Equipping the Future of Genomic Research

Animal rooms – Animal rooms are approximately 225 sf (12×20’). Rooms are outfitted with a wash sink, centrally located floor drains, personnel lights, and a computerized LED animal lighting system. Each animal room has 2-4 dedicated 20-amp circuits with backup power, and an additional 4-6 dedicated 20 amp circuits. Backup power is provided by a diesel generator serviced through Clemson Facilities.

Wash room – The washroom has an oversized sink for scrubbing tanks and large objects. Plastic totes and bleach are provided for tanks, nets, and miscellaneous equipment sanitation. There is a dedicated small tank washer from Tecniplast that can wash up to twelve 3.5-liter zebrafish style tanks per 25-minute cycle. There are dedicated freezers in the washroom for carcass disposal and food storage.

Water quality – The water quality laboratory is open for all facility users. Bench top pH and conductivity meters are available to test or verify inline aquatic system water quality probe values. A titration station is set up for alkalinity and hardness determinations. API colorimetric test kits are provided for nitrogen speciation determination. Several balances are on hand for weighing out salts or taking precise measurements. Select water quality salts are available along with MS-222 for euthanizing aquatic organisms. The water quality lab can also be used for dissection, necropsy, or other required procedures.

Microscopy laboratory and injection room – The microscopy laboratory is outfitted with three Leica S9i stereomicroscopes. One is equipped with a color camera and hooked up to a 36” TV monitor for training and student observation.  Two Leica M80 stereomicroscopes are set up specifically for embryo injections. The injection workstations use a Narishege MN-151 joystick micromanipulator combined with either a Harvard Apparatus BTX Microject 1000A, or a MinJ-D all digital microinjector by TriTech Research. One of the injection stations is outfitted with a camera and a video monitor for training and student observation.  Also housed in the microscopy laboratory is a Leica M165 fluorescence microscope using the LAX operating system with mCherry, GFP, and GFP LP filters.

Growth chamber and incubators – Two small bench top Yamato convection type incubators with a viewing window are available for embryo incubation. Normal temperature is set at 28° C. A larger Caron 25 cubic foot growth chamber is also available for embryos.  This is a closed system with an internal narrow range (400-500 nm) lighting system and a 24-hour timer for day/night simulation. The Caron growth chamber is a chiller or an incubator with a temperature range of 10-40° C.

Water source and purification – Water is sourced from the Anderson Regional Joint Water System and comes into the facility with a chlorine concentration of 1 mg/l.  Water purification for culture and animal use is performed at the room level. Water is purified through a process of sediment and carbon filtration, followed by reverse osmosis.

The CCGT manages ESRI’s campus-wide license, providing the research community with access to a suite of geospatial analysis, mapping, and data management technologies. These technologies encompass desktop, enterprise, and cloud-based solutions, available at no cost. The center offers a hybrid cyberinfrastructure that enables researchers to utilize high-throughput computing through the local GIS cluster (GalaxyGIS), virtual machine (VM) technologies for desktop GIS, high-performance computing via the Palmetto cluster, and cloud GIS and data services through ArcGIS Online and locally managed servers. CCGT encompasses a dedicated training facility that serves as a space for GIS training, workshops, seminars, summer school, webinars, class support, and customized training sessions. The training room is equipped with 20 student workstations, each featuring dual monitors. Additionally, the center maintains and supports access to ground and air drone technologies for imagery and LiDAR data collection.

Clemson University hosted resources for CloudLab include a 316-node compute cluster and a 6-node storage cluster. The CloudLab cluster nodes contain a mix of Intel Xeon, AMD EPYC, and IBM Power PC architectures, and offer a variety of co-processors such as NVIDIA Tesla GPUs, NVIDIA BlueField-2 SmartNICs, and Xilinx FPGAs. The latest expansion of the CloudLab cluster contains 32 nodes with 36-core Intel Ice Lake CPUs featuring Speed Select and SGX capabilities, and 32 nodes with 32-core AMD EPYC Milan CPUs featuring SEV capabilities. All 64 new nodes contain 256GB of RAM, NVMe local storage, and 100GbE Networking. Four of the storage nodes contain dual 10-core CPUs, 256GB memory, 8 1TB HDDs, and 12 4TB HDDs, and 2 of the storage nodes contain dual 6-core CPUs, 128GB memory, and 45 6TB HDDs.

Scanning Electron Microscopes (SEM) – Tabletop Variable Pressure SEM TM3000, Variable Pressure SEM S3400, Variable Pressure SEM SU5000, Variable Pressure SEM SU6600, High Resolution SEM Regulus8230, Ultra High-Resolution SEM SU9000, Nanodue’t Double Beam Microscope NB5000.

Transmission Electron Microscope (TEM) – Variable Energy TEM HT7830, TEM H9500.

