CORE Descriptions

ACCRE – Advanced Computing Center for Research & Education

The Advanced Computing Center for Research and Education (ACCRE) is a collaboratory built by and for Vanderbilt faculty. ACCRE offers computing resources flexible enough to enable High Performance Computing applications in a wide variety of research and education areas. Researchers from thirty campus departments and four schools use ACCRE for their computation needs.

All ACCRE hardware resources are housed in the University’s secure data center. In addition to the High Performance Computing system (described in detail below), ACCRE has multiple terabytes of disk space and a robotic tape storage system. Vanderbilt University is an Internet2 member and is a founding participant in Southern Crossroads (SoX) in Atlanta which provides access to a large number of research and high performance networks. Vanderbilt has a 10 Gigabits per second external network connection.

The ACCRE High Performance Computing cluster has about 3,000 processor cores and has a theoretical peak performance of 12 TeraFLOPS and is in the process of upgrading the compute hardware to provide over 20 TeraFLOPS. The processors are x86-based AMD Opterons and Intel Nehalem with clock speed at 1.8 GHz, 2.0 GHz and 2.4 GHz. All processors run a 64-bit Linux OS. Each compute node has 2−48 GB of memory. Compute nodes all have a disk drive (ranging from 40 – 250 GB) and dual copper gigabit Ethernet ports. Each node is monitored via Nagios. Resource management, scheduling of jobs, and usage tracking are handled by an integrated scheduling system by Moab/Torque. These utilities include an “advance reservation” system that allows a block of nodes to be reserved for pre-specified periods of time (e.g., a class or lab session) for educational or research purposes.

IBM’s General Parallel File System (GPFS) is used for user home directories and scratch space and can sustain 10 Gb/s to the cluster. The ACCRE file system provides over 200TB of disk space, 144GB of disk cache, and can sustain 60Gb/s of disk bandwidth to the cluster. The home directories of all users are backed up daily. The disk arrays are attached to a SAN fabric along with the storage nodes which then export the file system to the rest of the cluster using a fully redundant design with no single point of failure. The internal network design is a classic tree with an Extreme Networks x650 switch fabric at the root. All of the disk servers and management nodes are connected to the top level.

The daily operation and maintenance of ACCRE is provided by ten support personnel, including eight system administrators, programmers and researchers with a combination of more than 60 years of computing experience. Support for system services is provided on a 24/7/365 basis, with on-call pager based support on nights and weekends. Cluster uptime has been better than 95% over the past three years. Support, training and education are available for all members of the ACCRE community – from novice to expert.

Biostatics Collaboration Center

The Biostatistics Collaboration Center at Vanderbilt (BCC) is a university sponsored core resource whose goal is to provide for, enhance, and/or facilitate statistical collaborations involving the design, conduct, analysis or publication of biomedical research at the university. The BCC is comprised of biostatisticians and computer systems analysts from the Department of Biostatistics who are available to work with faculty on a variety of projects. They offer a wide range of highly trained experts with unique expertise for almost any collaboration. The BCC has considerable expertise in the design, conduct, and analysis of large scale clinical trials and research design for basic biomedical research. Varying levels of expertise are also available for consultation, from bachelors and masters level trained biostatisticians and computer systems analysts to full professors.

The BCC is a revenue neutral university resource. Rates are based on the complete cost of performing collaborative services including, but not limited to, salaries, administrative costs, supplies, computing (software, hardware, and shared resources such as the Advanced Computing Center for Research and Education (ACCRE)), information technology support, and relevant professional development costs. ACCRE offers computing resources flexible enough to enable high performance computing applications in a wide variety of research and education areas, and also provides access to high performance storage resources. Rates have been calculated based on 1500 hour work year, explicitly excluding common professional activities not related to this specific project (e.g., seminars, meeting attendance etc.). Vanderbilt University annually reviews the BCC to ensure that it is in compliance with all applicable federal and state regulations, including OMB Circulars A-21, A-110 and A-133. Rates are adjusted annually to ensure that the BCC is operating on a strict non-profit cost recovery basis.

Typically, faculty biostatisticians who are listed as key personnel have supporting staff statisticians that are funded through the BCC. As a result, faculty recoverables, staff recoverables, and staff salary+fringe costs are bundled into one core cost.

