Principal Investigator/Program Director (Last, first, middle):
Bunnell, H. Timothy
RESOURCES
FACILITIES: Specify the facilities to be used for the conduct of the proposed research. Indicate the performance sites and describe capacities,
pertinent capabilities, relative proximity, and extent of availability to the project. Under “Other,” identify support services such as machine shop,
electronics shop, and specify the extent to which they will be available to the project. Use continuation pages if necessary.
Laboratory:
The Nemours Bioinformatics Core Facility (BCF) is located at the Nemours/Alfred I. duPont Hospital for
Children in Wilmington, Delaware. The main facility in Rockland Center I occupies about 550 square feet of
work space including four offices, two workstation cubicles, and a shared conference room equipped with
videoconferencing capability. An additional 273 sq. ft. computer and network facility room is maintained in the
Administration and Research Building. The BCF is wheelchair accessible and barrier-free.
Clinical:
The Nemours/Alfred I duPont Hospital for Children is a 195-bed Children's Hospital that is the academic
partner for Thomas Jefferson University and Pediatric provider for the Jefferson Health system. It serves
inpatient and outpatient needs for children in Delaware, New Jersey, Eastern Pennsylvania and Maryland
communities. There are outpatient clinical services that include active Genetics, Neurology and Developmental
Pediatrics divisions. All facilities are accessible and barrier-free.
Animal:
Animals are housed in the Nemours Life Science Center (LSC) that is immediately adjacent to the hospital
building. This vivarium space is a specific pathogen-free environment and includes several rodent rooms as
well as separate rodent surgical suites. The Life Science Center building also has office space for the staff
which includes veterinarian, technical supervisor and staff (3), and a research surgical assistant. The PhD
director maintains direct contact with principal investigators and provides scientific consultations related to
transgenic/chimeric experimental designs.
Computer:
BCF computational resources are based on Linux (Ubuntu) servers supporting over 300 Windows, Mac OSX,
Android and iOS computing devices and printers in the Nemours Biomedical Research department. Within the
BCF, there are six Intel i5/i7 computers including laptops that support remote data collection and staff travel
needs. Six Android, iOS, and Windows tablets are available for application testing.
The BCF manages the primary web, email and database servers for asel.udel.edu and NemoursResearch.org
with 10 computing cores, 16GB of RAM and 5TB of disk space for user accounts. Additional Ubuntu-based
research servers provide 100 CPU cores, 430 GB of RAM and 52 TB of RAID disk space for research lab
fileshares, application development and testing. Up to 32 CPU cores and 256G of memory can be used for
traditional parallel computing tasks and a dedicated 8-node 192 core Apache Spark/Hadoop computing cluster
is available for big data related projects. A comprehensive backup system provides hourly backups of email,
daily disk backups of file volumes, and weekly LTO5 tape backups which are stored off-site. Additionally, BCF
operates a dedicated Ubuntu PostgreSQL database server (32 cores, 128G RAM, and 11TB of RAID6 storage)
on the protected, internal enterprise network for managing Nemours PEDSnet CDM data. All servers are
housed in the hospital’s datacenter which is environmentally-controlled with redundant power backup.
The BCF also maintains five RedHat Enterprise (RHEL) Linux Virtual Machines (VMs) in the Nemours/CSX
secure enterprise computing cluster, providing application support and testing for REDCap, i2b2, MySQL, and
an internally developed research-based timekeeping system. These database facilities support a large number of
user-defined clinical research databases.
PHS 398 (Rev. 05/01)
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Resources Format Page
The BCF is part of the Delaware Center for Translational Research (ACCEL DE-CTR) and manages a thirdparty hosted Centos Linux-based web/mail/database server. Via this server, BCF supports several software
applications for the DE-CTR including instances of REDCap, VIVO, and custom dashboards within a Drupalbased platform. The BCF is also part of the Bioinformatics Network of Delaware (BiND) that is integrating
bioinformatics and biostatistics resources across six Delaware INBRE partner institutions. Computing facilities
are available from the University of Delaware including access to SAS statistical software, MATLAB, and
online journals.
Office:
Three offices, ranging in size between 100-130 sq. ft. provide office and work space for the core facility
director and key personnel. One furnished office cubicle provides additional work space for bioinformatics
personnel. A 186 sq. ft. shared conference room is equipped with videoconferencing capability.
Other:
In addition to the BCF, Nemours Biomedical Research supports other core laboratory facilities that provide
services such as DNA sequencing and oligonucleotide synthesis, real-time RT/PCR with ABI Prism robotic
apparatus, protein analysis, imaging facility including upright and inverted fluorescent digital photomicroscopes
(Leica), confocal microscope (Leica), phosphorimager (Molecular Dynamics Storm system), general histology,
cytogenetics, and molecular diagnosis. The Department of Research also maintains a staffed photography
facility and editorial staff. These core facilities are available on a fee for service basis to projects needing them.
MAJOR EQUIPMENT: List the most important equipment items already available for this project, noting the location and pertinent capabilities of each.
Computer facilities (see above) for bioinformatics use