Genomics Drowning in Data

By Michael Feldman

December 1, 2011

The leap forward in genomics technology promises to change health care as we know it. Sequencing a human genome, which costs millions of dollars just a few years ago, now costs thousands. And the prospect of mapping a genome for under a thousand dollars is on the horizon.

But cheap gene sequencing, by itself, won’t usher in a health care revolution. An article in the New York Times  this week points out that turning those sequenced genomes into something useful is the true bottleneck. Doctors would like to be able to use their patients genome to determine their susceptibility to specific diseases or to devise personalized treatments for conditions they already have.

Sequencing all the DNA base pairs is really the easy part of the problem. It just reflects the ordering of these bases — adenine (A) , thymine (T), guanine (G), cytosine (C) — in the chromosomes. The bioinformatics software necessary to extract useful information from this low-level biomolecular alphabet is much more complex and therefore costly, and necessitates a fair amount of computing power.

According to David Haussler, director of the center for biomolecular science and engineering at the University of California, Santa Cruz, that’s why it costs more to analyze a genome than to sequence it, and that discrepancy is expected to grow as the cost of sequencing falls.

The NYT article reports that the cost of sequencing a human genome has decreased by a factor of more than 800 since 2007, while computing costs have only decreased by a factor of four. That has resulted in an enormous accumulation of unanalyzed data that is being generated by all the cheap sequencing equipment.

According to the article, the current capacity of sequencers worldwide is able to 13 quadrillion DNA base pairs per year. For this year alone, it is estimated that 30,000 human genomes will be sequenced, a figure that is expected to rise to the millions within just a few years.

Not only is that too much data to analyze in aggregate, it’s also too difficult to share that volume of data between researchers. Even the fastest commercial networks are too slow to send multiple terabytes of information in anything less than a few weeks. That’s why BGI (Beijing Genomics Institute), the largest genomics research institute in the world, has resorted to sending computer disks of sequenced data via FedEx.

Cloud computing may help alleviate these problems. In fact, some believe that Google alone has enough compute and storage capacity to handle the global genomics workload. Others believe that there is just too much raw data and researchers will have to pre-process it to reduce the volume or just hold onto the unique bits.

But there are even more challenging problems ahead. Metagenomics, which aggregates DNA sequences of a whole population of organism, is even more data-intensive. For example, the microbial species in the human digestive tract represent about a million times as much sequenced data as the human genome. And since that microbial population can have a profound effect on the its human host, that genomic data becomes a pseudo-extension of the person’s genetic profile.

On top of that is all is the data associated with the RNA, proteins and other various biochemicals in the body. To get a complete picture of human health, all of this data has to be integrated as well.  Data deluge indeed.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

HPC Iron, Soft, Data, People – It Takes an Ecosystem!

December 11, 2017

Cutting edge advanced computing hardware (aka big iron) does not stand by itself. These computers are the pinnacle of a myriad of technologies that must be carefully woven together by people to create the computational c Read more…

By Alex R. Larzelere

IBM Begins Power9 Rollout with Backing from DOE, Google

December 6, 2017

After over a year of buildup, IBM is unveiling its first Power9 system based on the same architecture as the Department of Energy CORAL supercomputers, Summit and Sierra. The new AC922 server pairs two Power9 CPUs with f Read more…

By Tiffany Trader

PEZY President Arrested, Charged with Fraud

December 6, 2017

The head of Japanese supercomputing firm PEZY Computing was arrested Tuesday on suspicion of defrauding a government institution of 431 million yen (~$3.8 million). According to reports in the Japanese press, PEZY founde Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

Unleash the Next Generation of HPC with Memory-Driven Compute

Today’s enterprises are faced with an ever-growing volume of data that contains immense value and intelligence for those who can properly collect, process, and store it. Read more…

Azure Debuts AMD EPYC Instances for Storage Optimized Workloads

December 5, 2017

AMD’s return to the data center received a boost today when Microsoft Azure announced introduction of instances based on AMD’s EPYC microprocessors. The new instances – Lv2-Series of Virtual Machine – use the EPY Read more…

By John Russell

HPC Iron, Soft, Data, People – It Takes an Ecosystem!

December 11, 2017

Cutting edge advanced computing hardware (aka big iron) does not stand by itself. These computers are the pinnacle of a myriad of technologies that must be care Read more…

By Alex R. Larzelere

IBM Begins Power9 Rollout with Backing from DOE, Google

December 6, 2017

After over a year of buildup, IBM is unveiling its first Power9 system based on the same architecture as the Department of Energy CORAL supercomputers, Summit a Read more…

By Tiffany Trader

Microsoft Spins Cycle Computing into Core Azure Product

December 5, 2017

Last August, cloud giant Microsoft acquired HPC cloud orchestration pioneer Cycle Computing. Since then the focus has been on integrating Cycle’s organization Read more…

