Bioinformatics Core

Cloud Resources

• Amazon Web Service (AWS) Computing: 2 t4g.xlarge EC2 instances 

• AWS storage: The Sharing Tier has a current capacity of over 400 TB (expandable to 1 PB) and the Archival Tier’s current capacity is over 1 PB (expandable to 4.5 PB).

• AWS Academy standing membership: platform for student computing project (free $100 resource for each student project)

Servers Hosting

• University of South Dakota IT – Bioinformatics Core on Site owned Servers:

  • vCPU 6; Memory 16GB; Storage 350GB

  • vCPU 4; Memory 8GB; Storage 100GB

  • vCPU 32; Memory 32GB; Storage 500GB

  • vCPU 4; Memory 8GB; Storage 200GB

  • vCPU 24; Memory 24GB; Storage 2.8 TB 

• Lenovo Thinkpad with GTX 1080 GPU: 2 Laptops with Remote Access for big data science taks (research and student).

HPC GPU Node for big data and machine learning training

• Lawrence: 2,500 CPU cores, including systems with 1.5TB of memory, Nvidia P100, V100 and A100 GPU accelerators, and over 400TB of ZFS network storage accessible via a 56Gb FDR InfiniBand network. Lawrence has an estimated performance of over 100TFLOPS 

Lab Equipment

• 10x Chromium: Single cell genomics and metagenomics library prep.

• Scanning Electron Microscope (SEM): The SEM Laboratory at the GEAR Center is equipped with the FEI Quanta 450 to enable imaging at the nanometer length scale in three modes (high vacuum, low vacuum and ESEM). It is equipped to characterize conductive and non-conductive samples with the large field low vacuum secondary electron (LFD) detector, Gaseous secondary electron detector (GSED-use in ESEM mode), Scanning Transmission electron microscopy (STEM) detector and low voltage high contrast detector vCD and the Gaseous Back scattered electron detector for high pressures used in ESEM mode.

• Fluorescence Microscope: Zeiss Axiovert 200 inverted fluorescence microscope equipped with an Axiocam MRc5 camera and IOOW Halogen source. This microscope is configured with the following objectives-I OX, 20X and 40X and standard filter sets DAPI, Alexa Fluor 488 (FITC), and Texas red (Rhodamine). It is also equipped with a temperature-controlled stage for imaging live and fixed cells. Fourier Transform Infrared Spectroscopy (FTIR): A Thermo Scientific Nicolet 6700 FT-IR Spectrometer is available with ETC EvergloTM source, wherein the temperature of the source during normal operation is electronically controlled. It has an optical resolution of 0.09cm-1. This spectrometer can be configured for multiple spectral ranges (far-IR to UV-VIS) with the option of gold coated or aluminum optics. Sampling parameters, beam path, spectral ranges and experiment types can be automatically configured. 

• Tissue Culture Facilities: Two separate cell culture rooms each equipped with Thermo Scientific 1300 Series A2-Biosafety Cabinets (6 foot), C02 incubators (Thermo Scientific Forma Steri-cycle & Sanyo Safe Cell with built in IR sensor), Zeiss Primovert inverted microscope, Hettich Rotofix 32A centrifuge and Fisher Scientific Isotemp water bath. Third cell culture room equipped with The Baker Company Sterile ChemGARD Ill Advance Biosafety Cabinet.

• Molecular Biology Research: DNA sequencing electrophoresis kits and accessories; Electrophoresis apparatus (horizontal and vertical); lyophilizer (Labconco); Perkin Elmer Gene Amp 2400 PCR System; Motic Digital BA 210 Biological Binocular Microscope, Eppendorf Micro-Centrifuge 5417R; Tecan Infinite@ M200 microplate reader, Fisher Scientific Isotemp Water Bath; Fisher Scientific Accumet Basic pH meter; Bench top Orbital Shaker, MaxQ4450 (Thermo Scientific Corp) and deep freezer (-800C, Thermo Scientific Corp).