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June 5, 2013

Dell Boxes Up HPC for Life Sciences

Nicole Hemsoth

Dell has its sights set on a duo of trends unfolding around high-end computing. On the one side, the pace, price and practically of genomics is converging to create an exploding market. And on that note, the compute infrastructure required to push it all forward is facing some convergence of its own.

There are a range of figures demonstrating the rapid growth of genomics in the last decade, all of which coincide with the deepening dip in the cost to sequence genes. With more companies sequencing more genetic samples to aid in everything from drug discovery, disease cures and the creation of new materials, the time is ripe for an explosion of purpose-built all-in-one infrastructure approaches.

According to IDC, spending on converged systems is predicted to grow “at a compound annual rate of more than 54 percent over the 2011-2016 forecast period, driven by the cost advantages and efficiency related to operations and management of IT, simplification of vendor engagement and faster time to productivity with IT system updates.”

This week at their Dell Enterprise Forum, the company snapped these trends together with the unveiling of their Active Infrastructure for HPC Life Sciences offering. Set for release in August, the company describes their package as a “modular high performance computing and storage building blocks” which include the required bricks stacked into a single rack housing 32 nodes.

The packaged PowerEdge blades are orchestrated with Bright Cluster Manager and come with Intel inside, namely of the 8-core, dual socket Xeon E5-2400 ilk. On their own, these particular blades offer up 16 cores with 2.5 MB cache per core. With this power, Dell says one cabinet can support the data load of two to four sequencers.

In other words, if you have the practical know-how, a cool million bucks should be able to get you up and running with two sequencers (if they’re at the low end like the “commodity” ones set to be offered by Life Technologies) and a nice fridge from Dell to handle all your genomic data. While that may be a bit of a stretch, power costs and general practicality aside, Dell insists that there’s a hungry market of smaller companies eager to remove the IT hassle and stick to the sequencing.

Dell says that users can tap up to 512 cores, 1.5 terabytes of memory, 540 terabytes of Dell NFS and Lustre file system storage, all strung together with either a 10 GbE or Infiniband network.

The company claims that the impetus and research work behind their converged life science offering was based on their work with the Translational Genomics Research Institute (TGen), where they were able to shave genomic analysis time from one week to one day.

Dell is making a number of other big claims for their genomics-flavored tailoring, the most prominent of which is that users can cut their genomic analysis workflows from days to hours via the ability to optimize analytical software and data across the cluster and file system. The end result is the ability to process a reported 38 genomes per day on a single system.

They note that in addition to cutting down the processing time, acquiring, optimizing and maintaining a custom cluster built from commodity parts can add significant overhead to time and cost. Their $650,000 rack, when compared to what simple server math reveals isn’t stunning, but for users who simply want to shed the datacenter hassle and get back to research, the “plug and play” element could be rather attractive.

What will be interesting to watch over the coming couple of years is how the cost line of sequencing is affected by the IT side of the equation. As noted earlier, the sequencers themselves are becoming more widely available due to price point. If the server side of the genomics business follows suit in a more competitive way, the goals of personalized medicine could be closer than we think–and not just because of the work of a relatively few research institutions that had enough funding…Imagine an average clinician’s ability to tailor treatment based on a quick sequence effort at one-twentieth of the cost it would have been in 2009.

According to Jason Corneveaux, a bioinformatician in the neurogenomics division at the Translational Genomics Research Institute, “With diseases like neuroblastoma, hours matter.” He says that their Dell system allows them to score the needed processing in a “clinically relevant amount of time.”

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