Comet Supercomputer Assists With Genomic Research

November 3, 2016

Nov. 3 — One of the most detailed genomic studies of any ecosystem to date has revealed an underground world of stunning microbial diversity, and added dozens of new branches to the tree of life.

The bacterial bonanza comes from scientists who reconstructed the genomes of more than 2,500 microbes from sediment and groundwater samples collected at an aquifer in Colorado. The effort was led by researchers from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley. DNA sequencing was performed at the Joint Genome Institute, a DOE Office of Science User Facility, and analyses were conducted with the aid of the CIPRES gateway and the Comet supercomputer, based at the San Diego Supercomputer Center (SDSC) at the University of California San Diego.

As reported online October 24 in the journal Nature Communications, the scientists netted genomes from 80 percent of all known bacterial phyla, a remarkable degree of biological diversity at one location. They also discovered 47 new phylum-level bacterial groups, naming many of them after influential microbiologists and other scientists. And they learned new insights about how microbial communities work together to drive processes that are critical to the planet’s climate and life everywhere, such as the carbon and nitrogen cycles.

These findings shed light on one of Earth’s most important and least understood realms of life. The subterranean world hosts up to one-fifth of all biomass, but it remains a mystery.

“We didn’t expect to find this incredible microbial diversity. But then again, we know little about the roles of subsurface microbes in biogeochemical processes, and more broadly, we don’t really know what’s down there,” says Jill Banfield, a Senior Faculty Scientist in Berkeley Lab’s Climate & Ecosystem Sciences Division and a UC Berkeley professor in the departments of Earth and Planetary Science, and Environmental Science, Policy, and Management.

Added UC Berkeley’s Karthik Anantharaman, the first author of the paper: “To better understand what subsurface microbes are up to, our approach is to access their entire genomes. This enabled us to discover a greater interdependency among microbes than we’ve seen before.”

The research is part of a Berkeley Lab-led project called Watershed Function Scientific Focus Area (formerly Sustainable Systems Scientific Focus Area 2.0). The project is developing a predictive understanding of terrestrial environments from the genome to the watershed scale. The field research takes place at a research site near the town of Rifle, Colorado, where for the past several years scientists have conducted experiments designed to stimulate populations of subterranean microbes that are naturally present in very low numbers.

The scientists sent soil and water samples from these experiments to the Joint Genome Institute for terabase-scale metagenomic sequencing. This high-throughput method isolates and purifies DNA from environmental samples, and then sequences one trillion base pairs of DNA at a time. Next, the scientists used bioinformatics tools developed in Banfield’s lab along with those from the CIPRES Science Gateway to analyze the data.

“The CIPRES Science Gateway and the Comet supercomputer were instrumental to our work,” Banfield said. “Considering the unprecedented size of our sequence datasets, we were unable to complete any runs for inferring trees on other servers.” The CIPRES Science Gateway and Comet are available through the Extreme Science and Engineering Discovery Environment (XSEDE). Supported by the National Science Foundation, XSEDE is the most advanced, powerful, and robust collection of integrated advanced digital resources and services in the world.

The scientists’ approach has redrawn the tree of life. Between the 47 new bacterial groups reported in this work, and 35 new groups published last year (also found at the Rifle site), Banfield’s team has doubled the number of known bacterial groups.

With discovery comes naming rights. The scientists named many of the new bacteria groups after Berkeley Lab and UC Berkeley researchers. For example, there’s Candidatus Andersenbacteria, after phylochip inventor Gary Andersen, and there’s Candidatus Doudnabacteria, after CRISPR genome-editing pioneer Jennifer Doudna.

“Berkeley now dominates the tree of life as it does the periodic table,” Banfield says, in a nod to the sixteen elements discovered at Berkeley Lab and UC Berkeley.

Another big outcome is a deeper understanding of the roles subsurface microbes play in globally important carbon, hydrogen, nitrogen, and sulfur cycles. This information will help to better represent these cycles in predictive models such as climate simulations.

The scientists conducted metabolic analyses of 36 percent of the organisms detected in the aquifer system. They focused on a phenomenon called metabolic handoff, which essentially means one microbe’s waste is another microbe’s food. It’s known from lab studies that handoffs are needed in certain reactions, but these interconnected networks are widespread and vastly more complex in the real world.

To understand why it’s important to represent metabolic handoffs as accurately as possible in models, consider nitrate, a groundwater contaminant from fertilizers. Subsurface microbes are the primary driver in reducing nitrate to harmless nitrogen gas. There are four steps in this denitrification process, and the third step creates nitrous oxide—one of the most potent greenhouse gases. The process breaks down if microbes that carry out the fourth step are inactive when a pulse of nitrate enters the system.

