Bioinformatics Core

Overview of Services

The Bioinformatics Core at the University of Arkansas for Medical Sciences works closely with the UAMS Genomics and Proteomics Cores to provide faculty support in experimental design, data analysis, data visualization, and interpretation of large, complex genomic and proteomic data sets. The core provides quality checking, differential analysis, and pathway/gene set enrichment analysis. For additional services not listed below, please contact bioinformatics@uams.edu.

Bioinformatics Core Services

The UAMS Bioinformatics Core offers cutting edge analyses for genomics and proteomics experiments.

Genomics

  1. RNA-sequencing
  2. DNA methylation
  3. ChIP-sequencing
  4. 10x Genomics Single-cell RNA-sequencing

Proteomics

  1. Label-free quantitation – spectral counts or intensity based quantitation
  2. Tandem-Mass-Tag Multiplex quantitation – MS3 intensity based quantitation
  3. PhosphoTMT – identification and quantitation of phosphorylation modifications

UAMS Bioinformatics Equipment

Computational Resources include:

  • UAMS high Performance Computing (HPC) cluster: Our HPC is composed of 96 traditional Xeon CPU nodes each with 28 cores and 128 GB of memory (2688 CPU cores), 96 Xeon Phi nodes each with 64 cores, of which 80 have 384 GB of memory and 16 have 192 GB of memory (6144 Phi cores total), 4 Xeon nodes with 24 cores and 128 GB of memory plus 2 NVIDIA GPUs (96 CPU cores, 8 GPUs with 27,264 total cores), 6 management/login/storage interface nodes and 1.9 PB of high speed storage (DDN Gridscaler). All components are interconnected via 100Gbps Omnipath interconnects and attached to external storage and the Internet (both commercial and I2) with redundant 10Gbps Ethernet interfaces. Intermediate storage is provided by a 350TB NAS and long term/backup storage is provided by a 4.2 PB object storage system (Dell/EMC ECS appliances).

  • PowerStation GX2: We have two PowerStation GX2 Advanced Workstations (PSSC Labs). Each Linux workstation contains 40 Intel Xeon Scalable Processor Cores for a total of 80 cores with hyperthreading enabled, two GOLD 6148 processors, 128 GB of high performance memory, 22 TB of RAID5 storage, CentOS 64-bit operating system, and a maintenance kit from PSSC Labs.

  • Dell Windows PCs: The facility is equipped with three Precision Tower 7910, four Precision Tower 7810, three Precision Tower 7600, two OptiPlex 9010, and one OptiPlex 9020 Windows PCs.

Location and hours of operation

Staff Hours Shipping Address 

               
Available for Consultation

Monday - Friday
List Hours

    


UAMS Bioinformatics Core

WP Rockefeller Cancer Institute, Rm 9108

400 Jack Stephens Dr

Little Rock, AR 72205

Links and Resources

Contacts

Name Role Phone Email Location
Stephanie Byrum
Director
 
(501) 686-5783
 
sbyrum@uams.edu
 
Biomed 1, B402
 
Allen Gies
Bioinformatician
 
(501) 526-6000 Ext 24917
 
GiesAllenJ@uams.edu
 
WPRC2, 9108
 
Jordan Bird
Bioinformatician
 
(501) 526-6000 Ext 24915
 
JTBird@uams.edu
 
WPRC2, 9108