The Center for Quantitative Sciences – See separate document

BioVU - See separate document

Cell Imaging Shared Resource

The overall goal of the Cell Imaging Shared Resource is to support the full range of modern microscopy and digital imaging capabilities in order to enable and accelerate research that would otherwise be reduced in quantity and quality. Currently over 200 research groups use the facilities and services of the Resource, which maintains an active development program to keep the instrumentation and systems current, functional, accessible, and easy to use.  The laboratory is fully equipped to carry out numerous aspects of “routine” as well as specialized electron microscopy. Included in the specialized services available through the resource are: 1) preparative techniques, such as embedding and sectioning, critical point drying, high-resolution low angle and rotary shadowing, and cryo-EM; 2) research techniques, such as immuno- and enzyme-cytochemistry, autoradiography, and whole-mount microscopy; and 3) analytical techniques, such as on- and off-line microcomputer based systems for image processing, pattern analysis, and 3-D reconstruction. In addition, collaboration between the resource and the engineering department provide access to intermediate voltage electron microscopy, scanning electron microscopy, and X-ray microanalysis. The director has extensive knowledge of all of these techniques. In addition to microscopes and ancillary equipment, the facility has an extensive array of computer software for image processing and analysis.  The resource includes the following equipment:  Philips CM-12, 120 keV, with high-resolution eucentric goniometer state and Gatan cryotransfer stage and high-resolution CCD camera system to facilitate digital image collection and analysis; two Reichert Ultracut-3 microtomes; vacuum evaporator equipped with low angle shadowing capability; slam and plunge freezing equipment; critical point dryer and sputter coater for SEM sample preparation; computer imaging facilities for image processing and analysis, digital printing, 3-D reconstruction, pattern recognition, and quantitation. All computers are networked.  The resource also provides education and training in microscope operation, sample preparation, image analysis, and EM experiment design. In addition, the School of Engineering has a Philips CM-20 Intermediate Voltage Electron microscope with STEM capability and a Hitachi X-650 scanning electron microscope with both EDS and WDS capabilities. These instruments are available to all University users. Guidance and training in use of the equipment for biological samples is provided by the Electron Microscopy Resource.

Vanderbilt Center for Human Gentics Research – See separate document

CRC-Clinical Research Center

The purpose of the Vanderbilt Clinical Research Center is to provide the resources needed by clinical and translational investigators to carry out their research in an environment optimized for safety, comfort and convenience of the patient or volunteer, with the facilities and expertise to provide the most advantageous milieu in which to address the investigator’s experimental requirements. This includes outpatient space, inpatient beds, laboratories, equipment and supplies for clinical research by the faculty of Vanderbilt University, Meharry Medical College, and their collaborating investigators. The use of the center is justified on the basis of the quality and significance of the research and the special need for the Center’s facilities.

In the process of achieving its primary objective, the Clinical Research Center can also serve as a resource for teaching medical, graduate, and other multidisciplinary students, a site for research on the methodology of patient care systems, and an unique environment for the apprenticeship of young clinical investigators. The center is a component of the Vanderbilt Institute of Clinical and Translational Research (VICTR) organized under a Clinical and Translational Award (CTSA) made in 2007 by the National Center for Research Resources and the National Institute of Health.

Division of Animal Care – See separate document

Epidemiology Shared Resources (Biospecimen Core and Survey Research Shared Resources – See separate document

Flow Cytometry Core – See separate document

Human Immunology Core

The Human Immunology Core provides a wide-range of support and assays to assist investigators in their research with a primary interest in assessing cellular immune responses during clinical trials. We strive to assist investigators with sample processing, storage, shipping, documentation, assay design, assay development and evaluation of immune responses.  Our dedicated staff can provide consultation to investigators on the types of immune assays to choose for clinical trial monitoring and data interpretation. It is the goal of the core to monitor immune responses during clinical trials using the latest advances in technology and provide practical applications of this technology to evaluating immune responses.  We continue to develop new immune monitoring technology with industry and academic collaborators. The Immunology Core has extensive experience in assay development and optimization, and will assist in the selection of appropriate assays and antigens during the protocol/developmental phase of a study or trial.

Genome Sciences Resource – See separate document

Hormone Assay & Analytical Services Core

The purpose of this core is to assist investigators in the measurement of amino acid profiles and hormones in biologic fluids as related to diabetes and endocrine and metabolic research. The core provides space, equipment, and personnel for sample analysis and method development. Investigators pay a charge to cover the cost of reagents, supplies, and pro-rated service contracts.  Since its inception in 1973, the core has evolved into a state-of-the-art laboratory analyzing more than 60,000 samples/year from various sources. The primary techniques utilized for analysis are radioimmunoassay (RIA) and High Performance Liquid Chromatography (HPLC).  The core has expanded its services to include applications associated with flow cytometry.  Utilizing these methodologies, the core offers services in amino acid analysis and profiling, specific activity measurements of select amino acids, specific activity measurement of select glucose precursors, hormone assays, and multiple Luminex applications.

