Our Facilities at Wake Forest University
The subcontract research team at Wake Forest University Health Sciences (WFUHS) has access to considerable resources to conduct this project. Drs. Yu, Carr, and Register have affiliations with multiple research organizations at WFUHS and Virginia Tech (VT) that provide them with tremendous support in both intellectual and computational resources.
Wake Forest University School of Medicine: Wake Forest University was founded in 1834. The School of Medicine was established in 1902 and is part of Wake Forest University Health Sciences (WFUHS), a corporation begun in 2001. WFU Health Sciences and The North Carolina Baptist Hospital combine to form Wake Forest University Baptist Medical Center with John McConnell, M.D., the CEO. William Applegate, M.D., M.P.H., F.A.C.P., is President of WFUHS and Dean of WFUSM. The Wake Forest University Medical Center consists of 739 full-time faculty members, including 560 clinicians and 185 in the basic sciences and 3,501 other employees. It supports 981 beds and over 50,000 acute care and outpatient services annually.
Department of Radiology: Wake Forest Baptist Medical Center is committed to advancing clinical research specifically as relates to biomedical imaging. The Department of Radiology occupies more than 92,000 square feet at multiple sites across the campus and performs more than 363,000 diagnostic procedures each year providing sub-specialty care for adults and the Brenner Children’s Hospital. It is equipped with the most modern medical imaging systems, including state-of-the-art CT, MRI and PET scanners, digital vascular imaging systems, US, conventional and digital radiology. Particularly, a dedicated GE 16 slice CT scanner is available for research, and two PET/CT scanners are also in place (1 located in the radiology department and 1 for treatment planning located in the Cancer Center).
CT Lab (Director: Dr. Hengyong Yu, PhD): Founded in June, 2010, the lab currently has two PhD students and one post-doc. The Department of Radiology, Wake Forest University School of Medicine, is going through the paperwork to assign an old GE 2/4 slice CT scanner to the lab for research. In the framework of Biomedical Imaging Division, VT-WFU School of Biomedical Engineering and Sciences (SBES), the CT Lab shares an advanced multi-scale CT facility with the CT Lab in VT (directed by Dr. Ge Wang), which covers six orders of magnitude in terms of image resolution and sample size as shown in Fig. R2. The team at WFU may also leverage the High Performance Compute Cluster (HPCC) system.
Image Analysis Lab (Director: Dr. Jeffrey Carr, MD): The Imaging Analysis Lab occupies 2,600 square feet and performs advance image processing for cardiac CT, body composition, atherosclerosis and animal imaging. The Lab has more than 10 advanced 3D workstations from TeraRecon (2), General Electric (4), Apple Computer (4), Dell/Red Hat Linux (3). Besides using commercial software, the Lab participates in the open source community supporting the NIH-NCI CaBig project and the MIRC project (www.rsna.org/mirc). The Lab has an extensive computing infrastructure including a secure gigaethernet LAN, climate controlled computer room, robotic backup facility, database programming core, research picture archival and communications systems, over 10 Terabytes of online storage, as well a secure vault for off-site backup of image archives.
Department of Biomedical Engineering (BME): The subcontract PI Dr. Yu’s office physically locates in BME. Total space allocated exclusively to BME comprises 8451 square feet. Academic space consists of office and general use space for faculty students and staff Total academic area space is 3738 square feet and comprises offices, work areas, and a teleconference/teleclassroom used primarily for real time conferences and classes with Virginia Tech. BME Centers and labs comprise 4713 square feet. BME maintains or has access to computing and network resources typical to a major research institution including Internet, cluster computing, and secure scalable RAID storage with daily backup. Service is provided by Information Services, Academic Computing, and BME staff. All faculty, staff, and students have adequate workstations on their desktop and servers are for the most part consolidated at the Medical Center Data Center.
Virginia Tech-WFU School of Biomedical Engineering and Sciences (SBES): The Department of Biomedical Engineering is a part of SBES and the faculty members from the two campuses work closely together on teaching and research in biomedical engineering, electrical engineering and mechanical engineering. The BME department at Wake Forest has full access to the resources at the Virginia Tech including its engineering labs, library and high performance computing facilities. Further information can be found at (http://www.sbes.vt.edu).
Center for Biomolecular Imaging (CBI): The CBI is a multi-technology, Medical School Facility comprised of state-of-the-art imaging modalities. The CBI occupies the ground and first floors (13,200 square feet) of the MRI building, 1,400 square feet of the Comprehensive Cancer Center, 2,000 square feet in the Nutrition Research Center, and 1,500 in the BRF-1 Building downtown. Several large bench Labs and multiple small bench Labs, an Image Analysis Lab and a cyclotron are included. These Labs are well-equipped with current technologies. The Center has two cutting-edge cardiac CT systems (Light Speed Scanner by GE and Aquilion CT Scanner by Toshiba), two MRI scanners ( GE 1.5T human scanner, Bruker 7T small animal scanner) and two PET scanners (GE Advance, Micro PET), which are all solely dedicated to research. Also available for research are a PET/CT scanner and 3T MRI scanner, located in the Department of Radiation Oncology. The Center houses two GE Advantage Windows workstations for image analysis. A state-of-the-art 4D imaging TeraRecon workstation infrastructure was recently acquired, and will be added to the Informatics branch of the CBI for every investigator to use from desktop.
