A PDF version of the MiniLims poster presented at the 2011 AGBT meeting is now available. Click on the image above or use this direct download link:
http://www.bioteam.net/wp-content/uploads/2011/02/AGBT_poster_2011.pdf

(photo credit: iontorrent.com) Bioteam is partnering with Life Technologies to offer a support package for the Ion Torrent compute server, called the Torrent Server. We’re all pretty excited to get moving now that the deal is inked and the press release (PDF version below) is public.

The short version is that customers will be able to purchase either a three month or a full year support contract with Bioteam from the Ion Torrent web store. This will provide:

* An initial phone consultation, after the system is installed and delivered by Ion Torrent
* Support and training via phone and email for initial integration with the lab network and data storage
* Ongoing email support for issues that may arise between the Torrent Server and the lab IT environment.

It’s important to note that Bioteam is not claiming to support the Personal Genome Machine. That’s wholly and entirely the field engineering team from Ion Torrent. Our goal is to provide expertise and experience at the integration layer between torrent server and the local IT resources.

Here’s a slightly broader take on it:

Ever since lab instruments have been connected to IT networks, the question of “where the instrument vendor stops,” has been a challenge. Second and third generation DNA sequencers brought this challenge front and center. These machines are complex piles of robotic chemistry. They generate massive amounts of data, which creates computational load. All of these instruments contain some sort of on-board compute server – and some contain entire compute clusters. Most of them come with software which can be charitably described as “custom.”

Most instrument vendors don’t particularly want to be dragged into the world of building compute clusters and large data storage. They also don’t necessarily want to be really really good at writing software. Most instrument vendors recognize their core competency is, well, in the chemistry and perhaps the robotics. On the other side, very few life sciences IT organizations want to populate their network closets with a series of one-off instrument-specific gear. Nobody wants to see a central IT group driven around by the compute server or network layout chosen by an instrument vendor.

Things have gotten a lot better on this front in the last few years – and Bioteam has been in the thick of it that whole time. We’ve approached the situation from a number of fronts. I’ve re-built existing compute clusters to support primary and secondary pipelines of off-instrument analysis. I’ve also done some serious tinkering under the hood of sequencing instruments to get them to connect to existing systems in a sensible way. While I do get tired of using our marketing tag-line, Bioteam’s specialty of “bridging the gap,” really applies here.

In my (somewhat biased) opinion, Ion Torrent has struck exactly the right balance with the Torrent Server. They have drawn an architectural separation between the lab instrument and the server that does primary analysis. They provide a single working server that the end user is not expected to tinker with. They provide recipes and protocols for integrating that server into generic networks and data storage environments. Finally, they partnered with Bioteam to cover whatever gap remains.

Bioteam has been involved with the Ion Torrent team for some time now. We’re confident both in the system and in our ability to provide real value where it meets the lab information management layer.

Ion Torrent Press Release

Amazon made a very important announcement today, releasing new EC2 server types and network configurations that significantly enhance the Amazon AWS environment for people who are interested in cluster computing, compute farming and high performance computing (HPC) on the cloud.

The announcement is here for those who are interested:

http://aws.typepad.com/aws/2010/07/the-new-amazon-ec2-instance-type-the-cluster-compute-instance.html?

I’m thrilled that this news is now public, the service is up for use and I can finally start testing, blogging and benchmarking in the “real” production environment.

In the next few days I’ll be blogging over on http://www.bioteam.net, concentrating initially on seeing how storage and storage IO speeds differ on the new instance types. For life science types like myself, one of the biggest hassles in the cloud is due to the fact that we tend to be more performance bound by the speed of storage and file IO than anything else. The 10GbE networking changes and non-oversubscription of the network links along with the ability to group nodes together may mean very very interesting things are now much more feasible on the AWS platform.

Because I’m going to first concentrate on storage and IO stuff on the new offering I wanted to quickly show Grid Engine running on the new server types.

Even a single node SGE cluster can do reasonable work now as the cc1 instance type includes a pair of quad-core Nehalem CPUs along with ~23GB memory and a 10GbE ethernet backend.

We will be blogging and talking much more about how to use Chef Server to orchestrate self-assembling Grid Engine clusters and compute farms on this new service but since that may not happen until later — I just wanted to throw up a teaser post showing SGE 6.2u5 running in single-node mode on the new HPC offerings from Amazon.

qstat output showing 16 CPUs (click for full-size):

qhost output showing system resources (click for full-size):

Excerpt:

“IT MAY NO LONGER BE FAIR to characterize large pharmaceutical firms as late adopters of information technology (IT).

Having spent the past five years catching up to other industries in the deployment of enterprise software systems that link researchers and laboratories companywide, big drug firms are now starting to push data storage and processing onto the Internet to be managed for them by companies such as Amazon, Google, and Microsoft on computers in undisclosed locations…“

Article link: http://pubs.acs.org/cen/email/html/cen_coverstory_87_8721cover.html

Simply put, Amazon is now willing to accept delivery of eSATA and USB disks for large-scale data ingestion into the S3 storage cloud service. This is far faster than internet based methods, particularly if you are dealing with daily terabyte-scale data that you’d like to park in some sort of external utility service.

I think this may be a big deal for life science and can forsee quite a bit of scientific data making “1-way” trips into the cloud for long term storage and even secondary processing via cloud server instances. We’ll see.

These links cover the just-launched service in detail:

• http://aws.typepad.com/aws/2009/05/send-us-that-data.html
• http://aws.amazon.com/importexport/

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/