Dr Paddy Tighe, from the Department of lmmunology and Division of Ophthalmology and Visual Sciences at the University of Nottingham, is using Apple’s Workgroup Cluster for Bioinformatics to get to the heart of the human genome.

The surface of the human eye is an incredible place. Not only does the healthy eye produce lubrication, but there are cells here that take on an anti-bacterial role, ready to kill bacteria that might otherwise cause damage. To help with its research into ophthalmology and other aspects of the human body, the University Hospital, Nottingham, has invested in a five-node Apple Workgroup Cluster for Bioinformatics. The technology has brought on-site the power the hospital needs to carry out the analytical study of DNA and proteins, the genes that make up every human being.

Dr Paddy Tighe is senior lecturer in molecular biology at the Department of Immunology at the University of Nottingham, and is responsible for the installation and maintenance of the Workgroup Cluster. “Apple has a good standing within the research community”, he says. “I see a lot of people presenting using PowerBooks and there is more and more biology software being developed to run on Mac OS X”.

The university was already equipped with two Xserve G5s and a 1U rackmount cabinet. Its latest investment has resulted in a system comprising four compute-only Xserve G5 cluster nodes with 2GB of RAM each, plus an Xserve head node, which will soon be upgraded to hold 4GB of RAM. In addition to this, two Xserve RAIDs give the system a total of 4TB of storage with the hardware linked together by a gigabit Ethernet switch.

“For the raw power we get from the solution, it’s very good value. Especially with the addition of the Xserve RAID arrays for mass storage, which have been of great benefit to us — ultra-reliable and very easy to set up.”

“For the raw power we get from the solution, it’s very good value”, says Dr Tighe. “Especially with the addition of the Xserve RAID arrays for mass storage, which have been of great benefit to us — ultra-reliable and very easy to set up and to manage user access. I only have to restart the machine when there are system updates, so I consider the cluster to be very low maintenance overall”.

Setting up the Workgroup Cluster was quick and easy, says Tighe, not least because it ships with BioTeam iNquiry software, which automatically configures the cluster for optimum use, and makes it easy to deal with Web and private network interfaces. Adding new users to the system is also a straightforward task. Tighe has only once needed help from the AppleCare Premium Service and Support team, and they swiftly diagnosed a failed component and immediately arranged for a replacement to be shipped out to the university.

BioTeam iNquiry offers 170 bioinformatics applications including BLAST (Basic Local Alignment Search Tool), a DNA sequence comparison programme. Alongside this, Dr Tighe has installed the open source programme BASE (BioArray Software Environment), a cluster-enabled programme that manages microarray data. “I’m very keen on open source initiatives, so its nice to have MySQL, PHP, Perl and the Apache server at my fingertips”, he explains. “Generally, I rate my Macs for the fact I can have the best of UNIX and Mac OS X running together. They are very reliable and, of course, I get a beautiful user interface”.

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