The Genomics and Bioinformatics Core Facility provides many levels of support for the successful completion of projects in several ways, including genomics support, bioinformatics support, and access to computing resources. We also provide grant support to assist investigators in accelerating their research programs.
Genomics Facility Statement
The facilities at University of Notre Dame will support the successful completion of this project in several ways. The Notre Dame Genomics and Bioinformatics Core Facility (GBCF) is a 1500 square foot facility that houses specialized equipment for DNA and RNA sequencing and microarray applications including an Applied Biosystems 3730xl 96-capillary sequencer, Agilent 2100 Bioanalyzer, Affymetrix GeneChip System (including the GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450, and GeneChip Scanner 3000 7G), Roche NimbleGen 4 and 12‐bay hybridization systems, Roche NimbleGen MS 200 scanner, Qubit 2.0 Fluorometer, BioRad CFX384 Real-Time PCR Detection System, Nanodrop 2000 Spectrophotometer, Sage Science BluePippin, Invitrogen E-Gel iBase Power System, Covaris S220 high-intensity acoustic transducer shearing equipment, and an Ilumina MiSeq sequencer. Cost effective sequencing for large-scale sequencing projects is achieved by outsourcing through negotiated contracts. A Managing Director and 2 research technicians are employed full-time in the genomics lab and are responsible for operating and maintaining the equipment listed above and have received training from respective manufacturers in machine maintenance and experimental methods.
Bioinformatics Facility Statement
Providing bioinformatics support, Dr. Scott Emrich serves as the Bioinformatics Director and Associate Research Faculty, in the Department of Compuer Science and Engineering. Dr. Emrich has expertise in sequence assembly, next-generation sequence analysis, and parallel computing. His role includes high-level oversight of bioinformatics staff, facilities and equipment, and strategic planning for maintaining state-of-the-art bioinformatics capabilities. The GBCF has developed pipelines for downstream data analysis of next-generation short-read sequencing data. Currently, the GBCF has developed a quality control pipeline, a SNP discovery pipeline, and a population structure pipeline to assist with collaborative research. These pipelines involve procedures including image processing, base calling, genome and transcriptome assembly, and reference mapping. Particularly relevant to most projects is the availability of well-developed pipelines to assemble short read sequences, extract SNPs, and analyze population genomic data.
There are three primary classes of computing resources that the GBCF uses: 1) the core facility cluster, comprising an 8 core machine with 32 GB of RAM and high-memory platforms including two 512 GB and one 1 TB RAM machines; 2) the campus computing grid, a shared computational resource containing over 1,000 compute nodes accessible through a Condor workload management system; 3) the university’s Center for Research Computing (CRC), a large shared computational resource with hardware including 4 compute clusters with interactive front ends topping out with a Sun X4600 server with the following specifications: 8 Quad core AMD Opteron Model 8356 (2.3 GHz) processors (32 cores) 64/32 bit, 64 GB RAM, and 146 GB drive. The CRC also provides 3 general access compute clusters including 100 Sun X2200 servers and 288 Sun X2100 servers. The CRC also provides research data backup and archival storage via a high-speed disk cache and tape storage silo. Current components include distributed scratch space with 4 data ONTAP GX systems (each has 28- 500 GB SATA drives per server) and 2 Sun x4500 “Thumper” servers with 24TB raw storage each. In addition, Notre Dame is a member of the virtual organization called Open Science Grid, which allows access to shared computing resources at other institutions.