HPC for Life: Genomics, Brain Research, and Beyond

By Warren Froelich

July 19, 2018

Editor’s note: In part I, “HPC Serves as ‘Rosetta Stone’ for the Information Age,” we explored how high-performance computing is transforming digital data into valuable insight and leading to amazing discoveries. Part II follows the path of HPC into new areas of brain research and astrophysics.

During the past few decades, the life sciences have witnessed one landmark discovery after another with the aid of HPC, paving the way toward a new era of personalized treatments based on an individual’s genetic makeup, and drugs capable of attacking previously intractable ailments with few side effects.

Genomics research is generating torrents of biological data to help “understand the rules of life” for personalized treatments believed to be the focus for tomorrow’s medicine. The sequencing of DNA has rapidly moved from the analysis of data sets that were megabytes in size to entire genomes that are gigabytes in size. Meanwhile, the cost of sequencing has dropped from about $10,000 per genome in 2010 to $1,000 in 2017, thus requiring increased speed and refinement of computational resources to process and analyze all this data.

In one recent genome analysis, an international team led by Jonathan Sebat, a professor of psychiatry, cellular and molecular medicine and pediatrics at UC San Diego School of Medicine, identified a risk factor that may explain some of the genetic causes for autism: rare inherited variants in regions of non-code DNA. For about a decade, researchers knew that the genetic cause of autism partly consisted of so-called de novo mutations, or gene mutations that appear for the first time. But those sequences represented only 2 percent of the genome. To investigate the remaining 98 percent of the genome in ASD (autism spectrum disorder), Sebat and colleagues analyzed the complete genomes of 9,274 subjects from 2,600 families, representing a combined data total on the range of terabytes.

As reported in the April 20, 2018, issue of Science, DNA sequences were analyzed with Comet, along with data from other large studies from the Simons Simplex Collection and the Autism Speaks MSSNG Whole Genome Sequencing Project.

“Whole genome sequencing data processing and analysis are both computationally and resource intensive,” said Madhusudan Gujral, an analyst with SDSC and co-author of the paper. “Using Comet, processing and identifying specific structural variants from a single genome took about 2 ½ days.”

SDSC Distinguished Scientist Wayne Pfeiffer added that with Comet’s nearly 2,000 nodes and several petabytes of scratch space, tens of genomes can be processed at the same time, taking the data processing requirement from months down to weeks.

In cryo-Electron Microscopy (cryo-EM), biological samples are flash-frozen so rapidly that damaging ice crystals are unable to form. As a result, researchers are able to view highly-detailed reconstructed 3D models of intricate, microscopic biological structures in near-native states. Above is a look inside of one of the cryo-electron microscopes available to researchers at the Timothy Baker Lab at UC San Diego. Image credit: Jon Chi Lou, SDSC

Not long ago, the following might have been considered an act of wizardry from a Harry Potter novel. First, take a speck of biomolecular matter, invisible to the naked eye, and then deep-freeze it to near absolute zero. Then, blast this material, now frozen in time, with an electron beam. Finally, add the power of a supercomputer aided by a set of problem-solving rules called algorithms. And, presto! A three-dimensional image of the original biological speck appears on a computer monitor at atomic resolution. Not really magic or even sleight-of-hand, this innovation – given the name of cryo-electron microscopy or simply cryo-EM — garnered the 2017 Nobel Prize in chemistry for the technology’s invention in the 1970s.

Today, researchers seeking to unravel the structure of proteins in atomic detail, in hopes of treating many intractable diseases, are increasingly turning to cryo-EM as an alternative to time-tested X-ray crystallography. A key advantage of the cryo-EM is that no crystallization of the protein is required, a barrier for those proteins that defy being turned into a crystal. Even so, the technology didn’t take off until the development of more sensitive electron detectors and advanced computational algorithms needed to turn reams of data into often aesthetically pleasing three-dimensional images.

“About 10 years ago, cryo-EM was known as blob-biology,” said Robert Sinkovits, director of scientific computing applications at SDSC. ”You got an overall shape, but not at the resolution you would get with X-ray crystallography, which required working with a crystal. But it was kind of a black art to create these crystals and some things simply wouldn’t crystalize. You can use cryo-EM for just about anything.”

