Biology Faculty
Updated Jan 30, 2014, 10:57 PM
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EGG Resources

We have two high performance computing (HPC) clusters for bioinformatics data storage and analysis: NGS Galaxy cluster for next generation sequencing (NGS) data analysis and iNquiry biocomputing cluster for general bioinformatics data analysis. 

NGS Galaxy Cluster:
Recently we assembled a new NGS Galaxy cluster for NGS data analysis to support new ION Torrent PGM sequencer at Molecular Research Core Facility (MRCF). This cluster is rack-mounted and includes:
  • A head node with one Xeon quad-core X3370 (3.0GHz) processor, 8GB RAM, and 2TB local storage space.
  • Two compute nodes with dual eight-core Xeon E5-2680 processors (2.7GHz), 128GB RAM and one NVIDIA K20 Tesla GPUs.
  • One compute node with dual six-core Xeon X5650 processors (2.66GHz) and 24 GB RAM
  • Four compute nodes with dual quad-core Xeon E5620 processors (2.4GHz), 12 GB RAM, and 1TB local storage space.
  • A RAID with 16 TB storage space.
  • A 16-port Gigabit Ethernet switch.
    Total cluster cores: 156
    Total cluster storage: 22TB

NGS Galaxy Cluster software:
  • The Galaxy cluster is designed for analysis of next-gen sequencing data. The web workflow system called Galaxy is used as the interface for users to access the cluster. Command-line access to the cluster is possible too. A whole suite of NGS programs are installed on the cluster for next generation sequencing data analysis. Those programs include sequence assembly programs, RNA-seq data analysis programs, ChIP-seq data analysis programs, and many other NGS data analysis tools.
  • To use the NGS cluster, your need to obtain an account by registering through the link http://pig.egg.isu.edu/

iNquiry Biocomputing Cluster: 
We have assembled the ISU-EGG Apple Xserve computational biology cluster for comparative genomics. The cluster is rack-mounted (APC NetShelter VX 42U) and includes:
  • A head node with two G5 processors running at 2.3GHZ with 4GB RAM and 1.2TB hard drive storage space, and is used to assign computational tasks to the cluster nodes and store critical system databases.
  • Twenty-four Apple dual processor XServe G5 nodes (each with 2.3GHZ with 2GB RAM and one 80GB hard drive)
  • A tape-drive back-up, rack-mounted monitor & keyboard, and a 3COM 24-port Gigabit Ethernet switch
    Total cluster storage: 4 Terabytes
    Total cluster processor power: 195 gigaflops (floating-point operations per second)


Other EGG-associated servers:






iNquiry Biocomputing Cluster software:
We have installed and configured the iNquiry suite containing over 200 bioinformatics applications for comparative & functional genomics, proteomics, and phylogenetics. LOG IN HERE. These are many of the same tools in the EMBOSS package. This software suite is optimized for the Xserve multiple-CPU computational biology cluster, and uses Sun GridEngine to automatically distribute submitted processes to one or more compute nodes as needed. We modified the iNquiry suite to cater to the needs of local users and reflect the unique local research environment. These modifications include adding tools (especially for phylogenetics) and databases of interest to registered users.

    We installed LAM/MPI and PVM parallel computing environment on EGG. Many applications like MrBayes, Migrate, Clustalw, MPI-BLAST, TreePuzzle, HMMER, fastDNAml, PAUPBOOT etc. can run in parallel. These parallel applications can utilize all the CPUs of the EGG cluster at the same time.