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Core Facilities and Instrumentation for Biomedical Sciences at UNF

Instrumentation to facilitate Biomedical Sciences Research

For use of any of these instruments, contact the respective chairs/Directors first.

Department of Biology

Two Real Time-PCR Machines (Bio-Rad) for qPCR, Eppendorf Mastercycler Pro, Amersham Imager 600 RGB for protein/DNA gel imaging and analysis, Gel documentation system (Gel Logic 1500 uv/vis) for DNA gel visualization, Plate spectrophotometer (BioTek Powerwave XS, uv/vis) for protein assays and a Take3 Plate for Nucleic Acid quantification in small volumes (Includes dual injectors for dual-luciferase assays, Spectrophotometer (ThermoScientific Biomate 3 with microcell) for DNA quantification and purity, Beckman Ultracentrifuge with rotors, for sample preparations, Refrigerated centrifuge (Beckman Optima LE-80K) for sample preparations, two Beal Mill Homogenizers (FastPrep24) for sample homogenization, two Liquid Scintillation Counters (Beckman 6500) for isotope detection, Speed-vac with vacuum pump (Eppendorf) for sample drying, Biotek Synergy 2 Plate Reader with Chemiluminescence and UV/Vis Capability, Olympus FV 1000 Laser Scanning Confocal Microscope for visualization of protein localization, and Eppendorf Refrigerated Benchtop Centrifuge (Model 5810R) with fixed angel and swing bucket rotors for sample preparations, PerkinElmer AD 6 Autobalance microgram balance weighs down the 1 ug for samples <20 ug, and down to the 10 ug for samples <2000 ug.

See https://www.unf.edu/coas/biomed/Core_Facilities.aspx

Department of Chemistry

Varian 500 MHz Nuclear Magnetic Resonance (NMR) Spectrometer, Single Crystal Bruker D8 Venture X-ray Diffractometer with micro-focus Mo X-ray source for low temperature data collection, and high pressure data collection (up to 50GPa) using a diamond anvil cell, LTQ XL High Performance Linear Ion Trap Mass Spectrometer with ESI probe and UltiMate 3000 HPLC, Varian Saturn 2100 Gas Chromatograph Ion-Trap Mass Spectrometer (GC-MS), Hewlett-Packard HP Agilent 5890 Gas Chromatograph with FID/ECD detection (dual column), Agilent 1200 Quaternary Liquid Chromatograph with Variable Wavelength Detector, Perkin Elmer Lambda35 UV/Vis Spectrophotometer, Perkin Elmer SpectrumOne Infrared Spectrometer (FT-IR) with ATR accessory, Thermo Scientific Nicolet iS10 FTIR,, Shimadzu IR Affinity I (with HATR ZnSe), Pine Instruments Bipotentiostat with rotator for voltammetry, Perkin Elmer AAnalyst 800 Flame/Graphite Furnace Atomic Absorption Spectrometer, Perkin Elmer FIMS 400 Cold Vapor Mercury Analyzer, Quanta Master 30 PTI Spectrofluorometer with high-power Xe flash lamp, ThermoFisher Evolution UV Vis Spectrophotometer with NanoDrop Lite Accessory, TA SDT 650 Discovery Series TGA-DSC, Agilent Bio 100 UV/Vis Spectrophotometer and High Performance Computing Cluster featuring nine dual Intel 12 core Xeon processor computing nodes.

 

See https://www.unf.edu/coas/chemistry/Instrumentation.aspx and

https://www.unf.edu/coas/chemistry/Analytical_Services.aspx

Department of Physics

FEI Scanning Electron Microscope (SEM)+EDAX for chemical analysis, a SQUID magnetometer for measuring magnetic fields, Raman spectroscopy for fingerprinting molecules, and a high-resolution atomic force microscope (AFM). Other resources include a helium liquefier for changing material properties and thermal and electron beam thin film deposition Equipment (AFM), PPMS (heat capacity, thermal and electrical conductivity) and RAMAN SPECTROMETER.

 

See https://www.unf.edu/coas/physics/Physics_Instrumentation_Service_Center.aspx

Department of Psychology

NIRX NIRScout functional Near-Infrared Spectroscopy (fNIRS) system for cortical imaging (16 sources, 12 detectors) along with analysis software that integrates with MATLAB, Cedrus Stimtracker to mark stimulus events, 12 EEG caps in various sizes, Powerlab (ADInstruments Inc. Colorado Spring CO) neurophysiological unit (electrodermal activity, electroencephalography, electrocardiography, skin temperature, electromyography), two Faros wireless ECG units (Mega Electronics, Kupio, Finland), Matscan pressure mat (Tekscan Inc., South Boston, MA), Oscilla 310 model audiometer (Otometrics, Denmark), four GP3 HD eye tracking units (Gazepoint, Vacouver, BC), 10 operant chambers (small animal), Geovision video recording system, Marantz Professional PMD-661 digital recording system, digital and analog CCTV cameras, RFID proximity readers/passive integrated transponder tags, small wireless heart rate and microphone transmitters (3 grams), air quality sensors, raspberry pi's with computer vision software systems installed, software defined radio system for transmitting encrypted audio/video files over FM frequencies, custom built reprap 3D printing system, equipment to program microcontrollers/FPGA boards and other custom electronic systems.

