Advancing Genomic Science

The Aquatic Animal Research Laboratory CORE facility is a 4,000 square foot facility comprised of 12 animal rooms, a zebrafish quarantine laboratory, a general washroom, a water quality and procedural laboratory, and a microscopy laboratory for embryo injections, imaging, sorting, and incubation.

CCIT is the primary provider of computing resources and IT support for Clemson University. CCIT consists of key services including Internal Operations, Information Security, and IT Strategic Planning. Operational services include Enterprise Systems and Applications, Customer Services, Infrastructure Services and Operations, Research Computing & Data, and Medicaid IT Services. Within this framework, the groups that manage the various aspects of these areas leverage the common synergies and provide comprehensive solutions, to the benefit of faculty, students, and the greater user community. CCIT is committed to providing an integrated approach to high-performance computing environments and traditional computing. CCIT services include accounts and access; business and information systems; email and messaging; mobile, network, phones and cable; research and high-performance computing; security; software and hardware; teaching and learning; web development and web systems; and servers, hosting and data storage.

The Research Computing and Data (RCD) group is a centrally funded support organization inside Clemson Computing and Information Technology (CCIT). RCD provides general and advanced research computing support, training, and outreach. RCD faculty and technical staff are a highly successful group of research scientists who lead research in high-performance computing applications, high throughput computing, high-performance networking, data access and interpretation, geospatial data, visualization, artificial intelligence (AI), machine learning, social and biological sciences, humanities computing, and software environments for cyber-communities.

The CCGT offers specialized expertise and capabilities in geospatial research and support. It provides comprehensive solutions to meet various GIS-related needs, including technical workshops, project support, interdisciplinary collaboration, and innovative research at Clemson University and throughout the state of South Carolina. It enables geospatial research across all colleges and departments while supporting access to geospatial software and hardware technologies. The center is staffed by a dedicated team of enterprise and desktop GIS experts who provide education and research support to the Clemson community. This team consists of both full-time and part-time staff members. The CCGT team actively supports and trains over 2,000 students, staff, and faculty annually through various academic and research initiatives. They engage in grant collaborations, manage cloud-computing and cyberGIS platforms, and establish partnerships with industry stakeholders to foster innovation and knowledge exchange.

Clemson University is one of the three major sites participating in the NSF-funded CloudLab project (www.cloudlab.us); a network testbed that gives researchers a wide range of environments in which to develop, debug, and evaluate their systems. The project enables researchers to provision experimental distributed infrastructure with administrative privilege for over 1,500 computing nodes and computing resources.

The Cooper Library provides access to 1.2 million print volumes, complemented by over 500,000 eBooks and 82,000+ electronic journal subscriptions. Holdings are easily searched from the search box at the top of the library home page, and online holdings are available 24/7. Some older materials are stored in the Library Depot location in Clemson Research Park, retrievable upon request. Resource sharing agreements are in place with South Carolina academic libraries through PASCAL, and other libraries through interlibrary loan, to facilitate access to material not held in the Cooper Library.

The Electron Microscopy (EM) facility is a short distance from the main campus (3.5 miles north of I-85 on SC 187). This multi-user core facility has advanced high resolution transmission electron microscopes, scanning electron microscopes and a Focused Ion Beam microscope. Surface science instrumentation category has time-of-flight secondary ion mass spectrometry, X-ray photoelectron spectroscopy, Auger electron spectroscopy, ultraviolet photoelectron spectroscopy, low energy inverse photoelectron spectroscopy capabilities with Ar+ and C60 sources, Energy Dispersive X-ray Spectroscopy, Electron Backscatter Diffraction and Wavelength Dispersive Spectroscopy. It has several state-of-the-art high resolution transmission electron microscopes, scanning electron microscopes and a combined Focused Ion Beam scanning electron microscope. The microscopes have Energy Dispersive X-ray Spectroscopy, Electron Backscatter Diffraction, Wavelength Dispersive Spectroscopy, sample manipulation and surface modification capabilities.

The Clemson University Genomics and Bioinformatics Facility (CUGBF) helps investigators use the latest genomics technologies in their research. For a full description of this resource, see the Research Core component.

The Godley-Snell Research Center (GSRC) is a centralized animal facility in close proximity to the Life Science Facility. The GSRC has 22,000 sq. ft. dedicated to maintaining a variety of laboratory animal species used in research and teaching programs at Clemson University; and to providing resources and support services for those programs. GSRC is managed by the Office of Animal Services and provides facilities, equipment, caging, and veterinary and technical support to facilitate animal research and teaching programs. The GSRC has housing space for large and small laboratory animals, including two suites of individually ventilated isolation cubicles. Facilities and caging are available for housing laboratory rodents, rabbits, chickens, goats, swine, and other species as required. Ventilated cage rack systems and micro-isolator cages are available for housing mice. All animal rooms have centrally controlled temperature, humidity, air-flow, pressure differentials, and lighting. Environmental parameters are monitored continuously using a computer controlled monitoring system with dial out alarms. Laboratory animals are procured from pre-approved sources of specific pathogen free animals. Research Services staff includes laboratory animal trained veterinarians and animal care technicians. Animal care staff provide seven day a week animal care and health surveillance. The surgical facility has two large operating rooms, nursing station, sterile prep, recovery room, procedure and surgical prep room, and radiology. Anesthetic delivery and monitoring equipment are available for various animal species. Animals are maintained in accordance with all animal welfare regulations and federal guidelines to ensure humane care. Clemson University animal research facilities and programs are registered by USDA and have received full accreditation from the Association for Assessment and Accreditation of Laboratory Animal Care, International (AAALAC). The Office of Animal Services strives to provide and promote the highest standards of animal care and the humane and responsible use of animals in the advancement of knowledge which will benefit the health and welfare of man or animal.

