College of Medicine
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University of Nebraska Medical Center
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Resources

Our laboratory is equipped with state-of-the-art infrastructure for computational analysis of huge volumes of data generated from biological experiments.  Analysis of NGS-based (next-generation sequencing) data is demanding both in terms of computation and memory usage.  We have several servers dedicated to our laboratory for day-to-day usage, and we access super computers at the Holland Computing Center for more demanding jobs.

Tools and Software

Bioinformatics Tools & Software Developed / Maintained by the Guda Lab.

Software
Supported Tools
  • LocSigDB -A catalog of protein sorting signals
  • ngLOC - A Bayesian method for predicting protein subcellular localization
  • ECemble - an ensemble machine learning method to predict enzyme and enzyme classes from unannotated protein sequences
Discontinued Tools
  • pTARGET - A Prediction Server for Protein Subcellular Localization
  • CE-MC - Multiple Protein Structure Alignment Server
  • MITOPRED: a web server for the prediction of mitochondrial proteins
  • SledgeHMMER: A web server for batch searching of Pfam database
  • DMAPS: A Database of Multiple Alignments for Protein Structures
Other Databases Developed

Servers

The lab is equipped with state of the art computer facility. The lab currently owns three Dell servers used for bioinformatics research in the lab. The IT support for all of the servers is provided by the ITS Department at University of Nebraska Medical Center. All the servers are loaded with all essential bioinformatics tools and software.

Husker(HPC-Cluster)
  • Number of nodes: 4
    • Intel Xeon Gold 6138 2.0G, 20C/40T, 10.4GT/s , 27M Cache, Turbo, HT (125W) DDR4-2666
    • 512GB memory/node, RDIMM 2666MT/s Dual Rank
    • 80 Cores/node
  • Total memory: 2TB
  • Total # of CPU: 320
  • Storage: 208TB - 15K RPM SAS 12Gbps 512n 2.5in Hot-plug Hard Drive
Golgi
  • Intel XeonE5620 2.4Ghz, 12M Cache,Turbo, HT, 1066MHz Max Mem
  • 16GB Memory (4x4GB), 1066Mhz Dual Ranked RDIMMs for 2 Processors
  • 6TB: 6 * 1TB 7.2K RPM Self-Encrypting Near-line SAS 6Gbps 2.5in Hot-plug Hard Drive,FIPS140-2
Carcinoma
  • 24 Cores - Intel Xeon X5670, 2.93Ghz, 12M Cache,Turbo, HT, 1333MHz Max Mem
  • 64GB Memory (16x4GB), 1066MHz Dual Ranked RDIMMs for 2 Processors, Optimized
  • 2.9TB: 5 X 600GB(2.9TB) 15K RPM SA SCSI 6Gbps 3.5in Hotplug Hard Drive
Metastasis
  • 48 Cores - 2x Intel Xeon E7540 2.00GHz, 18M cache, 6.40 GT/s QPI, Turbo, HT, 6C, 1066MHz Max Mem
  • 128GB Memory (32x4 GB), 1066MHz, Quad Ranked RDIMMs for 2 or 4 Processors
  • 8TB: 4 * 2TB 7.2K RPM Near-line SAS 6Gbps 3.5in Hot-plug Hard Drive, Customer Installation
CBSB
  • 160 cores - Intel(R) Xeon(R) CPU E7- 8850 @ 2.00GHz
  • 512GB Memory
  • 202TB SATA RAID
Firefly/Tusker

Computational resources form collaborative projects

NNTC/CHARTER servers

  Test database Test app Production database Production app
Operating system CentOS Linux release 7.2.1511 (Core) CentOS Linux release 7.2.1511 (Core) CentOS Linux release 7.2.1511 (Core) CentOS Linux release 7.2.1511 (Core)
Model Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz
Total storage 2.31527G 3.23043G 1.97243G 2.99978G
Used storage 2.80502G 3.3661G 14.5154G 14.5154G
Processors 1 2 1 8
Memory 1840 7823 7823 7822
Jboss n.a. 5.1.0.GA n.a. 5.1.0.GA
Java version n.a. 1.7.0_79 n.a. 1.7.0_79