The purpose of the CBI is to support cutting-edge imaging research while facilitating multi-disciplinary collaborations. The Center is committed to keeping Wake Forest University School of Medicine on the cutting edge of imaging research, and changing the imaging research paradigm from pathoanatomy to physiologic/functional and molecular imaging.
High Performance Compute Cluster (HPCC): The team may also leverage the HPCC system. The HPCC system is a collection of servers running as one. This system is made up of 18 Dell servers (compute nodes) working together under the direction of one head node. The head node utilizes Sun Grid Manager to distribute jobs to the compute nodes thus allowing jobs to be split up and run simultaneously amongst many CPUs. The cluster is made up of the following components:
- Head Node
- 1 Dell 2650 Dual 2.8GHz Xeon processors 2GB RAM and 290GB internal storage
- Compute Nodes
- 2 Dell 1750 Dual 2.4GHz Xeon processors 8 GB RAM and 36 GB internal storage
- 16 Dell 1750 Dual 2.4GHz Xeon processors 4 GB RAM and 36GB internal storage
- Sun Grid Engine
- Ganglia system performance monitoring
- System Imager for node re-creation
- Gigabit Ethernet interconnect
Machine Shop at WFU: The machine shop provides SBES students and faculty with access to tools for prototyping, phantom fabrication, and development of fixtures required for experimental work. The shop is equipped with a milling machine, table saw, lathe, band saw, and drill press, and a variety of standard hardware tools.
WFU Data Center: The Center is a newly-designed, highly resilient, state of the art, fully monitored facility that is the electronic backbone for our research enterprise and for the ongoing digital communications revolution far into the future. The Center houses high-performance cluster computers, storage area networks and especially the fiber hub. All the telecommunication fiber optics from all the buildings in the Park, along with the fiber from other Wake Forest University Baptist Medical Center locations, Wake Forest University’s Reynolda campus and all the connections from telecommunications vendors that give access to the outside world from the Park begin and end here. This is also the site where these vendors, in addition to community organizations such as WinstonNet, have their physical presence.
WFU Primate Center (WFUPC): For more than four decades, Wake Forest University has maintained an extensive nonhuman primate research program, located primarily on the School’s Friedberg Campus, the home of the Wake Forest University Primate Center (WFUPC) and the section of Comparative Medicine (Pathology). The WFUPC is a 200-acre site, located nine miles south of the Medical Center/Hawthorne Campus. This complex includes 32 buildings, 120 employees, and about 1,000 nonhuman primates. This campus has 15 housing buildings for nonhuman primates, along with animal housing for sheep, animal support areas, totaling more than 80,000 net square feet of animal housing space, not including pastures. Additionally, the Primate Center provides office space for faculty and staff, research laboratories, conference rooms, and administrative support areas. At the WFUPC, faculty are committed to the principle of using animal models, primarily nonhuman primates, to conduct research designed to further our understanding of the mechanisms, prevention, and treatment of human diseases.
Veterinary Care at the WFUPC: The Animal Resources Program (ARP) of Wake Forest University Health Sciences is directed by Dr. Richard Young, an ACLAM-certified veterinarian with over 25 years of experience. The WFUPC veterinary care is headed by Melaney K. Gee, D.V.M. and supported by professionals with long experience in caring for nonhuman primates and other animal models (Janice D. Wagner, D.V.M., Ph.D., DACLAM, clinical medicine/diabetology, Thomas B. Clarkson, D.V.M., DACLAM, primatologist, Cynthia J. Lees, D.V.M., Ph.D., clinical medicine/surgery, Susan E. Appt, D.V.M., reproductive medicine, J. Mark Cline, D.V.M., Ph.D., DACVP, oncology/pathology, Kelly F. Ethun, DVM, clinical medicine; Tyler Aycock, D.V.M., clinical medicine) and four veterinary technicians. Diagnostic pathology support is directed by Dr. Cline, Assistant Director of the ARP. In addition veterinary residents and fellows provide both clinical and pathological assistance for animal care.
Data Services Unit at the WFUPC: The Data Services Unit (DSU) supports all research and animal care activities on the Friedberg Campus and is responsible for the management, archiving, and security of all clinical and research data derived from the animals housed at this location. As such, this unit will play a central role in managing the data repository (the Primate Information Retrieval System – PIRS) associated with the SPF colony. Its role is supported through the per diem mechanism and through institutional support. The unit is staffed by 13 individuals, including programmers, web developers, hardware technicians, research methods specialists and data entry experts. The DSU has the Primate Information Retrieval System & RS/1 as its primary software tools for fulfilling its obligations to researchers and clinicians.
