The signal processing phase for 454 (Titanium) data is computationally intensive, and is most efficiently done using the UA ICE cluster. The sequence assembly phase can also be done on ICE. In many cases, the sequencing facility will run the signal processing step on your data, and contig assembly may also be included for you. Annotation may be done via the RAST and/or NCBI PGAAP servers.
The who, what, when, where and why of AutoFACT. AutoFACT is a perl script that reads a FASTA sequence file and corresponding BLAST output files and performs automatic functional annotation.
The U of A UITS (formerly CCIT) group maintains High Performance Computing systems for use in research applications. A shared memory supercomputer (marin) and a Linux cluster (ICE) are available for running jobs requiring a large amount of memory, parallel processing, and certain visualization and scientific applications. ICE is a large cluster of Silicon Graphics Altix machines (8 cpus per node); for more details see: http://www.sgi.com/products/servers/altix/ice/. The UA News article http://uanews.org/node/20578 discusses the HPC systems, including their world ranking in terms of power and "green-ness".
The U of A UITS (formerly CCIT) group maintains High Performance Computing systems for use in research applications. A shared memory supercomputer (marin) and a Linux cluster (ICE) are available for running jobs requiring a large amount of memory, parallel processing, and certain visualization and scientific applications. ICE (Integrated Computing Environment) is a large cluster of Silicon Graphics Altix machines (8 cpus per node); for more details see: http://www.sgi.com/products/servers/altix/ice/. The UA News article http://uanews.org/node/20578 discusses the HPC systems, including their world ranking in terms of power and "green-ness". Other HPC systems are described here: http://www.hpc.arizona.edu
** NOTE: All BIO5 researchers are encouraged to take advantage of the availability of high priority CPU hours resulting from dedicated ICE cluster compute nodes funded by a TRIF grant (see below for details).
Grid Computing is a useful tool for long-running data analysis computing jobs. Below is more information on what grid computing is and how you can use it for you research.
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