Penn Neurodegeneration Genomics Center


Information technology (IT) Core
The PNGC IT Core is located at the Richards Medical Research Laboratories. Designed by the late Louis Kahn, a Philadelphia-based architect and former Penn faculty member, the building was completed in 1960 and is now a designated National Historic Landmark.  The Core team occupies the first floor of the D Tower and has access to office and workstations for up to 20 members.

To support the large amounts of computation in human genomic studies, the IT Core has the following resources:

  • Four high-performance Linux servers (three with 16-core/256GB/2TB, one with 8-core/64GB/1TB hard drive space) for software development and bioinformatics analysis.
  • One Linux cluster consisting of two Linux workstations with 20-core/256GB/5TB hard drive space and three Linux workstations with 4-core/16GB/1TB hard drive space for high performance computing.
  • A 700 TB Network Attached Storage (NAS) with RAID 6 configuration for redundancy and data loss recovery capability.
  • A high capacity hybrid storage with
    • Quantum Xcellis Storage Workflow for file management.
    • 1.3PB Spectrum LTO-7 Tape Library (with plans to extend the capacity substantially in the next few years).
    • 120TB hard drive storage in RAID-6 configuration for staging and file caching.
    • Two servers for file management and running the Aspera Server high-speed file transfer software.

For computational tasks that require very large computing capacity (e.g. processing deep sequencing data from 1,000 human genomes), the IT core uses the PMACS high performance computing cluster and the Amazon Elastic Compute Cloud extensively.

The high capacity storage and high-performance servers are physically located at the University Data Center facility.  Penn Medicine Academic Computing Services (PMACS) provides full-time systems administrative support to our lab’s computational resources. All computers/clusters are connected to the Internet through 100Mb or 1Gb Ethernet protected by Firewall.

Genomics Core
The Genotyping/Sequencing/Sample Management Core is in the Stellar Chance building at the University of Pennsylvania Medical School. The entire laboratory space is 1,760 sq ft (including a 166 square foot separate tissue culture room and a 164 Square foot computer room).  Shared space on the same floor includes three 4 degree C rooms, a darkroom and a common equipment room (398 square feet).

The Core is well equipped to perform molecular biology and genetics studies, and has all the equipment needed to prepare samples for Illumina DNA sequencing.  Major equipment includes

  • Sequencers:
    • 1 ABI3130xl 16 capillary fragment analyzer and DNA sequencer
    • 1 single capillary ABI310 fragment analyzer and sequencer
  • RT-PCR:
    • 1 ABI 7900HT Real Time PCR System
  • Thermocyclers:
    • 1 ABI GeneAmp 9600, 384 well format thermocycler
    • 1 ABI Veriti 96 well cycler
    • 1 MJQuad cycler
  • Biobanking:
    • 3 -70 centigrade Revco freezers
    • 1 Fotodyne Foto/Analyst Visionary image capture/analysis system
    • 1 Biorad CHEF-DRIII pulsed field gel electrophoresis apparatus
    • 1 Tomy refrigerated MTX-150
    • 1 Biorad CHEF-DRIII pulsed field gel electrophoresis apparatus
    • 1 UV 1800 Shimadzo spectrophotometer.
  • Tissue culture:
    • 2 laminar biohazard hoods
    • 5 CO2 37oC incubators for cell growth
    • 1 clinical centrifuge
    • 1 Nikon TMS inverted microscope.
  • Other equipment:
    • 1 Covaris S2 sonicator
    • 1 Nanodrop 3300 fluorospectrophotometer
    • 1 Agilent 2100 Bioanalyzer
  • Shared equipment in the immediate vicinity:
    • 1 L8 70M Bechman ultracentrifuge and rotors
    • 1 Optima TL Beckman Ultracentrifuge and rotors
    • 1 RC5C Sorvall preparative centrifuge.

Shared Resources

Next Generation Sequencing Core (NGSC)
The Perelman School of Medicine (PSOM) NGSC provides sequencing and first-pass analysis services for all PSOM and University investigators. Services include experimental design planning, library preparation training, basic analysis, data visualization, and data submission to public repositories. The NGSC currently has 4 Illumina Hi-Seq 2000 and 1 MiSeq sequencer.

Penn Medicine Academic Computing Services (PMACS)
PMACS provides a variety of IT services to groups affiliated with the medical school.  In addition to the administrative support provided by PMACS, PNGC accesses the following two PMACS resources for big data analysis:

PMACS maintains centralized High-Performance Computing Cluster (HPCC) with 2,048 cores from 128 computing nodes, 1PB of data storage on Tier-2 storage disks, and 1.5PB for duplicate long-term data archival on a ~1,900 automatic tape library. 

PMACS has negotiated a master contract between Perelman School of Medicine and Amazon Web Services (AWS).  The new partnership with AWS includes elements such as Elastic Cloud Computing (EC2), Elastic Block Storage (EBS), and Simple Storage Service (S3).  HPCC uses the IBM Platform Load Sharing Facility (LSF) job scheduling software to automatically transfer additional computing jobs to Amazon EC2 when HPCC computational load is high.

The University Data Center facility
Most of the servers and data storage are located at the University Data Center.  This Data Center is an ISO9001:2008 certified Tier 2+ Data Center, centrally located on Penn's campus at 3401 Walnut Street.  Data Center Operations support is provided 24 hours a day, 365 days a year.  The School of Medicine's assessment is that the security level of this site is at or above FISMA standards.  

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