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.
Users of the campus Sequencing Facility may choose to have their sequences sent directly to their BioDesk account folders.This How-To assumes that you already have a BioDesk account and are familiar with BioDesk.
Become familiar with basic UNIX commands
for listing files, moving around the directory structure and viewing
output files. There are numerous free Tutorials available on the web –
go to Google and search for ‘Unix Tutorials’ to find some of these.
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).
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