Several molecular biologists and chemists at UC San Diego are taking advantage of the university’s cryo-EM laboratory and SDSC’s computing resources, to reveal the inner workings and interactions of several targeted proteins critical to the understanding of diseases such as fragile X syndrome and childhood liver cancer.

“This will be a growing area for HPC, in part, as we continue to automate the process,” said Sinkovits.

Machine Learning and Brain Implants

It’s a concept that can boggle the brain, and ironically is now being used to imitate that very organ. Called “machine learning,” this innovation typically involves training a computer or robot on millions of actions so that the computer learns how to derive insight and meaning from the data as time advances.

Recently, a collaborative team led by researchers at SDSC and the Downstate Medical Center in Brooklyn, N.Y., applied a novel computer algorithm to mimic how the brain learns, with the aid of Comet and the Center’s Neuroscience Gateway. The goal: to identify and replicate neural circuitry that resembles the way an unimpaired brain controls limb movement.

The study, published in the March-May 2017 issue of the IBM Journal of Research, laid the groundwork to develop realistic “biomimetric neuroprosthetics” – brain implants that replicate brain circuits and function – that one day could replace lost or damaged brain cells from tumors, stroke or other diseases.

The researchers trained their model using spike-timing dependent plasticity (STDP) and reinforced learning, believed to be the basis for memory and learning in mammalian brains. Briefly, the process refers to the ability of synaptic connections to become stronger based on when they are activated in relation to each other, meshed with a system of biochemical rewards or punishments that are tied to correct or incorrect decisions.

“Only the fittest individual (models) remain, those models that are better able to learn better, survive and propagate their genes,” said Salvador Dura-Bernal, a research assistant professor in physiology and pharmacology with Downstate, and the paper’s first author.

As for the role of HPC in this study: “Since thousands of parameter combinations need to be evaluated, this is only possible by running the simulations using HPC resources such as those provided by SDSC,” said Dura-Bernal. “We estimated that using a single processor instead of the Comet system would have taken almost six years to obtain the same results.”

On the Horizon

Other impressive data producers are waiting in the wings posing further challenges on tomorrow’s super facilities. For example, an ambitious upgrade to the Large Hadron Collider will result in a substantial increase in the intensity of proton beam collisions, far greater than anything built before. From the mid-2020s forward, the experiments at the LHC are expected to yield 10 times more data each year than the combined output of data generated during the three-years leading up to the Higgs discovery. Beyond that, future accelerators are being discussed that would be housed in 100-km long tunnels to reach collision energies many times that of the LHC, while still others are suggesting the construction of colliders based on different geometric shapes, perhaps linear rather than ring. More powerful machines, by definition, will translate into torrents of more data to digest and analyze.

The future site of the Simons Observatory, located in the high Atacama Desert in Northern Chile inside the Chajnator Science Preserve (photo licensed under CC BY-SA 4.0)

Under an agreement with the Simons Foundation Flatiron Institute, SDSC’s Gordon is being re-purposed to provide computational support for the POLARBEAR and successor project called the Simon Array. The projects — led by UC Berkeley and funded first by the Simons Foundation and then the NSF under a five-year, $5 million grant — will deploy the most powerful cosmic microwave background (CMB) radiation telescope and detector ever made to detect what are, in essence, the leftover ‘heat’ from the Big Bang in the form of microwave radiation.

“The POLARBEAR experiment alone collects nearly one gigabyte of data every day that must be analyzed in real time,” said Brian Keating, a professor of physics at UC San Diego’s Center for Astrophysics & Space Sciences and co-PI for the POLARBEAR/Simons Array project.

“This is an intensive process that requires dozens of sophisticated tests to assure the quality of the data. Only be leveraging resources such as Gordon are we able to continue our legacy of success.”

“As the scale of data and complexity of these experimental projects increase, it is more important than ever before that centers like SDSC respond by providing HPC systems and expertise that become part of the integrated ecosystem of research and discovery,” said Norman.

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!