Mass Spectrometry Research Center - See separate document

Molecular Cell Biology Resource Cores

This resource provides custom DNA and RNA synthesis as well as custom cell culture media at a fraction of the cost of commercial sources. The supply arm of this resource stocks freshly prepared bacteria growth plates with or without antibiotics, transformation competent bacteria, and commercial kits and reagents for molecular biology research.  On-line ordering is available and there is free delivery to the lab. The Bioanalytics Facility houses state-of–the-art instrumentation for imaging and quantitation of fluorescent, radioactive, luminescent, and chemiluminescent signals from gels, membranes, or multiple well plates. Gels and membranes stained with visible dyes or ethidium bromide can also be analyzed. Digitized images can be saved to transportable storage for further analysis in the lab or prints can be made on site. This facility also has two “real-time” PCR instruments available on a sign-out basis.

Mouse Metabolic Phenotyping Center

The Mouse Metabolic Phenotyping Center provides investigators wishing to address hypotheses related to diabetes and metabolism with a range of animal model systems. Assistance with mouse experimentation falls under the auspices of the Mouse Metabolic Phenotyping Center, which branched off from this core in 2001. Expertise of core personnel reflects the need to assist in both small and large animal experiments.  Services provided are surgical, experimental, with limited analytical capacity (blood glucose, serology).  Emphasis is on procedures needed to study conscious, unrestrained animals.  Equipment available to investigators includes infusion pumps, blood flow meters, blood pressure monitors, gas analyzers, centrifuges, and glucose analyzers. The Animal Resources Core is experienced in developing new procedures and animal models to accommodate evolving research needs. Many of the procedures conducted in this core are novel. For this reason, training of investigators is an important responsibility of the Animal Resources Core.

Rat and Mouse Neurobehavior Cores

Murine Neurobehavioral Laboratory

This facility provides infrastructure and guidance to support the assessment of behavior in genetically altered mice. Automated, computer-controlled instrumentation provides for assessment of motor and cognitive behavior as well as drug responses. MNL core personnel consult with investigators on experimental design and train core users in animal handling, data acquisition, and statistical analysis.  Core personnel may also assist with writing methods and results sections for manuscripts or grants.

Rat Neurobehavioral Laboratory – see separate document

Neurochemistry Core Laboratory

This core offers services for neurochemical profiling of brain, peripheral tissues and body fluids. The core provides analytical services for the quantitation of multiple biogenic amine neurotransmitters (e.g. dopamine, norepinephrine, serotonin, acetylcholine), biogenic amine metabolites, amino acids and amino acid neurotransmitters (e.g. glutamate, GABA). Analyses on vertebrate and invertebrate (e.g. Drosophila, C. elegans) preparations are available. Investigators provide primary tissue samples or extracts stabilized for analysis.  Customized HPLC services are also available. The Core also oversees tools for neurotransmitter release from brain slices, neurotransmitter receptor quantitation, scintillation spectrometry, and gamma counting.

Sleep Research Core

The Vanderbilt Sleep Research Core offers two hard-wired sleep systems with synchronized video-polysomnography and 21 channels of EEG, with dedicated registered sleep technologists. A sleep core/sleep reading center manager and the core director (Dr. Beth Malow) assist investigators with protocol development. It offers polysomnography, titrations with continuous positive airway pressure, multiple sleep latency testing, and wrist actigraphy (wireless devices that measure sleep-wake patterns non-intrusively based on accelerometers that measure activity vs. rest). The core provides for centralized scoring of polysomnography and actigraphy data for multicenter trials.  In addition to the scoring component, emphasis is placed on the quality of the sleep recordings at the individual sites with close communication among the individual site technologists and the sleep core manager.

