Biomedicine Soars on HPC’s Wings

By Tiffany Trader

September 30, 2013

Computing and simulation methods have had a transformative effect on science and research. From computational biology to the recently coined petascale humanities, the computer sciences are pervasive throughout the academic and research landscape. And as the computer resources become both more powerful and easier to use, this transformative potential is even greater. The biomedical research sector is perhaps particularly illustrative of this on-going paradigm shift.

At a recent conference, prominent experts in biomedicine from government, academia and industry gathered to discuss HPC’s role in transforming bioscience. The event, titled “Current Challenges in Computing 2013: Biomedical Research,” or CCubed, was held earlier this month in Napa thanks to support from Lawrence Livermore National Laboratory and funding from IBM.

The attendees identified two key points:

+ The latest generation of high performance computers has the potential to transform the biomedical field in ways unthinkable just a few years ago.

+ There are further opportunities for accelerating the development of biomedical tools using petaflop class supercomputers.

“Computing is at a tipping point where it can play a much larger role in biomedical research,” said Fred Streitz, director of LLNL’s Institute for Scientific Computing Research and the High Performance Computing Innovation Center. “This is because of the level of computing power we’re now reaching and the fact that the biomedical community is becoming aware of HPC potential.”

Streitz added that “the promise of computing in the biology space was overhyped 10 years ago.” According to him the claims were on-target, but a decade too early. The best systems of the time were outmatched in terms of scale and sophistication. In the last ten years, however, both biology and computing have improved sufficiently to tackle these complex modeling challenges.

The current generation of leadership-class machines has crossed over into new territory by being able to model entire systems and not just parts of a system. For example, scientists can now model organs, like the human heart, beating in almost real-time. “The field is starting to realize they can use computing as a tool in a way they were not able to five years ago,” observed Streitz.

The inflection point does not only apply to computing; the event also emphasized the co-occurring need for data-based insight. The big data aspect of bioscience is the purview of bioinformatics. The two sides – HPC and big data – will inform and shape each other.

As Anna Barker, director, Transformative Healthcare Knowledge Networks, said: “Events like CCubed help advance biomedical research by bringing together eclectic thinkers who offer fresh perspective on how we can begin to manage and analyze this data, and how we can turn it into real knowledge.”

Related Items

Iowa State Accelerates Science with GPU-Phi Supercomputer

TACC’s Hadoop Cluster Breaks New Ground 

Czech Republic has a National Supercomputing Center

Sequoia Supercomputer Pumps Up Heart Research

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!

SC17 Student Cluster Competition Configurations: Fewer Nodes, Way More Accelerators

November 16, 2017

The final configurations for each of the SC17 “Donnybrook in Denver” Student Cluster Competition have been released. Fortunately, each team received their equipment shipments on time and undamaged, so the teams are r Read more…

By Dan Olds

Student Clusterers Demolish HPCG Record! Nanyang Sweeps Benchmarks

November 16, 2017

Nanyang pulled off the always difficult double-play at this year’s SC Student Cluster Competition. The plucky team from Singapore posted a world record LINPACK, thus taking the Highest LINPACK Award, but also managed t Read more…

By Dan Olds

Student Cluster LINPACK Record Shattered! More LINs Packed Than Ever before!

November 16, 2017

Nanyang Technological University, the pride of Singapore, utterly destroyed the Student Cluster Competition LINPACK record by posting a score of 51.77 TFlop/s at SC17 in Denver. The previous record, established by German Read more…

By Dan Olds

HPE Extreme Performance Solutions

Harness Scalable Petabyte Storage with HPE Apollo 4510 and HPE StoreEver

As a growing number of connected devices challenges IT departments to rapidly collect, manage, and store troves of data, organizations must adopt a new generation of IT to help them operate quickly and intelligently. Read more…

Hyperion Market Update: ‘Decent’ Growth Led by HPE; AI Transparency a Risk Issue

November 15, 2017

The HPC market update from Hyperion Research (formerly IDC) at the annual SC conference is a business and social “must,” and this year’s presentation at SC17 played to a SRO crowd at a downtown Denver hotel. This w Read more…

By Doug Black

SC17 Student Cluster Competition Configurations: Fewer Nodes, Way More Accelerators

November 16, 2017

The final configurations for each of the SC17 “Donnybrook in Denver” Student Cluster Competition have been released. Fortunately, each team received their e Read more…

By Dan Olds

Student Clusterers Demolish HPCG Record! Nanyang Sweeps Benchmarks

November 16, 2017

Nanyang pulled off the always difficult double-play at this year’s SC Student Cluster Competition. The plucky team from Singapore posted a world record LINPAC Read more…

By Dan Olds

Student Cluster LINPACK Record Shattered! More LINs Packed Than Ever before!

November 16, 2017

Nanyang Technological University, the pride of Singapore, utterly destroyed the Student Cluster Competition LINPACK record by posting a score of 51.77 TFlop/s a Read more…

By Dan Olds

Hyperion Market Update: ‘Decent’ Growth Led by HPE; AI Transparency a Risk Issue

November 15, 2017

The HPC market update from Hyperion Research (formerly IDC) at the annual SC conference is a business and social “must,” and this year’s presentation at S Read more…

By Doug Black

The Betting Window is Closed: Final Student Cluster Competition Betting Odds are in!

November 15, 2017

The window has closed and the bettors are clutching their tickets, anxiously awaiting the results of the SC17 Student Cluster Competition. We’ve seen big chan Read more…

By Dan Olds

2017 Student Cluster Competition Benchmarks, Workloads, and Pre-Planned Disasters

November 15, 2017

The students competing in the 2017 Student Cluster Competition in Denver are facing a grueling 48 hour marathon of HPC benchmarks and real scientific applicatio Read more…

By Dan Olds

Nvidia Focuses Its Cloud Containers on HPC Applications

November 14, 2017

Having migrated its top-of-the-line datacenter GPU to the largest cloud vendors, Nvidia is touting its Volta architecture for a range of scientific computing ta Read more…

By George Leopold

HPE Launches ARM-based Apollo System for HPC, AI

November 14, 2017

HPE doubled down on its memory-driven computing vision while expanding its processor portfolio with the announcement yesterday of the company’s first ARM-base Read more…

By Doug Black

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

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

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

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

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in Read more…

By Tiffany Trader

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

Leading Solution Providers

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

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

Cray Moves to Acquire the Seagate ClusterStor Line

July 28, 2017

This week Cray announced that it is picking up Seagate's ClusterStor HPC storage array business for an undisclosed sum. "In short we're effectively transitioning the bulk of the ClusterStor product line to Cray," said CEO Peter Ungaro. 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

IBM Advances Web-based Quantum Programming

September 5, 2017

IBM Research is pairing its Jupyter-based Data Science Experience notebook environment with its cloud-based quantum computer, IBM Q, in hopes of encouraging a new class of entrepreneurial user to solve intractable problems that even exceed the capabilities of the best AI systems. Read more…

By Alex Woodie

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This