Department of Nutrition and Dietetics and Public Health

One VWR UV-3100PC Spetrophotometer, a Biotek Epock microplate spectrophotometer, Biotek microplate washer ELX 405, Biotek fluorometer, benchtop Freeze Dry System, Labconco FreeZone 2.5 L.

 

See https://www.unf.edu/brooks/nutrition/

Materials Science and Engineering Research Facility (MSERF)

Housed in the School of Engineering, the MSERF includes focused ion beam scanning electron microscopy (FIBSEM), field emission microscopy (FE-SEM), variable pressure microscopy (VP-SEM), and a transmission electron microscope (TEM) capable of examining detail as small as a single column of atoms.

 

See https://www.unf.edu/ccec/MSERF/Home_Page.aspx.

College of Computing, Engineering & Construction (CCEC)

See https://www.unf.edu/ccec/computing/Facilities/Labs___Equipment.aspx

 

RF-Smart Lab

Building 15 Room 3130

Hours: SoC Lab Calendar.

The School of Computing Lab is open to all UNF students, but the installed software is tailored for software development. A lab assistant is on duty to answer basic questions and assist with Pay-4-Print. We also offer tutoring services for most programming languages. The installed software includes Eclipse, Microsoft Visual Studio, Microsoft SQL Tools, Netbeans, Oracle Client, SSH, MyITLab, SimUaid, LogicAid, Bitvise, Matlab, Microsoft Baseline Security Analyzer, WebDrive, Orcad Lite, CodeBlocks, PowerDVD, JGrasp, Notepad++, Quicktime, Real Player, and more.

 

Data Engineering Lab

Building 15 Room 3124

The Data Engineering Lab is highly configurable based on the needs of the students and instructor. Along with requisite software is the flexible display option with both an LCD projector and a wall-mounted LCD.

 

iMobile3

Building 15 Room 3126

Equipment: 24 iMacs

The iMobile3 Labis equipped with current iMacs and applicable software used primarily for application development.

 

Bio / Health Informatics Lab

Building 15, Room 3120

This space is currently used for faculty led practicum using software similar to the SOC Computer Lab. This space will be growing to approximately 20 computers and student capacity.

 

PAX Technology Cybersecurity Lab

Building 15, rooms: 2202 & 2204

Primarily used for cybersecurity classes, students will be working with computer viruses, trojans and worms. As such, the lab can be isolated from our campus network. This is a reconfiguarble lab equipped with tables and lockers.

 

Student Research Lab

Building 15 Room 3122

The Student Research Lab is a special-purpose lab that focuses on student research and study. Graduate and advanced Undergraduate research is supported. This is a 'bring your own device' lab (Building 15 Room 3122).

Engineering & Construction Management Computing Laboratory

The Engineering & Construction Computing Laboratory provides premier computing environments for engineering and construction students to learn and explore. The lab is located on the 2nd floor in Building 4, Skinner - Jones Hall, in room 2307 on the UNF campus.

 

See https://www.unf.edu/ccec/facilities/ECC_Lab.aspx

Engineering Fabrication Laboratory

The School of Engineering Fabrication Laboratory provides faculty, staff, and students safe, supervised access to tools and machinery for use in research and development. The School of Engineering Fabrication Laboratory is located in the Science & Engineering Building #50 on the UNF campus.

 

See https://www.unf.edu/ccec/facilities/Fabrication_Lab.aspx

Opus High-Performance Computing Cluster

Access to High Performance Research Computing

 

The Opus High-Performance Computer (HPC) provides the UNF Taylor Engineering Research Institute with access to massively parallel computing capabilities for ocean and atmospheric modeling. Opus was purchased in 2012 and custom built by Penguin Computing.

 

Opus is a Beowulf-type cluster with 16 compute nodes. Each node consists of dual, 12-core AMD Opteron 6234 2.4 GHz CPUs, 64 GB RAM, and 450 GB local scratch space. Eight of these nodes include nVidia Tesla M2070 6 GB GPUs, significantly enhancing the capabilities of the HPC on some types of computation. In addition, Opus has access to about 50 terabytes of high-performance storage.