Clemson’s high-performance computing resources include a “condominium” style cluster, known as Palmetto, developed to serve the university’s wide-ranging research needs. Designed and deployed by the CCIT Research Computing and Data Infrastructure (RCDI) group in collaboration with faculty researchers across the university, Palmetto provides a shared platform that optimizes resources for the benefit of all users. Named for South Carolina’s state tree, the Palmetto Cluster was designed to suit many different research applications, with many powerful multi-core nodes, each with a significant amount of memory.

Indigo is a Clemson University research data repository and processing platform. The system is backed by an all-flash scalable storage system provided by VAST Data. Indigo has roughly 3PB of raw storage, but it is anticipated to exceed 5.5PB of data leveraging data reduction and de-duplication technologies. The data lake can support large numbers of simultaneous clients by leveraging an aggregate of 800 Gbps of network throughput over InfiniBand and 400 Gbps over ethernet. Indigo is accessible from all RCD-managed resources via NFS, SMB, or S3 protocols. Students, faculty, and staff can access their storage via the SMB protocol over the campus network. A 500TB partition of the filesystem has been made available as scratch space to all users of the Palmetto Cluster at no charge. Each user is limited to 5TB or 5 million files, whichever comes first. This partition is automatically purged of stale data and is not intended for long-term storage. Faculty can purchase persistent storage on Indigo that also features backups and snapshots. Indigo storage owners will no longer need to copy data to scratch space before processing and can run directly against their partition.

The CCIT Information Technology Center (ITC) is the primary data center for Clemson University. The ITC contains 20,000 sq. ft. of raised floor space, with roughly 10,000 sq. ft. allocated for Research Computing and Data Infrastructure (RCDI). The data center’s electrical system features two 2.5MW transformers fed from redundant power feeds. In the event of a power outage, the facility has UPS and generator backup systems, including two 2.5MW generators with a guaranteed 24-hour supply of diesel fuel on-site. Equipment in the facility is cooled by three 250-ton chillers, which produce 500 tons of cooling capacity. Only two chillers are active simultaneously, leaving the third chiller available as a reserve in case of failure. 275 tons of liquid cooling capacity is provided to RCDI through a tertiary loop, with temperature maintained through building automation and three-way mixing valves. The ITC is the home of RCDI’s hardware resources, including the Palmetto HPC Cluster and the Indigo Data Lake. The ITC is also home to the Network Operations Center (NOC), which has staff on-site 24x7x365 to monitor Clemson’s critical IT infrastructure, including RCDI resources.

The Life Sciences Facility (LSF), completed in 2012, is a 100,000 sq. ft. building comprised of 3 floors of state-of-the-art research space (25 “wall-less” laboratories). Each laboratory has an interior 150 sq. ft. room with tissue culture facilities. The shared laboratory space, multiple collaboration white board spaces and integrated conference rooms increase ease of interactions among all faculty, postdocs and students. The CUGBF and the Clemson Light Imaging Facility are located in this building, as are faculty participating in the EPIC COBRE. The Biological Sciences and Genetics and Biochemistry Departments collectively supply secretarial services (four staff members), a budget center for grant account management and engineering services (two staff members responsible for maintenance and repair of departmental and laboratory equipment).

The Light Imaging Facility (CLIF) is a multi-user 2,642 sq. ft. core facility located in the Life Sciences Facility. CLIF houses an array of advanced light microscopes, cytometry equipment, a histology suite, and a fully functional molecular biology laboratory. Users have access to multiple confocal microscopes, a stereoscope, a laser microdissection system, and a polarized light microscope. Additionally, researchers can use an Olympus laser measuring microscope, a DSX Digital Microscope, and a BioRad S3E cell sorter. A specimen preparation area houses all the equipment necessary for sample preparation, including a cell culture hood, incubators, a chemical fume hood, and specimen rotators. Users also have access to common equipment, including automatic dishwashers, autoclaves, and cold rooms. The CLIF provides individualized research support, from sample preparation to image acquisition and analysis. CLIF has a dedicated classroom which seats 20 people.

The Micro Fabrication Facility is located within The Center for Optical Materials Science and Engineering Technologies (COMSET) at the Advanced Materials Research Lab (AMRL) in Anderson, SC. This facility provides academic and industry researchers easy access to a complete microelectronic, optoelectronic & MEMS fabrication facility. Processing includes cleaning wafers and photolithography to metal and oxide deposition as well as plasma etching, metrology, and device singulation. Complete fabrication of microelectronic, micro-optic & MEMS devices can be accomplished at this facility.

