below the Ness laboratory and the ATG genomics shared resource, close to other researchers who specialize in computational, statistical and database approaches (e.g. V. Cristini: computational modeling; C. Wiggins: New Mexico Tumor Registry).

Computational Facilities

The ATG Shared Resource maintains a bioinformatics-focused mini-cluster dedicated to the analysis of next-generation sequencing data. The cluster is an extension of the cloud computing facilities operated by Penguin Computing, and is configured so large jobs can 'burst to the cloud' if additional computing resources are needed.

The UNM Center for Advanced Research Computing (CARC), directed by Dr. Susan R. Atlas, provides parallel supercomputing, high-speed networking, large-scale storage and visualization capabilities to the entire UNM research community and houses a total of about 5 Tflops/sec (peak) of computing power and just under 400 TB of storage, including a new state-of-the-art 281 TB multi-tier, RAID storage system (integrated by Hewlett-Packard). The system is designed to scale to 16 PB. Several large memory supercomputers (e.g. Nano; Pequena) connect to the storage system via a secure high-speed network. This internal network serving data to the CARC supercomputers is further connected to the central campus Core and thus to the UNM Cancer Research Facility. It provides redundant switching capabilities for high availability in connecting the storage array to CARC parallel supercomputers.

A recent NSF Major Research Instrumentation grant was awarded to Dr. Atlas from the NSF Office of Cyberinfrastructure. The grant supported the acquisition of a new general-purpose GPU (graphical processing unit)-based supercomputer, Xena, which was installed in December 2011; this supercomputer consists of 256 processing cores, 96 nVidia Tesla GPUs, and .5 TB distributed RAM, networked by Infiniband. The new computer joins the 32-node Nano, 16 node .25 TB shared-memory machine (‘R’ server) Poblano, 160-core Ristra, and 176-core Pequena parallel supercomputers. CARC provides gateway access to the Encanto machine, housed at the statewide supercomputing center, the New Mexico Computing Applications Center. The NMCAC is managed by a consortium of the three New Mexico research universities (UNM, New Mexico Tech and New Mexico State University), Los Alamos National Laboratory and Sandia National Laboratories. Encanto is a 1792-node/14,336-core SGI Altix ICE 8200 system, of identical architecture to Pequena. Codes developed at CARC on Pequena are thus easily scaled up to run on the Encanto machine on a fee-for-service basis.  Encanto’s Infiniband I/O network presents a 172 TB scratch space in a Lustre file system.  The resources of three new machines, the 88-core Galles cluster and two 256-core NSF PRObE systems provided to UNM/CARC by the NM Consortium and Los Alamos National Laboratory, will also be available for use by this project. CARC connects to Internet1, Internet2 and the National Lambda Rail (NLR) via UNM’s 10 gigabit/sec backbone network.