University of Chicago Researchers Generate First Computational Model of Entire SARS-CoV-2 Virus

January 15, 2021

Over the course of the last year, many detailed computational models of SARS-CoV-2 have been produced with the help of supercomputers, but those models have largely focused on critical elements of the virus, such as its Read more…

By Oliver Peckham

Pat Gelsinger Returns to Intel as CEO

January 14, 2021

The Intel board of directors has appointed a new CEO. Intel alum Pat Gelsinger is leaving his post as CEO of VMware to rejoin the company that he parted ways with 11 years ago. Gelsinger will succeed Bob Swan, who will remain CEO until Feb. 15. Gelsinger previously spent 30 years... Read more…

By Tiffany Trader

Roar Supercomputer to Support Naval Aircraft Research

January 14, 2021

One might not think “aircraft” when picturing the U.S. Navy, but the military branch actually has thousands of aircraft currently in service – and now, supercomputing will help future naval aircraft operate faster, Read more…

By Staff report

DOE and NOAA Extend Computing Partnership, Plan for New Supercomputer

January 14, 2021

The National Climate-Computing Research Center (NCRC), hosted by Oak Ridge National Laboratory (ORNL), has been supporting the climate research of the National Oceanic and Atmospheric Administration (NOAA) for the last 1 Read more…

By Oliver Peckham

Using Micro-Combs, Researchers Demonstrate World’s Fastest Optical Neuromorphic Processor for AI

January 13, 2021

Neuromorphic computing, which uses chips that mimic the behavior of the human brain using virtual “neurons,” is growing in popularity thanks to high-profile efforts from Intel and others. Now, a team of researchers l Read more…

By Oliver Peckham

AWS Solution Channel

Now Available – Amazon EC2 C6gn Instances with 100 Gbps Networking

Amazon EC2 C6gn instances powered by AWS Graviton2 processors are now available!

Compared to C6g instances, this new instance type provides 4x higher network bandwidth, 4x higher packet processing performance, and 2x higher EBS bandwidth. Read more…

Intel® HPC + AI Pavilion

Intel Keynote Address

Intel is the foundation of HPC – from the workstation to the cloud to the backbone of the Top500. At SC20, Intel’s Trish Damkroger, VP and GM of high performance computing, addresses the audience to show how Intel and its partners are building the future of HPC today, through hardware and software technologies that accelerate the broad deployment of advanced HPC systems. Read more…

Honing In on AI, US Launches National Artificial Intelligence Initiative Office

January 13, 2021

To drive American leadership in the field of AI into the future, the National Artificial Intelligence Initiative Office has been launched by the White House Office of Science and Technology Policy (OSTP). The new agen Read more…

By Todd R. Weiss

Pat Gelsinger Returns to Intel as CEO

January 14, 2021

The Intel board of directors has appointed a new CEO. Intel alum Pat Gelsinger is leaving his post as CEO of VMware to rejoin the company that he parted ways with 11 years ago. Gelsinger will succeed Bob Swan, who will remain CEO until Feb. 15. Gelsinger previously spent 30 years... Read more…

By Tiffany Trader

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

By John Russell

Intel ‘Ice Lake’ Server Chips in Production, Set for Volume Ramp This Quarter

January 12, 2021

Intel Corp. used this week’s virtual CES 2021 event to reassert its dominance of the datacenter with the formal roll out of its next-generation server chip, the 10nm Xeon Scalable processor that targets AI and HPC workloads. The third-generation “Ice Lake” family... Read more…

By George Leopold

Researchers Say It Won’t Be Possible to Control Superintelligent AI

January 11, 2021

Worries about out-of-control AI aren’t new. Many prominent figures have suggested caution when unleashing AI. One quote that keeps cropping up is (roughly) th Read more…

By John Russell

AMD Files Patent on New GPU Chiplet Approach

January 5, 2021

Advanced Micro Devices is accelerating the GPU chiplet race with the release of a U.S. patent application for a device that incorporates high-bandwidth intercon Read more…

By George Leopold

Programming the Soon-to-Be World’s Fastest Supercomputer, Frontier

January 5, 2021

What’s it like designing an app for the world’s fastest supercomputer, set to come online in the United States in 2021? The University of Delaware’s Sunita Chandrasekaran is leading an elite international team in just that task. Chandrasekaran, assistant professor of computer and information sciences, recently was named... Read more…

By Tracey Bryant

Intel Touts Optane Performance, Teases Next-gen “Crow Pass”

