Chris Dagdigian recently test-drove Univa UD’s UniCluster Express, integrated it with the Amazon Elastic Compute Cloud (EC2).

Links to the Howto Whitepaper and various screencast video recordings are available via the gridengine.info post:

http://gridengine.info/articles/2008/07/14/univa-ud-unicluster-express-and-amazon-ec2

Congratulations are in order for Mike who was announced as the winner of the “Win your Genome” contest being run by 23andMe. The announcement can be read online here:

http://spittoon.23andme.com/2008/05/14/and-the-winner-is/

Click on the image to download the full article in PDF form.

“… The wikiLIMS system is
“something of a shared brain”
for a lab, “where we can all
agree on a common dialog, a
common vocabulary, common
semantics, and we have the
infinite memory of a hard
drive.”

The full article in PDF form is available here:

As Principal Investigator, Dr. Osborne will work with clients to deliver solutions to challenges in high performance computing, informatics, and next-generation sequencing.

Dr. Osborne comes to BioTeam from his own consulting company ZBIO. Prior to ZBIO, he held the positions of both Chief Technology Officer and Director of Informatics at Cognia and Director of IT at OSI Pharmaceuticals. Osborne earned his PhD in Biology at MIT and his Bachelor’s degree from Hampshire College. He was also Group Leader for Bioinformatics at Cadus Pharmaceuticals and worked within the plant genome sequencing lab at UC Berkeley. “We are very pleased to have Brian at BioTeam. The depth of scientific knowledge and experience he brings is exciting and a great fit for our clients,” said William Van Etten, Ph.D. BioTeam Founding Partner and Director of Services.

The above image shows a pair of Illumina Genome Analyzer systems installed in a laboratory setting. The Illumina systems are one example of what people are calling “Next Generation” systems for doing DNA and whole-Genome analysis. Everyone is working hard to produce the fabled “$1000 Genome” and there is a fantastic scientific and technology race currently ongoing to see which system, which platform and which vendor will succeed. There is even a $10 Million Dollar X-Prize for the first team to do 100 human genomes in the space of ten days. Exciting times!

What does this have to do with Grid Engine? Well, each one of these instruments is individually capable of producing terabyte-level volumes of data in just a few instrument runs. The compute power required to analyze the data coming off of these lab instruments greatly exceeds the capacity of the workstation class machines that drive the instrument. In fact, the 2 instruments you see in the image above are supported by a cluster in the basement with more than 40 terabytes of raw online storage attached.

In the case of the above Illumina/Solexa machines, Grid Engine is actually a key part of the analysis pipeline. In order to operate the instruments shown above, a working SGE installation is required. My employer has been doing quite a lot of consulting and systems integration work these days helping users and labs integrate these devices into local infrastructures and workflows. Along the way we’ve met a number of people who have expressed an interest in a small mailing list or community for swapping tips and best practices.

I also believe (but can’t speak in public on the topic …) that the Illumina/Solexa devices are just the first wet-lab oriented SGE-using instruments to enter the market. There will likely be more.

Thus was born a small google group forum:

http://groups.google.com/group/sge-lifescience-sig

The goal of the group is to build a tightly focused community that can share knowledge and tips on how to integrate these SGE-using devices into new or existing settings. Many vendors also assume that their customers will exclusively buy their technology platform and will use their analysis systems on dedicated hardware — this is not what we see out in the real world where we are already trying to support multi-vendor sequencing environments and shared cluster/storage resources for the back end analysis pipelines.

We’ve made the group name generic rather than making it Illumina/Solexa specific in order to accommodate future products and technologies. If interested, visit http://groups.google.com/group/sge-lifescience-sig and sign up.