Translational Pathology Shared Resource

This resource provides access to human tissue samples, histology services, and specialized equipment to researchers. Human tissues are collected prospectively from routine surgical resections and autopsies for use by investigators in basic, translational, and clinical research studies.  Only remnant tissue samples not needed for diagnostic purposes are collected.  These tissues are available fresh, snap frozen, or in a variety of fixatives as requested by the investigator.  Normal, neoplastic, and other diseased tissues are available for study. Additional clinical information can be obtained without compromising patient confidentiality. The resource also provides tissue collection and storage services for several research groups.  All of the tissue samples are organized and distributed utilizing relational databases designed by the Tissue Clinical Informatics Shared Resource. Our full service research histology laboratory offers paraffin embedding, sectioning, automated Hematoxylin and Eosin staining, frozen sectioning and a large selection of special stains. The laboratory also offers specialized processing and sectioning services including cell block preparations, RNase free sectioning, special processing for lacZ stained samples, and tissue microarray sectioning. The lab is continually developing new protocols to meet the special needs of requesting investigators. The facility also offers access to a laser capture microdissection system, tissue microarray equipment for making microarray blocks, and a Bacus Laboratory slide scanner (BLISS system).

Vanderbilt Center for Structural Biology – see separate document

Vanderbilt Center for Stem Cell Biology

Transgenic Mouse/ES Cell Shared Resource

The Transgenic Mouse/ES Cell Shared Resource (TMESCSR) facilitates the generation, maintenance, and/or storage of genetically modified mice, thereby providing new and useful animal models for the study of cancer, diabetes, and neurobiological and other diseases. This resource, which has been in existence for nearly 20 years, provides eleven categories of services. This includes pronuclear DNA microinjection, mouse ESC microinjection into blastocysts, assisted reproduction to maintain transgenic and knockout mouse lines, gene targeting and recombinase-mediated cassette exchange (RMCE) in mouse ESCs, embryo cryopreservation, karyotyping of mouse ESCs, and BAC recombineering to assemble targeting vectors and transgenes. This facility has generated over 2475 transgenic founder mice from 674 different DNA constructs and 4200 chimeric mice from 724 different mouse ES cell clones. The TMESCSR has assisted in the generation of over 160 different gene-targeted mice. The facility also works closely with investigators to provide any needed advice and instruction on the screening strategies, maintenance, and analysis of the animals generated.

Vanderbilt Institute of Chemical Biology (VICB)

VICB Chemical Synthesis Core

The Chemical Synthesis Facility supports the Vanderbilt community in all aspects of medicinal and organic synthesis. The primary focus of the core is to facilitate biology-orientated projects within the medical center and the university by assisting with the chemistry aspect of the project. The core works independently or in collaboration with the VICB High Throughput Screening Center on the synthesis of literature-cited compounds (including patented ones) as well as full scale lead optimization of a compound.

VICB High-Throughput Screening Facility – see separate document

Vanderbilt Antibody and Protein Resource

The VAPR is a shared resource dedicated to the generation, purification and characterization of monoclonal antibodies, polyclonal antibodies, and recombinant proteins.  The core’s mission is to make state of the art antibody and protein technologies cost effective and readily available to Vanderbilt Investigators.  Additionally, the facility provides access to many related technologies such as protein:protein affinity measurement, protein:small molecule affinity measurement, CHO cell expression optimization, cell line sub cloning, and recombinant antibody generation and expression. The facility also serves as a low cost center for purification, quality control and distribution of useful antibodies to researchers inside Vanderbilt.

Vanderbilt University Institute of Imaging Science (VUIIS)

VUIIS supports advances in physics, engineering, computing and other clinical and basic sciences for the development and application of new and enhanced imaging techniques to address problems in biology and medicine, in health and disease.  Faculty and trainees pursue research in developing new imaging methods and techniques, as well as in diverse applications. The addition of a 7 tesla magnet, one of only about eight in the United States, has enabled researchers to generate images down to the molecular level and will ensure Vanderbilt remains at the forefront of research in magnetic imaging. Some of the core areas of current interest are the development of methods for the assessment of structure, function, and metabolism including imaging in broad areas such as cancer, brain physiology, transgenic mice, cellular and molecular as well as research into the physics of imaging and spectrometry. The Institute also provides an exemplary training environment for postdoctoral fellow, graduate and medical students and undergraduates.

ZCORE – Zebrafish Aquatic Facility

The current zebrafish facility is composed of approximately 100 research tanks available for short and long-term studies, and a significant expansion project is underway.  The facility enables investigator access to the unique advantages of the zebrafish model, which provides hundreds of mutant and transgenic zebrafish with unique properties suited for specific experiments. This core’s essential mission is to provide a reliable mechanism for incorporation and propagation of new and existing zebrafish lines into the core.