 

The operating system, like over 95% of high-performance computing systems, is GNU/Linux (specifically, CentOS). The primary application hosted by Opus is ADCIRC, a system of computer programs for solving time-dependent, free surface circulation and transport problems in two and three dimensions. Additional software applications can be compiled to run on Opus, utilizing a variety of implementations of message-passing interface and compiler suites.

 

Early LINPACK benchmarks rate Opus at 3.7 TFLOPS (CPUs only) and up to 7.8 TFLOPS with GPUs.

 

The Opus HPC is managed by UNF's Research Technology Services unit in the College of Computing, Engineering & Construction.

 

See https://www.unf.edu/ccec/rts/opus_hpc.aspx

 

VMWare ESX Memory Management

See https://www.unf.edu/~sahuja/cloudcourse/VMWareESXMemoryManagement.pdf 

Research Technology Services

The Office of Research Technology Services (RTS) is an administrative unit of the College of Computing, Engineering & Construction.

 

RTS has proven experience is the following:

  • Experiment Design
  • Systems Design
  • Systems Integration
  • Software Development
  • Optimization
  • Algorithm Development
  • Data Management
  • Data Analysis
  • Visualization
  • Technology Management
  • Services Management
  • Project Management
  • Systems Administration
  • Collaboration & Communications
  • Virtualization & Cloud Services
  • High-Performance Computing  
  • Mobile Computing
  • and much more

See https://www.unf.edu/ccec/rts/

 

The Information Technology Services- ITS (https://www.unf.edu/its/) also runs a newer cluster with the following specs:

 

Beowulf High Performance Computing Cluster (HPCC)

single cluster head node for submitting jobs

fourteen compute nodes for running jobs

392 CPU cores (Xeon processors)

1.8 TB RAM

7 TB of shared storage

 

HPCC resources are accessed via the head node which is connected to our internal UNF network via 10Gb Ethernet. The head node is connected to the compute nodes by a private, dedicated 10Gb Ethernet compute network. HPCC management and operations are accomplished with the Bright Cluster Manager 7.3 (BCM) product and job submission and scheduling is handled by the bundled SLURM workload management software. The head node and compute nodes run Red Hat Enterprise Linux (RHEL) operating system, version 7.3.

3-D Printing Polymer Lab

The School of Engineering at the University of North Florida provides hands-on learning in coastal engineering, or in material science research and, for the past three year, in the Johnson & Johnson 3-D Printing Laboratory. This space provides cooperative educational and research opportunities for University undergraduate and graduate students as well as faculty researchers in the engineering, chemistry, biology and physics disciplines. The Laboratory will also assist MD&D Global Services, LLC in its efforts to personalize health care delivery through 3-D printing technologies.

 

See https://www.unf.edu/ccbl/Johnson___Johnson_3-D_Printing_Center_of_Excellence.aspx

Cutting-Edge GENI Rack Computing Resource

Facilitated by grants from the National Science Foundation and Cisco Corporation, UNF has acquired and activated a GENI (Global Environment for Network Innovations) rack, which is linked to similar racks, a group of physical servers, at leading universities in the United States and internationally.

 

See https://www.unf.edu/publicrelations/media_relations/press/2016/UNF_Acquires_Cutting-Edge_GENI_Rack_Computing_Resource.aspx

FSU RESEARCH COMPUTING CENTER

The FSU HPC system is comprised of 12,492 x86 64-bit compute cores linked together by low-latency infiniband networks for MPI communication. The aggregate peak performance of the system is 264.6 TFLOPS. Compute nodes support between 2 and 16GB of memory per core, with servers up to 256GB. A redundant cluster of specialized nodes serves as the user entry points for the system.

 

The cluster utilizes the Slurm scheduler for job submission and scheduling. Slurm is an open source scheduling system that automates the job submission, allocation, and management process for HPC users. To maximize the utility of the system we offer, a broad set of compilers, math/communication libraries, and software applications are available to users. Users can request the installation of new software by RCC staff. Using container technologies such as Docker and Singularity, users are free to configure their own software environments.

 

Florida State University is a founding member of the Sunshine State Education and Research Computing Alliance (SSERCA), which was created in 2010 to bring together Florida's geographically distributed educational institutions in a way that maximizes their collective impact on research and education. SSERCA provides the management and technology framework to share and access resources distributed across the State of Florida.

 

The alliance currently supports several projects with sophisticated workflows and complicated data and compute requirements. More details regarding how SSERCA is accelerating research in the State of Florida are available at http://sserca.org. Current member organizations include FAMU, FIT, FIU, FSU, UCF, UFL, UM, UNF, and USF. The Florida LambdaRail provides connectivity to all institutions in the alliance.

 

See https://rcc.fsu.edu/facilities