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The Turnkey Appliance Revolution Evolution in Genomics


By Joe Stanganelli

June 29, 2016 | The past couple of years in genomics IT have seen the rise of turnkey appliances and similar purpose-dedicated devices that can be hosted locally.  These appliances offer powerful solutions for handling genomics data on premises in a single box instead of in the cloud.  Recent developments mark a watershed in their increasing usefulness and—perhaps—looming ubiquity.

"The Intel of Genomics"

Edico Genome made some major announcements last month related to the DRAGEN Bio-IT Processor—a dedicated chip the company makes for genomic analysis.  For starters, Edico Genome will now offer DRAGEN pre-installed with a hardware-accelerated version of the Broad Institute's Genomic Analysis Toolkit (GATK) for high-throughput sequencing data—known as "Accelerated GATK."  Additionally, Edico Genome will be making DRAGEN—replete with Accelerated GATK—available on the IBM Power Systems S822LC for HPC.  Gavin Stone, Edico Genome's Vice President of Marketing, told Bio-IT World in an email interview last month that according to Edico’s internal testing, the DRAGEN-boosted IBM systems powered by GATK can improve the speed of variant-calling analysis by about 10,000% compared to a standard software version of GATK running on the same server without DRAGEN.

One week after these revelations, the company further announced the award of its latest patent related to DRAGEN; Edico Genome's CEO, Pieter van Rooyen, noted that DRAGEN has seen "brisk customer adoption…in our first year of commercialization."

EdicoReleased two years ago, DRAGEN was originally a tool strictly for on-premises genome mapping and alignment—at reported speeds far greater than dozens of HPC servers working in tandem.  Variant calling, however, was always the next step; van Rooyen told Bio-IT World as much in an interview two years ago at Boston's Bio-IT World Conference & Expo 2014 (where the company unveiled its DRAGEN prototype) when he laid out the market strategy for DRAGEN—calling Edico Genome "the Intel of genomics."

Whether or not Edico Genome is worthy of that title, it is hard to argue with DRAGEN's success in meeting van Rooyen's goals and increasing its market penetration.  And DRAGEN is but one example of the movement in genomics toward dedicated, on-premises "console" devices.

The Cloud in the Box

In earlier days of their development and marketing, as turnkey appliances and their ilk were all the rage at Bio-IT World Conference & Expo two years ago, one of the primary use cases for turnkey appliances in genomics and bioinformatics was as an alternative for nephophobes to cloud-hosted solutions.  The genomics-console revolution provided researchers a way to optimize performance on premises through a customized marriage of software and hardware compatibility.  The siren song of the power of the cloud was thus muted for those afraid of smashing against the rocks of data-stewardship compliance presented by HIPAA, HITECH, CLIA, and a myriad of other laws and regulations.  Back then, some major cloud services—like Amazon Glacier—did not provide BAAs to ensure and memorialize this sort of compliance.

What's more, the cloud continued to decrease in popularity (at least in the short term) after NSA whistleblower Edward Snowden's revelations about US and UK surveillance practices.

Turnkey appliances, conversely, offered efficiency benefits without presenting the privacy, security, or compliance worries of their cloud counterparts (no more so, anyway, than any other on-premises tool).  They weren't just mini-HPC units with preinstalled bioinformatics software.  Each one was a "cloud in a box."

"They don't have to staff up with IT people," Stan Gloss, CEO of BioTeam, said in an interview at Bio-IT World Conference & Expo 2014 about users of his company's then-nascent SlipStream Appliance for next-generation sequencing (NGS) data management.  "[E]verybody wins[.]"

Even today, these benefits are powerful incentives for going with an on-premises turnkey-appliance solution.

"If you're a researcher, your job is that you don't want to deal with IT," noted Ketan Paranjape, General Manager of Life Sciences and Analytics at Intel, in an on-site interview at this year's Bio-IT World Conference & Expo.  "[You] don't want to deal with compute."

Intel—which actually is the Intel of genomics—began collaborating with BioTeam on the SlipStream Appliance four years ago.  Intel likewise worked with GENALICE on the company's VAULT variant-calling appliance, as well as with a plethora of tech heavies like Dell, IBM, and SGI on other turnkey appliances.

Intel also collaborated with Knome on a genome-interpretation appliance released in 2012 that was billed as a "lab in a box"—the knoSYS 100.  Not quite as agile as genomics appliances to come, the knoSYS 100 weighed in at nearly 600 pounds and was larger than a large nightstand.

Indeed, the Intel-Knome appliance partnership appears to have been but a one-night stand.  This past fall, Tute Genomics acquired Knome for what biotech pundit Alex Lash has estimated to be pennies on the dollar.  Tute, incidentally, offers a cloud-based service.

Intel, too, has had its own woes.

"We haven't seen that traction we were hoping to see," admitted Paranjape when asked about Intel's own lagging foray in the turnkey-appliance business in genomics.  "We went after the IT, [but] if you're the CIO[,] you want to create something that is as 'general purpose' as possible."

Consequently, said Paranjape, the decision-makers that Intel was originally targeting in its sales and marketing efforts were naturally disinclined to pursue a specialty solution for research scientists.

"Researchers, bioinformaticians … We didn't go after these people," Paranjape lamented.

"Science on Day One"

CorrectGalaxyAppliance"There is a renewed interest in the need for appliances in the marketplace, [and] I think that one of the things that changed in two years with appliances [is that] people have realized there's an art to it," Aaron Gardner, one of BioTeam's senior scientific consultants, told Bio-IT World on site at Bio-IT World Conference & Expo 2016.  "BioTeam understands the C-suite buyer, [but] we primarily market this to scientists [who otherwise] get co-opted into…IT."

BioTeam's latest turnkey appliance, the BioTeam Appliance Galaxy Edition—preinstalled with Galaxy and a host of other bioinformatics tools—seeks to address this pain point.  While being interviewed, Gardner turned on the appliance and launched into a seamless demo—claiming that he had never before touched it.

"Immediately, their problems are informatics and not IT," said Gardner of BioTeam's customers.  "The thing that this is about is science on day one."

The appliance also includes a router and a wireless-antenna dongle, allowing researchers working with the appliance to use it semi-remotely on a tablet or smartphone via the appliance's own Wi-Fi.  Thus, the BioTeam Appliance Galaxy Edition is a mini-cloud unto itself.

Pivoting to the Cloud

Despite their cloud-in-a-box capabilities, however, genomic turnkey appliances need not be islands unto themselves.

"Now you have an on premise solution [and then] burst out into the cloud," burst Paranjape excitedly, noting that many turnkey appliances are designed for SaaS compatibility.  

Turnkey appliances are certainly more powerful when paired with complementary cloud solutions—but then the privacy, security, and regulatory headaches return.  This is not to say that turnkey appliances do not present their own similar issues.  Kryngle Daly, CEO of genomics startup KBioBox, said in a recent phone interview that his company put a temporary halt to development of the turnkey appliance it debuted at Bio-IT World Conference & Expo 2014 because of FDA compliance issues.  Daly told Bio-IT World that KBioBox has since "pivoted" to a SaaS model.

Meanwhile, Stone reports that Edico Genome, which operates on a leasing model, is "transitioning to also have DRAGEN available in the cloud now as part of an integrated hybrid-cloud offering, so [we] will also be adding some more granular pay-per-use pricing as well."

While Gardner agrees that the cloud will always have its place, he insists that the same holds true for turnkey appliances—isolated or no.

"[T]here's never gonna be one infrastructure…that just dominates," said Gardner.  "Local infrastructure [has] been neglected [and] turnkey appliances are important—because things are getting more complicated, not simpler."

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