Resources

Facilities and Research Environment

Laboratory: The Kim lab is a member of the Center for Computational Systems Biology at Prairie View A&M University funded by the Texas A&M Chancellor’s Research Initiative (CRI). The center brings together faculty in Electrical and Computer Engineering, Computer Science, Mathematics, Agriculture and Biology to accelerate biomedical informatics research, train students and commercialize discoveries.

<img align=”right” src=/images/misc/resources/CCSB-Genomics-Lab.png style=”float: right; width: 320px”> The Cell Biology Lab and Next Generation Sequencing Center supports the Center for Computational Systems Biology at Prairie View A&M University to further the research of all Center Investigators and the wider scientific community. The Cell Biology and Sequencing Center share 1,612 square feet of wet lab space. The wet lab is equipped for molecular and cellular studies and can validate computational results. The sequencing center is equipped with short read technologies for targeted re-sequencing, expression studies and transcriptome analysis. It also offers microarray technologies to analyze RNA expression and analysis of data.

There is a tissue culture room, large equipment room and general lab with areas for the sequencing center, molecular biology, cell biology and microarray processing and analysis. It contains standard laboratory equipment (stir plates, pH meter, vortexers, scales, water bath, centrifuges, shakers, autoclave, biosafety cabinet, incubators, chemical fume hood, refrigerators, freezers, -80ºC freezers and a Millipore water ultra-purification system), as well as equipment for protein and nucleic acid electrophoresis and detection, real-time PCR and microarray processing and analysis. There is a 576 sq ft dedicated conference room adjoining the labs.

The Next Gen Sequencing Center <img align=”right” src=/images/misc/resources/CCSB-NextSeq550.png style=”float: right; width: 320px”> offers Illumina sequencing by synthesis. It is equipped to isolate, quantitate, evaluate quality of nucleic acid preparations and prepare libraries for sequencing using a workflow that minimizes contamination. The Illumina sequencer is covered under an annually renewed PROD Care NSQ 550 Comprehensive service contract through Illumina. It guarantees an average 3 business day on-site response time by a field engineer, full coverage on parts and labor, and an annual preventative maintenance visit. The center also offers microarray processing and analysis. We will train, support, and provide fee-for-service work, access to ancillary equipment for sample preparation and bioinformatics support to Center investigators and the wider scientific community.

Next Generation Sequencing Data Specific Computing Resources: Resources specifically dedicated to the handling and analysis of DNA and/or RNA sequencing includes: BaseSpace Sequencing Hub with unlimited storage and computing and an in-house analytical pipeline to analyze NGS data.

The Cell/Molecular Biology Lab is equipped to study the function of gene products implicated in pathological processes. Facilities and experience in use of viral and mammalian expression vectors are in place.

Computer Resources: The lab has a dedicated 27” iMAC 16GB RAM workstation to process Bioanalyzer and Nanodrop data and a color inkjet printer.

Major Equipment

High throughput sequencing equipment:

  • Illumina NextSeq 550. Features include: reads up to 150 bp long; low cost/base; fast turn-around times; mid- or high-output modes (150M or 400M clusters/sample, respectively).
  • Agilent 2100 Bioanalyzer to analyze the quality of protein, DNA and RNA.
  • Nanodrop and Qubit 4 to determine the concentration of nucleic acids.
  • Real Time PCR for superior accuracy of quantification.

Cell biology equipment:

  • BSL2 biohazard containment hood
  • 2 controlled-atmosphere 37 degree C incubators (one O2 controlled for hypoxic studies along with a biological oxygen monitor 5300A
  • 765 Starr Mouse oximeter
  • 5331A YSI Oxygen probe and tissue tearer)
  • 5810R eppendorf tabletop centrifuge
  • Z series Coulter Counter
  • Inverted brightfield and phase contrast microscope
  • 3 upright refrigerators, 2 upright freezers and a -80 degree C freezer

Protein analysis equipment:

  • 4 vertical SDS-PAGE gel boxes
  • 2 dual-output power supplies
  • one orbital platform shake and a sonicator

Molecular and genetic studies:

  • Roche light cycler 96 real time qPCR System
  • GMI Amplitronix 4 thermal cycler
  • Two horizontal electrophoretic gel boxes
  • Vacuum concentrator centrifuge

Gel imaging:

  • Licor Odyssey FC.

Microarray analysis:

  • Agilent and Illumina hybridization ovens
  • Microsample incubators
  • GenePix Axon 4300 Scanner

High performance GPU-Workstation:

  • Silicon Mechanics workstation with
    • 2 x Intel Xeon E5-2683v4, 2.1GHz (16-Core, HT, 40MB Cache memory)
    • 256GB (8 x 32GB DDR4-2400 ECC Registered 2R 1.2V RDIMMs) Operating at 2400 MT/s Max
    • NVIDIA Quadro P4000 GPU, 8GB GDDR5
    • Micron 240GB 5100 Pro TLC (6Gb/s, 1.5 DWPD) 2.5-in SATA SSD
    • Seagate 6TB Exos 7E8 HDD
    • LG 4K display

High performance cluster:

The CCSB has full access to the Advanced Computing Lab equipped with

  • High performance computer cluster with 4 racks. The cluster consists of 56 IBM dual-core blade servers, 8 HP 16-core nodes with 16GB memory each, 24 IBM 16-core nodes with GPUs and 16GB memory each, as well as a 4 Dell nodes for setting up cloud virtual machine farm. There is also a shared data storage and archive system with 48-TB capacity connected to the cluster to support big data access and storage.
  • 4 x NVIDIA DGX-1 cluster equipped with
    • 2x Intel Xeon E5-2698 v3 (16 core, Haswell-EP)
    • 8x NVIDIA Tesla P100 (3584 CUDA Cores)
    • 512GB DDR4-2133 (LRDIMM)
    • 128GB HBM2 (8x 16GB)
    • 4x Samsung PM863 1.92TB SSDs
    • 4x Infiniband EDR and 2x 10GigE
    • GPU throughputs are: FP16 at 170 TFLOPs, FP32 at 85 TFLOPs, FP64 at 42.5 TFLOPs