“If microbes aren’t there to accept the nitrous oxide handoff, then the greenhouse gas escapes into the atmosphere,” says Anantharaman.

The scientists found the carbon, hydrogen, nitrogen, and sulfur cycles are all driven by metabolic handoffs that require an unexpectedly high degree of interdependence among microbes. The vast majority of microorganisms can’t fully reduce a compound on their own. It takes a team. There are also backup microbes ready to perform a handoff if first-string microbes are unavailable.

“The combination of high microbial diversity and interconnections through metabolic handoffs likely results in high ecosystem resilience,” says Banfield.

Other co-authors of the paper include Berkeley Lab’s Eoin Brodie, Susan Hubbard, Ulas Karaoz, and Kenneth Williams; and UC Berkeley’s Chris Brown, Cindy Castelle, Laura Hug, Alexander Probst, Itai Sharon, Andrea Singh, and Brian Thomas. The research is supported by the Department of Energy’s Office of Science.

About SDSC

As an Organized Research Unit of UC San Diego, SDSC is considered a leader in data-intensive computing and cyberinfrastructure, providing resources, services, and expertise to the national research community, including industry and academia. Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. SDSC supports hundreds of multidisciplinary programs spanning a wide variety of domains, from earth sciences and biology to astrophysics, bioinformatics, and health IT. SDSC’s Comet joins the Center’s data-intensive Gordon cluster, and are both part of the National Science Foundation’s XSEDE (Extreme Science and Engineering Discovery Environment) program.

About LBNL

Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit www.lbl.gov.


Source: SDSC

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!

Cray Introduces All Flash Lustre Storage Solution Targeting HPC

June 19, 2018

Citing the rise of IOPS-intensive workflows and more affordable flash technology, Cray today introduced the L300F, a scalable all-flash storage solution whose primary use case is to support high IOPS rates to/from a scra Read more…

By John Russell

Lenovo to Debut ‘Neptune’ Cooling Technologies at ISC

June 19, 2018

Lenovo today announced a set of cooling technologies, dubbed Neptune, that include direct to node (DTN) warm water cooling, rear door heat exchanger (RDHX), and hybrid solutions that combine air and liquid cooling. Lenov Read more…

By John Russell

World Cup is Lame Compared to This Competition

June 18, 2018

So you think World Cup soccer is a big deal? While I’m sure it’s very compelling to watch a bunch of athletes kick a ball around, World Cup misses the boat because it doesn’t include teams putting together their ow Read more…

By Dan Olds

HPE Extreme Performance Solutions

HPC and AI Convergence is Accelerating New Levels of Intelligence

Data analytics is the most valuable tool in the digital marketplace – so much so that organizations are employing high performance computing (HPC) capabilities to rapidly collect, share, and analyze endless streams of data. Read more…

IBM Accelerated Insights

Banks Boost Infrastructure to Tackle GDPR

As banks become more digital and data-driven, their IT managers are challenged with fast growing data volumes and lines-of-businesses’ (LoBs’) seemingly limitless appetite for analytics. Read more…

IBM Demonstrates Deep Neural Network Training with Analog Memory Devices

June 18, 2018

From smarter, more personalized apps to seemingly-ubiquitous Google Assistant and Alexa devices, AI adoption is showing no signs of slowing down – and yet, the hardware used for AI is far from perfect. Currently, GPUs Read more…

By Oliver Peckham

Cray Introduces All Flash Lustre Storage Solution Targeting HPC

June 19, 2018

Citing the rise of IOPS-intensive workflows and more affordable flash technology, Cray today introduced the L300F, a scalable all-flash storage solution whose p Read more…

By John Russell

Sandia to Take Delivery of World’s Largest Arm System

June 18, 2018

While the enterprise remains circumspect on prospects for Arm servers in the datacenter, the leadership HPC community is taking a bolder, brighter view of the x86 server CPU alternative. Amongst current and planned Arm HPC installations – i.e., the innovative Mont-Blanc project, led by Bull/Atos, the 'Isambard’ Cray XC50 going into the University of Bristol, and commitments from both Japan and France among others -- HPE is announcing that it will be supply the United States National Nuclear Security Administration (NNSA) with a 2.3 petaflops peak Arm-based system, named Astra. Read more…

