Storage Doesn't Matter for Bioinformatics? Not So Fast

Joe Stanganelli, Founder and Principal, Beacon Hill Law | 4/30/2012 | 28 comments

Joe Stanganelli
Last week, I wrote an article about how keynote speaker Martin Leach presented a convincing argument to Bio-IT World Conference 2012 attendees here in Boston as to why the biggest obstacle facing the health and life sciences industry in the age of "big-data" is not one of storage, but of computing.

Accessibility, analysis, and integration are the sole true bugaboos, says Leach, making storage issues but a petty distraction when it comes to genomics and others who work with intensive bioinformatics.

Turns out, not everyone here agrees.

Robert Bjornson is director of IT at the Yale Center for Genome Analysis (YCGA). "We spend almost no time thinking about computing. We spend all of our time thinking about storage," told Bjornson to a room of a few dozen conference attendees.

In a presentation about IT infrastructure and hardware, Bjornson talked about the technological challenges YCGA and similar organizations face.

"Drives," he aptly observed, "fail."

Even Leach does not dispute this fact of IT life. The Broad Institute of MIT and Harvard, where Leach is CIO, boasts the largest genomic datacenter in the world, with over 10 petabytes of data on spinning disks -- and every day to day-and-a-half, one of those disks fails.

"When you have 1,000 drives, expect failure," confirms Bjornson, by way of advice. What's more, backing up all of a genomics organization's data -- which can number in the petabytes -- just isn't practical.

Cost is also a factor (Moore's Law notwithstanding) for some customers, says Bjornson -- at least psychologically. Despite the price of storage falling, many enterprise and high-level organizational customers maintain a consumer market perspective. "I can't tell you how many times people have said, 'Why does this cost $1,000 a terabyte?' " says Bjornson, relating laughable characterizations of customers who protest that hard drives at Best Buy can go for about $65 per terabyte.

Big-data customers may be their own worst enemy in more ways than one. YCGA's customers use YCGA's storage and YCGA's cluster. Cautions Bjornson, however, "It's risky to let customers into the factory." They can crash the login node. They can overload the storage. They can "do any one of a number of things that people do when they get the chance," Bjornson says, and any of those things can interfere with their data management and data analysis.

To be fair, this is an example of a risk that falls under both the "storage" and the "accessibility" umbrellas -- and there are others.

For instance, Bjornson himself concedes that search is a huge problem in big data genomics, as he presents a slide that reads, " 'Find' does not work on 2PB on Storage." Genome sequencing, of course, is a data-intensive field -- yet the field of genomics lacks a truly effective data identification solution ("a Google search for data," as Leach called it on Tuesday), says Bjornson. "We don't have it. We really need it."

Nonetheless, "storage, for us, is by far the hard part," maintains Bjornson.

Both sides of the accessibility vs. storage discussion raise very valid points -- and have very real concerns. Alas, the hardware presentation series here at Bio-IT has been somewhat sparsely attended compared to other sessions. Conversely, so many Bio-IT attendees clamored to see the opening keynote speeches on Tuesday that dozens were relegated to an overflow room with a live video feed.

With so many of the attendees here having heard only Leach's advocacy for accessibility, arguments like Bjornson's about the importance of storage seem to have become lost in the din of the conference -- and therefore, ironically, much less accessible.

View Comments: Newest First | Oldest First | Threaded View
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Sara Peters   Storage Doesn't Matter for Bioinformatics? Not So Fast   4/30/2012 4:31:51 PM
other genomic research institute
If you haven't already, check out the On the Case video documentary series we're doing about the Translational Genomics Research Institute. Storage is DEFINITELY a challenge for them -- but processing speed and data sharing are just as important. Check it out:

Sara Peters   Storage Doesn't Matter for Bioinformatics? Not So Fast   4/30/2012 4:22:03 PM
gold star
Joe you get extra credit simply for using the word "bugaboo."
Taimoor Zubair   Storage Doesn't Matter for Bioinformatics? Not So Fast   4/30/2012 2:51:05 PM
Re: Storage hubris
"What I've learned is it's the one leg in computer processing that is taken for granted until it fails."

@Lufu: I agree with you on this. Recently I had a meeting over a project's budget with finance. It took a whole while and considerable efforts convincing those non-technical folks why we needed redundant data disks inside a server and why can't normal disks replace a RAID controller.

LuFu   Storage Doesn't Matter for Bioinformatics? Not So Fast   4/30/2012 2:05:09 PM
Storage hubris
I worked in data storage for many years. What I've learned is it's the one leg in computer processing that is taken for granted until it fails. One of the first things I learned was the MTBF of a disk drive which is it's Mean Time Between Failure. It's a calibration in hours of a hard drive's expected lifetime. So, a manufacturer reports 1.5 million hours MTBF and you think that this will last a lifetime if not longer. Of course the drive spec should include the asterisk - *Your drive mileage may vary - since Murphy's Law is usually excluded from the MTBF equation. Ergo, I vote for Bjornson and his concern about storage. And when it's big storage then it becomes a larger issue. As we all know, size does matter.
tekedge   Storage Doesn't Matter for Bioinformatics? Not So Fast   4/30/2012 1:49:44 PM
Storage Doesn't Matter for Bioinformatics? Not So Fast
"What's more, backing up all of a genomics organization's data -- which can number in the petabytes -- just isn't practical. "

I am a bit confused with that statement. Does the poster mean to say, backing up petabytes of data daily? Yes that wd be a difficult task but surely on a periodic basis the entire database can be backed up and incremental backups on daily basis which should probably be in terrabytes should be possible.

syedzunair   Storage Doesn't Matter for Bioinformatics? Not So Fast   4/30/2012 12:21:44 PM
Re: What about Cloud?
It's at least better than backing up your data in a hundred Hard Drives when all the data can perish if a fire breaks out.

It seems much better than storing data on tapes or on hard drives. With storage on the cloud you get the option of storing your data in a geographically separate location as compared to your current business location. It will most certainly help in data recovery if the primary location goes down. 
David Wagner   Storage Doesn't Matter for Bioinformatics? Not So Fast   4/30/2012 11:46:08 AM
Re: What about Cloud?
It is tempting to think that perhaps the Broad Institute is just better at running its data center (or better funded) than Yale. Sure, drives fail. Sure backing up petabytes of data is hard and expensive.

But it isn't like this isn't being done.

On the other hand, what I really think Dr. Bjornson is probably feeling is the tightness of the standard academic budget. Hopefully, Dr. Leach is correct that prices continue to drop and academic datacenters can afford to do more.

In the meantime, I doubt there's a datacenter out there that doesn't feel the budget pinch.
nasimson   Storage Doesn't Matter for Bioinformatics? Not So Fast   4/30/2012 10:02:34 AM
What about Cloud?
We're no longer in the 70s when Bill Gates announced that a couple of kilobytes of storage space is more than enough for everyone.

Storage demands increase, and it goes for every kind of organization given today's storage needs.

With the inception of Cloud we sure have another pretty darn good alternative for storing. Storage providers aren't charging much at this point in order to commercialize Cloud. Perhaps this is the next wise step?

It's at least better than backing up your data in a hundred Hard Drives when all the data can perish if a fire breaks out.
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