MUAL is a multi-user mass spectroscopy core facility. The facility primarily focuses on mass spectrometry based experiments including characterization and quantitation of small molecules and oligomers from a variety of biological and environmental matrices; comprehensive metabolomic analysis, including extensive [isomer] profiling of sugars, lipids, amino compounds, and secondary metabolites in plants, microbes, and cells; characterization of biopolymers in biomass; quantitative and global proteomic analyses; isotope-based metabolic flux analyses; accurate mass measurement, isotope-modeling, and fragmentation for the structural elucidation of unknown compounds. The facility also offers researchers a wealth of post-analyses services including compound identification using in-house and online mass-spectral libraries, statistical analyses of complex data, and metabolic pathway analysis to contextualize the metabolomic data, as well as provides hands on training for graduate students and postdocs in sample collection, processing, method development, and instrument operation.

The SC-TRIMH COBRE supports this core, which provides support to build patient-specific and precision-care musculoskeletal systems through multiscale modeling at molecular, cellular, tissue, and body levels. The goals of the core are to develop, acquire, and maintain software tools/packages; utilize the Palmetto Cluster; and provide mentoring in multiscale modeling. Services include high-performance graphic workstations for imaging-based model creation (pre-processing) and simulation results visualization (post-processing); high-performance computing workstations for computational model solver optimization; commercial software licenses and modeling software capacities through open-source codes like FEBio (finite element analysis), OpenSim (multibody dynamics), and 3D slicer (imaging processing); full access to high-performance computing and data visualization capacities at Clemson through CCIT; provide general and project-specific assistances in multiscale computational – molecular, cellular, tissue-level modeling; and artificial intelligence/machine learning based modeling.

The Clemson University College of Engineering and Science maintains a well-equipped machining facility that is useful for instrumentation development.

At the core of Clemson’s local area network are two fully redundant, 100 Gbps-connected Juniper QFX10008’s. These have multiple 40 Gbps-connected links to Cisco Nexus 7700’s in diverse campus locations. The Nexus switches aggregate dual 10 Gbps connections from Cisco 9300 switch stacks that serve as building network distribution and access switches. The multi-gigabit Cisco 9300s allow end user connections of up to 5 Gbps. This network design has zero single points of failure in the core and distribution layers, is consistent across Clemson’s entire campus, is easy to troubleshoot, and behaves deterministically, should link or equipment failure occur. The C-Light Network is Clemson University’s upstream connection to the national research community via direct fiber between Clemson, Atlanta, and Charlotte. C-Light connects to Internet2, a national high-speed research and education network in Atlanta and Charlotte, including a dedicated 100Gbps connection to Internet2’s Advanced Layer 2 Service (AL2S) network, to provide Clemson University’s research community high speed and redundant connections for their research needs. C-Light currently provides over 160Gbps upstream capacity to its membership with geographically redundant connections in Atlanta, Charlotte, Clemson, Anderson, and Columbia. C-Light’s network brings Clemson the technological infrastructure that faculty and researchers need to collaborate nationally and internationally with colleagues and access resources, maintaining Clemson University’s in the national research conversation.

The SC-TRIMH COBRE supports this core, which uses large animal testing and human cadaver analyses to assess the in vivo function of novel devices, interventions, and therapeutics, plus to further validate the predictive computational models developed by SC-TRIMH investigators. Large animal imaging and motion and gait analysis are used for the functional assessment of the new devices, interventions, and therapeutics. These can also be tested using a fully functional human cadaver lab. Existing research facilities for animals within the Department of Animal and Veterinary Sciences, and human cadaver lab within the Clemson University Biomedical Engineering Innovation Campus are unified in this core. The services and facilities include: (i) Surgical support equipment located in the Godley Snell Research Center includes Shoreline stainless steel heated hydraulic tilt surgery tables; isoflurane anesthesia machines with mechanical ventilators; patient monitors with ECG and pulse oximeter; Bovie electrosurgical generators, defibrillator. The Godney-Snell Research Core provides laboratory animal housing for large and small research animals and other species as required. In addition to conventional caging, micro-isolator cages and metabolism cages are available. BSL-2 rooms are available for housing projects needing animal isolation. All animal rooms, operating and procedure rooms have 100% fresh air and centrally controlled temperature, humidity, airflow, pressure differentials and light cycles. Environmental parameters are monitored continuously using a computer-controlled monitoring system with dial out alarms. The Human Cadaveric Surgery Lab has 12 full dissection stations, seven of which are hardwired for arthroscopy. The lab has a full set of basic instruments for dissection, and can accept, store, prepare and dispose of cadaveric and human specimens. Each station has mounting equipment to position anatomic specimens for essentially all surgical approaches. Storage facilities include walk-in cooler and 5 floor model freezers. The lab has access to fluoroscopic equipment for radiographic analysis as well as ultrasound equipment. Dual plane fluoroscopy, electromagnetic tracking, and kinematics are available in the core at CUBEInC. The core provides full service for IACUC protocol development, consultation on veterinary and surgical protocols, and orthopedic surgery for musculoskeletal research.