January 5, 2021

Competition to leverage new memory and storage hardware with new or improved software to create better storage/memory schemes has steadily gathered steam during Read more…

By John Russell

Farewell 2020: Bleak, Yes. But a Lot of Good Happened Too

December 30, 2020

Here on the cusp of the new year, the catchphrase ‘2020 hindsight’ has a distinctly different feel. Good riddance, yes. But also proof of science’s power Read more…

By John Russell

Esperanto Unveils ML Chip with Nearly 1,100 RISC-V Cores

December 8, 2020

At the RISC-V Summit today, Art Swift, CEO of Esperanto Technologies, announced a new, RISC-V based chip aimed at machine learning and containing nearly 1,100 low-power cores based on the open-source RISC-V architecture. Esperanto Technologies, headquartered in... Read more…

By Oliver Peckham

Azure Scaled to Record 86,400 Cores for Molecular Dynamics

November 20, 2020

A new record for HPC scaling on the public cloud has been achieved on Microsoft Azure. Led by Dr. Jer-Ming Chia, the cloud provider partnered with the Beckman I Read more…

By Oliver Peckham

NICS Unleashes ‘Kraken’ Supercomputer

April 4, 2008

A Cray XT4 supercomputer, dubbed Kraken, is scheduled to come online in mid-summer at the National Institute for Computational Sciences (NICS). The soon-to-be petascale system, and the resulting NICS organization, are the result of an NSF Track II award of $65 million to the University of Tennessee and its partners to provide next-generation supercomputing for the nation's science community. Read more…

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Aurora’s Troubles Move Frontier into Pole Exascale Position

October 1, 2020

Intel’s 7nm node delay has raised questions about the status of the Aurora supercomputer that was scheduled to be stood up at Argonne National Laboratory next year. Aurora was in the running to be the United States’ first exascale supercomputer although it was on a contemporaneous timeline with... Read more…

By Tiffany Trader

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

By John Russell

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Programming the Soon-to-Be World’s Fastest Supercomputer, Frontier

January 5, 2021

What’s it like designing an app for the world’s fastest supercomputer, set to come online in the United States in 2021? The University of Delaware’s Sunita Chandrasekaran is leading an elite international team in just that task. Chandrasekaran, assistant professor of computer and information sciences, recently was named... Read more…

By Tracey Bryant

Leading Solution Providers

Contributors

Top500: Fugaku Keeps Crown, Nvidia’s Selene Climbs to #5

November 16, 2020

With the publication of the 56th Top500 list today from SC20's virtual proceedings, Japan's Fugaku supercomputer – now fully deployed – notches another win, Read more…

By Tiffany Trader

Texas A&M Announces Flagship ‘Grace’ Supercomputer

November 9, 2020

Texas A&M University has announced its next flagship system: Grace. The new supercomputer, named for legendary programming pioneer Grace Hopper, is replacing the Ada system (itself named for mathematician Ada Lovelace) as the primary workhorse for Texas A&M’s High Performance Research Computing (HPRC). Read more…

By Oliver Peckham

At Oak Ridge, ‘End of Life’ Sometimes Isn’t

October 31, 2020

Sometimes, the old dog actually does go live on a farm. HPC systems are often cursed with short lifespans, as they are continually supplanted by the latest and Read more…

By Oliver Peckham

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

Gordon Bell Special Prize Goes to Massive SARS-CoV-2 Simulations

November 19, 2020

2020 has proven a harrowing year – but it has produced remarkable heroes. To that end, this year, the Association for Computing Machinery (ACM) introduced the Read more…

By Oliver Peckham

Nvidia-Arm Deal a Boon for RISC-V?

October 26, 2020

The $40 billion blockbuster acquisition deal that will bring chipmaker Arm into the Nvidia corporate family could provide a boost for the competing RISC-V architecture. As regulators in the U.S., China and the European Union begin scrutinizing the impact of the blockbuster deal on semiconductor industry competition and innovation, the deal has at the very least... Read more…

By George Leopold

Intel Xe-HP GPU Deployed for Aurora Exascale Development

November 17, 2020

At SC20, Intel announced that it is making its Xe-HP high performance discrete GPUs available to early access developers. Notably, the new chips have been deplo Read more…

By Tiffany Trader

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This