Surface Sciences – X-Ray Photoelectron Spectroscopy (XPS) PHI VPIII, Auger Electron Spectroscopy (AES) PHI VPIII, Ultraviolet Photoelectron Spectroscopy (UPS) PHI VPIII, Low Energy Inverse Photoemission Spectroscopy (LEIPS) PHI VPIII, Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) PHI nanoTOF 3.

Porosimetry – Quantachrome Autosorb iQ Gas Sorption Analyzer.

Imaging and specialized equipment includes a Toshiba Aquilion TSX-101A 16-slice computed tomography unit capable of imagining animals up to 300 pounds; a Esaote Vet-MR Grande magnetic resonance imaging unit with a .25 tesla field for large animal magnetic resonance imaging; a Bruker SkyScan 1176 Micro CT unit capable of 9, 18, or 35µm resolution computed tomography imaging in rodents; a Perkin Elmer IVIS Lumina XR benchtop small animal optical (bioluminescent and fluorescent) imaging system and X-ray with up to 21 emission filter sets to capture emission from green to near-infrared; a Visual Sonics VEVO 2100 ultrasound ultra-high frequency unit; a GE Logiq e NextGen portable ultrasound unit (B-mode, M-mode, doppler, and color doppler capable; a Sound NEXT Equine DR portable radiology unit; a DigiGait Rodent Gait Analyzer to perform gait analysis for voluntary and treadmill walking over a range of speeds.

The Palmetto Cluster currently benchmarks at 3.01 PetaFLOPS using 11,280 CPU cores and 2,611,200 accelerator cores and was ranked #239 in the 61st edition of the Top500 list of HPC clusters. The benchmark utilized 220 compute nodes with either NVIDIA Tesla V100, or NVIDIA Tesla A100 GPU Accelerators, and HDR100 Interconnect. The Palmetto Cluster currently contains over 1800 compute nodes consisting of over 1000 CPU-only nodes, and more than 700 GPU accelerated nodes. GPU accelerated nodes are also interconnected with high speed Infiniband networking. The latest compute nodes contain dual 32-core Intel Ice Lake CPUs, 256GB of memory, dual NVIDIA Tesla A100 GPU Accelerators, and HDR100 100G Infiniband Networking. Palmetto also contains special resources such as large-memory nodes (1TB of memory or more), and NVIDIA DGX systems for large scale AI/ML workloads. Storage on the Palmetto Cluster consists of approximately 3 PB of large-scale, backed-up project space, and approximately 2 PB of high-speed scratch space provided by a Beegfs parallel filesystem. There is an additional 120 TB scratch space consisting of all NVMe flash storage. As of July 2023, a new 500TB all-flash scratch space is available on Palmetto as part of the Indigo Data Lake, providing up to 5TB of space or 5 million files per user. The Palmetto Cluster is housed at Clemson’s Information Technology Center (ITC). The ITC is a 24/7 monitored environment with proper power, cooling, and physical security. The Palmetto Cluster is UPS and generator backed to prevent unexpected interruptions to compute jobs.

Olympus DSX1000 digital microscope, Leica SPE confocal, Leica SP8X MP confocal with hyvolution, Leica GSD/TIRF widefield, Leica THUNDER model organism imager, Leica CM1950 cryostat, Leica laser microdissection, Leica M125 stereoscope, Leica DM750P polarized light, Olympus LEXT optical profiler, Cytoviva hyperspectral, Nikon eclipse Ti-E, Biorad S3E cell sorter, Invitrogen Tali image-based cytometer, Invitrogen Countess cell counter. The following preparatory equipment is housed in the laboratory: 1 cell culture hood, 1 chemical fume hood, two CO₂ incubators, two non-CO₂ incubators, incubator shaker, open-air platform shaker, microcentrifuge, four mini-centrifuges, three vortex mixers, four electronic pipets, two refrigerators, two -20°C freezers, -80°C freezer, two Mettler-Toledo balances, pH meter, two stirring hot plates, and three specimen rotators. Users also have access to common equipment, including automatic dishwashers, autoclaves, ultra-pure water systems, and cold rooms.

Thermo Orbitrap Fusion Tribrid mass spectrometer that combines quadrupole, ion trap and Orbitrap mass analysis; Thermo Orbitrap Exploris mass spectrometer; Shimadzu LCMS-8040 triple quadrupole mass spectrometer; Waters Xevo TQ Absolute triple quadrupole mass spectrometer; Agilent 7250 GC/QTOF Gas Chromatography – Quadrupole Time-of-flight mass spectrometer; Agilent 5975C Series GC/MSD single quadrupole mass spectrometer; ultra-high pressure liquid chromatographs (Thermo UltiMate 3000 UPLC; Thermo UltiMate 3000 RSLCnano; Waters ACQUITY UPLC I-Class PLUS; Thermo Vanquish) coupled to mass spectrometers and diode-array and florescence detectors; Shimadzu UFLC; Acquity e λ PDA Detector; gas chromatographs (Shimadzu 2010 plus, Agilent 7890B, 7890A); Waters DESI XS.