By John Russell

GlobalFoundries, Ayar Labs Team Up to Commercialize Optical I/O

December 4, 2017

GlobalFoundries (GF) and Ayar Labs, a startup focused on using light, instead of electricity, to transfer data between chips, today announced they've entered in Read more…

By Tiffany Trader

HPE In-Memory Platform Comes to COSMOS

November 30, 2017

Hewlett Packard Enterprise is on a mission to accelerate space research. In August, it sent the first commercial-off-the-shelf HPC system into space for testing Read more…

By Tiffany Trader

SC17 Cluster Competition: Who Won and Why? Results Analyzed and Over-Analyzed

November 28, 2017

Everyone by now knows that Nanyang Technological University of Singapore (NTU) took home the highest LINPACK Award and the Overall Championship from the recently concluded SC17 Student Cluster Competition. We also already know how the teams did in the Highest LINPACK and Highest HPCG competitions, with Nanyang grabbing bragging rights for both benchmarks. Read more…

By Dan Olds

Perspective: What Really Happened at SC17?

November 22, 2017

SC is over. Now comes the myriad of follow-ups. Inboxes are filled with templated emails from vendors and other exhibitors hoping to win a place in the post-SC thinking of booth visitors. Attendees of tutorials, workshops and other technical sessions will be inundated with requests for feedback. Read more…

By Andrew Jones

SC Bids Farewell to Denver, Heads to Dallas for 30th Anniversary

November 17, 2017

After a jam-packed four-day expo and intensive six-day technical program, SC17 has wrapped up another successful event that brought together nearly 13,000 visit Read more…

By Tiffany Trader

US Coalesces Plans for First Exascale Supercomputer: Aurora in 2021

September 27, 2017

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, in Arlington, Va., yesterday (Sept. 26), it was revealed that the "Aurora" supercompute Read more…

By Tiffany Trader

NERSC Scales Scientific Deep Learning to 15 Petaflops

August 28, 2017

A collaborative effort between Intel, NERSC and Stanford has delivered the first 15-petaflops deep learning software running on HPC platforms and is, according Read more…

By Rob Farber

Oracle Layoffs Reportedly Hit SPARC and Solaris Hard

September 7, 2017

Oracle’s latest layoffs have many wondering if this is the end of the line for the SPARC processor and Solaris OS development. As reported by multiple sources Read more…

By John Russell

AMD Showcases Growing Portfolio of EPYC and Radeon-based Systems at SC17

November 13, 2017

AMD’s charge back into HPC and the datacenter is on full display at SC17. Having launched the EPYC processor line in June along with its MI25 GPU the focus he Read more…

By John Russell

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Japan Unveils Quantum Neural Network

November 22, 2017

The U.S. and China are leading the race toward productive quantum computing, but it's early enough that ultimate leadership is still something of an open questi Read more…

By Tiffany Trader

GlobalFoundries Puts Wind in AMD’s Sails with 12nm FinFET

September 24, 2017

From its annual tech conference last week (Sept. 20), where GlobalFoundries welcomed more than 600 semiconductor professionals (reaching the Santa Clara venue Read more…

By Tiffany Trader

Google Releases Deeplearn.js to Further Democratize Machine Learning

August 17, 2017

Spreading the use of machine learning tools is one of the goals of Google’s PAIR (People + AI Research) initiative, which was introduced in early July. Last w Read more…

By John Russell

Leading Solution Providers

SC17 Booth Video Tours Playlist

Amazon Debuts New AMD-based GPU Instances for Graphics Acceleration

September 12, 2017

Last week Amazon Web Services (AWS) streaming service, AppStream 2.0, introduced a new GPU instance called Graphics Design intended to accelerate graphics. The Read more…

By John Russell

Perspective: What Really Happened at SC17?

November 22, 2017

SC is over. Now comes the myriad of follow-ups. Inboxes are filled with templated emails from vendors and other exhibitors hoping to win a place in the post-SC thinking of booth visitors. Attendees of tutorials, workshops and other technical sessions will be inundated with requests for feedback. Read more…

By Andrew Jones

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Tensors Come of Age: Why the AI Revolution Will Help HPC

November 13, 2017

Thirty years ago, parallel computing was coming of age. A bitter battle began between stalwart vector computing supporters and advocates of various approaches to parallel computing. IBM skeptic Alan Karp, reacting to announcements of nCUBE’s 1024-microprocessor system and Thinking Machines’ 65,536-element array, made a public $100 wager that no one could get a parallel speedup of over 200 on real HPC workloads. Read more…

By John Gustafson & Lenore Mullin

Flipping the Flops and Reading the Top500 Tea Leaves

November 13, 2017

The 50th edition of the Top500 list, the biannual publication of the world’s fastest supercomputers based on public Linpack benchmarking results, was released Read more…

By Tiffany Trader

Intel Launches Software Tools to Ease FPGA Programming

September 5, 2017

Field Programmable Gate Arrays (FPGAs) have a reputation for being difficult to program, requiring expertise in specialty languages, like Verilog or VHDL. Easin Read more…

By Tiffany Trader

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

Share This