Our Assets: Children’s Mercy Hospitals
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Shui Qing Ye, MD, PhD
Dr. Ye is a Professor in the Department of Pediatrics at Children’s Mercy Hospitals and Clinics and Department of Biomedical and Health Informatics, University of Missouri School of Medicine at Kansas City (UMKC) and the William R. Brown/Missouri Endowed Chair in Medical Genetics and Molecular Medicine at CMH and UMKC. Dr. Ye had served as the Director, Gene Expression Profiling Core in Center of Translational Respiratory Medicine in Johns Hopkins University School of Medicine from 2001 to 2005 and the Director, Molecular Resource Core in a NIH funded Program Project Grant on Lung Endothelial Pathobiology in University of Chicago Pritzker School of Medicine from 2005 to 2007. Dr. Ye edited a book entitled “Bioinformatics-A Practical Approach”, which was published in 2008 by CRC Press (www.crepress.com). This book enjoys a rave review by covering most translational bioinformatics topics with 25 expert contributing authors from nine different world-class institutions of six different countries. He is planning to work on the second edition of this book at the invitation of the publisher, Dr. Sunil Nair. Dr. Ye now serves as the Director in the Core of Genetic Research at CMH, which provides next generation sequencing and data analysis services for medical researchers at CMH. Last year, his lab published a demonstrative RNA-seq technology video article (Cheranova et al., 2013) in J Vis Exp, The First Scientific Video Journal, at the editor’s invitation.
The Core of Genetic Research, directed by Dr. Shui Qing Ye, is equipped with a compute cluster (Advanced Computer Clustering, Inc., Kansas City, KS). There is one head node with six compute nodes installed in a dedicated rack with room for several more nodes. It comprises a 96-core cluster with 384GB of DDR3 RAM and 48TB SATA hard drives (6 x dual 8-core Intel Xeon E5-2670 “Sandy Bridge” 2.6GHz processors), Quantum SuperLoader3 2U 16 tape library for backups. It is located within a dedicated data center with environmental controls, conditioned power, and hospital emergency back-up power. Deployed on the cluster are the latest versions of GATK, CASAVA, Bowtie, TopHat, Cufflinks, R with CummeRbund, Python with NumPy and SciPy, BreakDancer, Plink, and Haploview software applications.
Center for Pediatric Genomic Medicine, directed by Neil Miller, has five full time bioinformatics/IT staff. The Center’s compute resources are located within a dedicated data center with environmental controls, 15 tons of air conditioning, conditioned power, hospital emergency back-up power and 45kVa UPS capability. The compute resources comprise a 608-core Linux compute cluster with 6TB of DDR3 RAM and 20TB SATA hard drives (20 x 12-core Intel Xeon X5670, 8 x 16-core Intel Xeon E5-2650 and 12 x 20-core Intel Xeon E5-2660 ), redundant head nodes (12-core Intel Xeon X5670 with 48GB RAM and 500GB SATA drive), a pipeline server (12-core Intel Xeon X5670 with 96GB RAM and 1TB SATA hard drive), Isilon X400 storage system with 810TB usable capacity, SGI Infinite Storage Gateway disaster recovery and backup appliance with 160TB usable capacity, Spectra Logic T950 tape library with 2.4PB uncompressed usable capacity, redundant web servers (12-core Intel Xeon X5670 with 48GB RAM and 500GB SATA drive), and database server (12-core Intel Xeon X5670 with 96GB RAM and 16TB SATA drives) on which are deployed the LIMS, GATK, GSNAP, CASAVA, SSAGA, CMH variant warehouse, RUNES and VIKING software systems. The data center is adjacent to the room housing the DNA sequencers, which also features environmental controls to maintain ambient temperature at 65 degrees C, conditioned power, hospital emergency back-up power and substantial UPS capability.