GENE & PROTEIN ANALYSIS MODULE Space & equipment The GENE ANALYSIS SERVICE will use the newly organized Vanderbilt Technologies for Advanced Genomics (VANTAGE)). VANTAGE is a genomics core laboratory consolidation initiated by an $8.6 million ARRA funded NIH award to Vanderbilt University Medical Center. It is a new collaborative shared resource that accelerates discovery in genome sciences and personalized medicine, providing state-of-the art research shared resource facilities and technology. VANTAGE occupies 12,505 square feet of newly renovated laboratory space for new cutting edge scientific equipment. Renovation was completed in May 2012, and all the core labs are now fully operational. The consolidation includes the operational merger of the Vanderbilt DNA Resources and Genome Sciences Resource cores and offers lllumina genotyping (lllumina HiSeq2500 and lllumina MiSeqV2), DNA extraction and banking, Affymetrix-based genotyping and expression microarrays, Sanger sequencing and Next Generation Sequencing among many other specialized services. The lllumina HiSeq system includes the lllumina cBOT Cluster Generation System, an automated system that creates clonal clusters from DNA library templates, preparing them for sequencing on the lllumina HiSeq. These resources are now part of an overall structure that takes full advantage of physical co-location together. VANTAGE works closely with VANGARD (VANderbilt Technologies for Advanced Genomics Analysis and Research Design) to assist researchers in experimental design and results evaluation. VANTAGE/VANGARD holds weekly Genomic Design Studios, which offer a panel of experts to review research proposals set forth by those in the Vanderbilt research community. These occur each Tuesday at and host up to 7 researchers who register in advance online. Computing resources include ACCRE High Performance Computing with over 4000 processors, 17 TFLOPS, 300 TB GPFS storage via a BluArc Titan SAN storage system, and 70TB of fast-access and reliable storage space, scalable as-needed. Numerous workstations are available, ranging from six core to single core Xeon processors, with 6 to 24 gigabyte of RAM per workstation (Windows, Mac and Linux OS), and over 50 terabytes of file space. Complete backup of critical data performed nightly. Two Windows 2008 and five Ubuntu 64-bit dedicated servers, with 24 to 256 gigabyte of RAM per server. 50 terabytes of storage space are dedicated directly for research, backed up and verified daily. The Center for Quantitative Sciences utilizes an Ethernet network with Windows Server 2008 64 bit, Windows 7 (32 and 64 bit), Windows XP (32 and 64 bit), OS X, and GNU/Linux (32 and 64 bit) servers and workstations. The network includes fourteen Intel Xeon Quad core workstations, seventeen Intel Xeon workstations, eight Intel Pentium 4 workstations, two Intel Quad core workstations, two dual processor AMD Opteron 275 workstations, Three Intel Xeon eight core servers with 192, 64 and 24 gigabytes of memory, two Dual Intel Xeon 6 core with 48 and 128 gigabytes of memory, and Dual 12 core AMD server with 256 gigabytes of memory. These 46 computers contain more than 100 terabytes of storage capacity, which are backed up nightly by a Hewlett Packard Ultrium LT03 40 tape backup system. All campus-wide servers are accessible from these computers via the network. Software includes MATLAB, S-PLUS, SAS, SPSS, STATA, StatXact, Resampling Stats, EGRET, EPICURE, CART, MARS, TREE-NET, NCSS, nQuery, EaSt, PASS and other statistical applications, MS Visual Studio.Net, Digital Fortran, Visual Basic, MS Access 2010 and MySQL for Relational Database Projects, Ruby on Rails, BWA, GATK, Tophat, Cufflinks, Cuffdiff, DESeq, baySeq, GenomeStudio, zCall, optiCall, GALAXY instance, and others. Conversion of statistical data is accomplished using DBMS/Copy or Open Database Connectivity Drivers and the accompanying software packages. In addition to a fully equipped molecular biology laboratory with all standard benchtop equipment needed to routinely perform biomedical research, VANTAGE is equipped with the following state-of-the-art instrumentation: Geospiza and Clarity/GenoLogics LIMS ABI 3730XL and 3730 capillary array sequencers
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