September 28, 2012
Kevin Davies : The launch this week by Knome of the knoSYS 100 "genome supercomputer" has raised a lot of interest in the value and desirability of a dedicated hardware/software solution for NGS data analysis and interpretation.
As first reported at Bio-ITWorld.com, Knome executives clearly feel there is a niche for many users who want a turnkey solution for processing NGS data. I’m sure CEO Martin Tolar doesn’t literally believe that every NGS instrument – about 2,000 are estimated to be running currently around the world – will have a computer next to it, but that doesn’t stop him from raising the possibility.
Knome’s Jonas Lee says that the company, co-founded by George Church as the first personal genome sequencing firm, remains staunchly a software company. "But most institutions have trouble putting together the precise [IT] system to run the software, so why not take that burden off their hands? Not everyone has a really deep IT bench - so we did it for them."
The solution requires some forethought: the knoSYS unit weighs in at almost 600 pounds, and at $125,000, the price is higher than some benchtop sequencers. It contains four 2.4-GHz 8-core Intel Xeon E5-2665 processors, 64 Gigabytes of DDR3 memory, and 18 to 54 Terabytes useable disk storage. Running kGAP software, Knome executives are excited about the ability to create in silico gene "superpanels" for targeted analysis of subsets of a human genome (or exome) sequence, such as genes related to cardiomyoptathy or epilepsy.
But the system’s specs met with some mixed reviews, at least according to two experts interviewed in the Bio-IT World story. The decision to house the computer in a specially soundproofed unit that is wider than a standard data center rack wouldn’t appeal to some research IT folks, said the BioTeam’s Chris Dagdigian, suggesting that the unit really is intended to sit in the lab close to the NGS instruments.
Another NGS expert, HudsonAlpha’s Shawn Levy, felt that the quantity of storage was sub-optimal, and also felt that concerns about cloud security of patient data would be.
Leonid Kruglyak, a geneticist a Princeton University, reacted on Twitter: "Don’t all rush…"
While dedicated software/hardware offerings are rare, there are precedents. A few years ago, the Danish bioinformatics company CLC bio launched the CLC Genomics Machine, "a turnkey solution for large full genome analysis".
CLC bio’s VP communications, Lasse Görlitz, tells me the company is preparing to launch an upgraded version of the hardware, which will include two 8-core Intel Xeon E5-2650 CPUs; 64 Gigabytes RAM, 24 Terabytes storage, and a 64-bit Linux. That’s reasonably comparable with the specs on the new knoSYS, even though the machines have different goals.
Görlitz points out that the CLC Genomics Machine, which weighs about 70 pounds, fits perfectly in a rack or as a stand-alone device (it’s up to the customer). And he candidly states: "We're obviously selling more Genomics Workbench software licenses than these machines, but we find it's a rather popular item with labs and smaller companies who don't already have a huge IT infrastructure in place."
So is there is a true market for turnkey NGS data analysis? Do these solutions suit your group’s needs? If not, why not? We’d like to hear from you…