The Data Services Unit of the WFUPC is located in Building 8. It is composed of the computer room (240 sq.ft.) which includes room for the database administrator (80 sq. ft.) and programmer analyst (80 sq.ft.), data entry staff (160 sq.ft.), research specialist (80 sq.ft.), a data coordinator (80 sq.ft.), and Programmer Analyst (85 sq.ft.). In Building 12, the office areas accommodate the technical services manager (90 sq.ft.), research specialist (90 sq.ft.) and systems administrator (90 sq.ft.). In addition, a users’ area (80 sq.ft.) equipped with a personal computer, printer and scanner for general use are available. An important service for our Department is the computer support staff that helps faculty and trainees with computer program management and document preparation.
Software supported in this Windows and MAC environment include database engines -
ORACLE, SQL Server and Access; Imaging – Photoshop and Cumulus; Statistical analysis – BMDP, Statistica, RS/1 and SAS; Word Processing – Microsoft Word; Bibliographic database management – EndNote and Procite; Electronic Mail and WWW access – Outlook and Internet Explorer.
The computer room located at the Piedmont Triad Research Park Data Center is a state-of-the-art Level 2+ data center. The data center has an 18” raised floor. The room is laid out in a hot aisle / cold aisle design for temperature management and airflow regulation. The computer room air conditioners are N+1. The UPS room and computer room air conditioners have redundancy with a separate DX system. The data center is dual bus with two separate UPS rooms and two separate battery rooms. Batteries are wet cell battery strings with a 40 minute ride-through time. The UPS’s are designed to carry the load until the building generator starts, stabilizes and the electrical load is put onto the generator. The one Megawatt generator has the capacity to power the entire data center for as long as the diesel fuel holds out (about 72 hours); as long as the diesel fuel is supplied the data center will have power. The chillers are N+2 with a monitored chilled water loop. The data center has a monitored Sitescan remote monitoring system for monitoring and alarming. There are two smoke sensing systems: the under-floor air sampling system (VESDA) and the ceiling smoke detectors. There is also a pre-action sprinkler system and an HFC-125 clean agent fire extinguisher system. Physical access to the data center is badge-access only. The servers are equipped with an automatic notification feature to ensure response to unexpected system abnormalities. Backups are performed daily with monthly backup tapes stored outside the CPU area to ensure optimal disaster recovery.
The network is Ethernet-based (TCP/IP) and supports a wide variety of personal computers (PC compatible and MacIntosh) each with LAN connectivity. The entire WFUPC facility links to the Bowman Gray Campus LAN through a metro-E line. The processor hardware platforms that form the computing base of the Technical/Data Services Unit include:
HP DL585 G2 Server– Dual Core, 4 AMD 2ghz processors, 270GB RAID array, 4GB memory, Windows 2008 R2 used as a database server
2 HP DL380 G7 Servers – Quad Core Xeon processors, 5 TB SAN, 4gb memory, Windows 2008 R2 used as web and database servers
HP 7000 Server – 4 Pentium II Xeon processors, 50GB RAID array, 1GB memory, Windows 2000 used as a file server
1 HP 3000 Server – 2 Pentium II, 270GB RAID array, 512MB memory, Windows 2000 used as file and print servers
3 HP DL380 Servers – 2 Pentium processors, 270GB each, 1GB memory, Windows 2003 used as web, application and database servers.
Ethernet based networked Laser, Color Laser printers and Xerox copiers
Primate Information Retrieval Record System (PIRS): The Primate Information Retrieval System (PIRS) is a computerized database system established in 1975 to maintain the experimental, clinical, pathologic and demographic data for all nonhuman primates in our colonies, past and present. PIRS allows storage, processing and retrieval of information concerning an individual animal or a group of animals. The system contains vital information consisting of over 2,500,000 records on approximately 13,000 animals presently and formerly at the facility. Access to the system is available to all on-site users and authorized staff members. Users can request the transfer of selected PIRS data into Excel and/or RS/1 for analyses and graphics. All data is up to date and available for on-line access daily via a web-interface.
The software used in the management of this data is ORACLE. It has been used by the DSU over the last 20 years to coordinate colony management data and some research data. This software can program data entry screens and perform range checks upon entry. RS/1 provides a built-in interface to ORACLE to allow easy transfer and access to data. Data entry and correction procedures are consistent, regardless of which software package is used during DSU processing.
Collection and storage of data on nonhuman primates begin with the arrival of animals into our colonies either through acquisition from outside sources or birth at our institution. All important events from that time on are recorded such as origin, birth date, parentage, location, diet, illnesses, diagnostic tests, therapeutic interventions, experimental analyses and experimental manipulations. Data are categorized as informational, clinical, research or surveillance. Data collection continues until the animal is transferred to another institution or dies. Results of necropsy examinations on all primates are also stored in our computerized record system.