By Tiffany Trader

The Machine Learning Hype Cycle and HPC

June 14, 2018

Like many other HPC professionals I’m following the hype cycle around machine learning/deep learning with interest. I subscribe to the view that we’re probably approaching the ‘peak of inflated expectation’ but not quite yet starting the descent into the ‘trough of disillusionment. This still raises the probability that... Read more…

By Dairsie Latimer

Xiaoxiang Zhu Receives the 2018 PRACE Ada Lovelace Award for HPC

June 13, 2018

Xiaoxiang Zhu, who works for the German Aerospace Center (DLR) and Technical University of Munich (TUM), was awarded the 2018 PRACE Ada Lovelace Award for HPC for her outstanding contributions in the field of high performance computing (HPC) in Europe. Read more…

By Elizabeth Leake

U.S Considering Launch of National Quantum Initiative

June 11, 2018

Sometime this month the U.S. House Science Committee will introduce legislation to launch a 10-year National Quantum Initiative, according to a recent report by Read more…

By John Russell

ORNL Summit Supercomputer Is Officially Here

June 8, 2018

Oak Ridge National Laboratory (ORNL) together with IBM and Nvidia celebrated the official unveiling of the Department of Energy (DOE) Summit supercomputer toda Read more…

By Tiffany Trader

Exascale USA – Continuing to Move Forward

June 6, 2018

The end of May 2018, saw several important events that continue to advance the Department of Energy’s (DOE) Exascale Computing Initiative (ECI) for the United Read more…

By Alex R. Larzelere

Exascale for the Rest of Us: Exaflops Systems Capable for Industry

June 6, 2018

Enterprise advanced scale computing – or HPC in the enterprise – is an entity unto itself, situated between (and with characteristics of) conventional enter Read more…

By Doug Black

MLPerf – Will New Machine Learning Benchmark Help Propel AI Forward?

May 2, 2018

Let the AI benchmarking wars begin. Today, a diverse group from academia and industry – Google, Baidu, Intel, AMD, Harvard, and Stanford among them – releas Read more…

By John Russell

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

ORNL Summit Supercomputer Is Officially Here

June 8, 2018

Oak Ridge National Laboratory (ORNL) together with IBM and Nvidia celebrated the official unveiling of the Department of Energy (DOE) Summit supercomputer toda Read more…

By Tiffany Trader

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

Hennessy & Patterson: A New Golden Age for Computer Architecture

April 17, 2018

On Monday June 4, 2018, 2017 A.M. Turing Award Winners John L. Hennessy and David A. Patterson will deliver the Turing Lecture at the 45th International Sympo Read more…

By Staff

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

Google I/O 2018: AI Everywhere; TPU 3.0 Delivers 100+ Petaflops but Requires Liquid Cooling

May 9, 2018

All things AI dominated discussion at yesterday’s opening of Google’s I/O 2018 developers meeting covering much of Google's near-term product roadmap. The e Read more…

By John Russell

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

Pattern Computer – Startup Claims Breakthrough in ‘Pattern Discovery’ Technology

May 23, 2018

If it weren’t for the heavy-hitter technology team behind start-up Pattern Computer, which emerged from stealth today in a live-streamed event from San Franci Read more…

By John Russell

HPE Wins $57 Million DoD Supercomputing Contract

February 20, 2018

Hewlett Packard Enterprise (HPE) today revealed details of its massive $57 million HPC contract with the U.S. Department of Defense (DoD). The deal calls for HP Read more…

By Tiffany Trader

Part One: Deep Dive into 2018 Trends in Life Sciences HPC

March 1, 2018

Life sciences is an interesting lens through which to see HPC. It is perhaps not an obvious choice, given life sciences’ relative newness as a heavy user of H Read more…

By John Russell

Intel Pledges First Commercial Nervana Product ‘Spring Crest’ in 2019

May 24, 2018

At its AI developer conference in San Francisco yesterday, Intel embraced a holistic approach to AI and showed off a broad AI portfolio that includes Xeon processors, Movidius technologies, FPGAs and Intel’s Nervana Neural Network Processors (NNPs), based on the technology it acquired in 2016. Read more…

By Tiffany Trader

Google Charts Two-Dimensional Quantum Course

April 26, 2018

Quantum error correction, essential for achieving universal fault-tolerant quantum computation, is one of the main challenges of the quantum computing field and it’s top of mind for Google’s John Martinis. At a presentation last week at the HPC User Forum in Tucson, Martinis, one of the world's foremost experts in quantum computing, emphasized... Read more…

By Tiffany Trader

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