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EGG
Bioinformatics Computer Facilities
High Performance Biocomputing Cluster:We have assembled the ISU-EGG Apple Xserve computational biology cluster for comparative genomics. The cluster is rack-mounted and includes:
| - Twenty-four Apple dual processor XServe G5 nodes | |
| - a tape-drive back-up, | |
| - a rack-mounted monitor & keyboard, and | |
| - an APC NetShelter VX 42U Enclosure | |
| - a 3COM 24-port Gigabit Ethernet switch. | |
1. The cluster head node consists of 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.
2. Cluster nodes each consist of two G5 processors running at 2.3GHZ with 2GB RAM and one 80GB hard drive.
3. Total cluster storage: 4 Terabytes
Total cluster processor power: 195 gigaflops (floating-point operations per second)
Bioinformatics Servers
In addition to the high performance biocomputing cluster, there are other servers for bioinformatics and other analysis:
1. EGG.ISU.EDU : XServe G4 with dual processors running at 1.33GHz with 720GB hard drivers and 2GB memory. This server is running the EGG website (www.egg.isu.edu) and 4 virtual domains (www.byrp.isu.edu, www.ice.isu.edu, www.bgs.isu.edu, & www.ibri.isu.edu)
2. PIG.EGG.ISU.EDU : XServe G5 with dual processors at 2.0GHz, 4GB RAM and 750GB hard drive storage space, serving as a platform for student research and education
3. MRCF.ISU.EDU : XServe G5 (dual 2.0GHz, 2GB RAM, 750GB hard drive) , serving as a web and file server for the Molecular Research Core Facility (http://www.mrcf.isu.edu). A data management system called Finch (log in now) from Geospiza is running on this server for DNA sequencing.
4. ERROL.EGG.ISU.EDU XServe G5(dual 2.0GHz, 2GB RAM, 750GB hard drive), serving as a platform for evolutionary genomics research.
5. BAMBOO.BIOS.ISU.EDU XServe G5 (dual 2.0GHz, 1GB RAM, 500GB hard drive), serving as a server for bamboo phylogeny database system.
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Software: (full list of bioinformatics applications)
We have installed and configured the iNquiry suite (The BioTeam, log in now) containing over 200 bioinformatics applications for comparative & functional genomics, proteomics, and phylogenetics. 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, Clustalw, TreePuzzle, HMMER, fastDNAml etc. can run parallely. These parallel applications can utilize all the CPUs of the EGG cluster at the same time.
Databases: (complete list of sequence databases)
We installed many NCBI databases locally. These databases are updated regularly.
The EGG iNquiry suite – our local installation of over 200 bioinforamtics tools with web interface. To use the tools, you must first obtain an account from Luobin Yang or Mike Thomas. Accounts are available to ISU faculty & students, Idaho BRIN members, and collaborators. Please send an email to Luobin or Mike for more information.
Tutorials - read tuturials describing how to use the bioinformatics tools to solve common research problems.