TACC Highlights Its Upcoming ‘IsoBank’ Isotope Database

By Oliver Peckham

January 22, 2020

Isotopes – elemental variations that contain different numbers of neutrons – can help researchers unearth the past of an object, especially the few hundred isotopes that are known to be stable over time. However, isotope analysis can be expensive and time-consuming and researchers have lacked a central data repository, meaning that most isotopic research has been conducted independently, with the resulting data stored in silos. Now, in a new article, the Texas Advanced Computing Center (TACC) has offered a deep dive into the creation of IsoBank, a community isotope database funded by the National Science Foundation (NSF). 

“When people talk about the impact that technology has had on bioinformatics, they talk about genetic sequencing getting cheaper, but without the data becoming available through GenBank, the cost wouldn’t make much difference,” said Chris Jordan, manager for Data Management and Collections at the Texas Advanced Computing Center (TACC). “Unless you can compare your genome to all the other genomes that have been sequenced, you can’t make any sense of it. There is the potential here to do something similar with stable isotope data.”

Isotope sample collection in Argentina. Image courtesy of Pauli group, University of Wisconsin-Madison.

The IsoBank project began in 2017, when an NSF-funded workshop led to a team of researchers publishing an opinion piece outlining the need for a centralized repository of isotopic data. Just a year later, the NSF made a bigger contribution: a $1.5 million, three-year grant to that same research team, a collaboration spanning TACC, the University of Wisconsin-Madison, the University of New Mexico and the University of Utah. The objective of the grant: to develop a globally accessible archive of isotopic data and analysis tools for that data.

IsoBank faces a number of challenges, chiefly storing the isotopic data and organizing the metadata that needs to accompany each piece of sample data in order to make it useful to the broader community. TACC, which was selected as a partner based on its experiencing handling massive record collections, is focused on appropriately representing and storing that metadata.

“We’re isotope experts, but we’re not experts in designing, building, and curating such a large database like this,” said Jonathan Pauli, associate professor of forestry and wildlife ecology at the University of Wisconsin-Madison. “TACC is really central in providing the expertise for us to be able to build IsoBank the way it should be.”

The team hopes that IsoBank will help researchers use multiple datasets – even those produced to answer “very different questions” – in a cohesive and cross-compatible way. Seth Newsome, an animal ecologist at the University of New Mexico, suggested using IsoBank to combine isotope datasets and examine how isotopes of various organisms express differently in different areas or time periods. 

“There isn’t a field out there in natural science and medicine that’s not interested in isotopes,” Newsome said. “It’ll be cool to see this lead to collaborations of truly distant fields, like pharmacology and ecology, and biochemistry and archaeology.”

To read TACC’s Aaron Dubrow’s article on IsoBank, click here.

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!

Graphcore Introduces Next-Gen Intelligence Processing Unit for AI Workloads

July 15, 2020

British hardware designer Graphcore, which emerged from stealth in 2016 to launch its first-generation Intelligence Processing Unit (IPU), has announced its next-generation IPU platform: the IPU-Machine M2000. With the n Read more…

By Oliver Peckham

heFFTe: Scaling FFT for Exascale

July 15, 2020

Exascale computing aspires to provide breakthrough solutions addressing today’s most critical challenges in scientific discovery, energy assurance, economic competitiveness, and national security. This has been the mai Read more…

By Jack Dongarra and Stanimire Tomov

There’s No Storage Like ATGC: Breakthrough Helps to Store ‘The Wizard of Oz’ in DNA

July 15, 2020

Even as storage density reaches new heights, many researchers have their eyes set on a paradigm shift in high-density information storage: storing data in the four nucleotides (A, T, G and C) that constitute DNA, a metho Read more…

By Oliver Peckham

Get a Grip: Intel Neuromorphic Chip Used to Give Robotics Arm a Sense of Touch

July 15, 2020

Moving neuromorphic technology from the laboratory into practice has proven slow-going. This week, National University of Singapore researchers moved the needle forward demonstrating an event-driven, visual-tactile perce Read more…

By John Russell

What’s New in HPC Research: Volcanoes, Mobile Games, Proteins & More

July 14, 2020

In this bimonthly feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

By Oliver Peckham

AWS Solution Channel

INEOS TEAM UK Accelerates Boat Design for America’s Cup Using HPC on AWS

The America’s Cup Dream

The 36th America’s Cup race will be decided in Auckland, New Zealand in 2021. Like all the teams, INEOS TEAM UK will compete in a boat whose design will have followed guidelines set by race organizers to ensure the crew’s sailing skills are fully tested. Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and increase the vehicle’s speed and efficiency. These fluid dyn Read more…

By Oliver Peckham

Graphcore Introduces Next-Gen Intelligence Processing Unit for AI Workloads

July 15, 2020

British hardware designer Graphcore, which emerged from stealth in 2016 to launch its first-generation Intelligence Processing Unit (IPU), has announced its nex Read more…

By Oliver Peckham

heFFTe: Scaling FFT for Exascale

July 15, 2020

Exascale computing aspires to provide breakthrough solutions addressing today’s most critical challenges in scientific discovery, energy assurance, economic c Read more…

By Jack Dongarra and Stanimire Tomov

Get a Grip: Intel Neuromorphic Chip Used to Give Robotics Arm a Sense of Touch

July 15, 2020

Moving neuromorphic technology from the laboratory into practice has proven slow-going. This week, National University of Singapore researchers moved the needle Read more…

By John Russell

Max Planck Society Begins Installation of Liquid-Cooled Supercomputer from Lenovo

July 9, 2020

Lenovo announced today that it is supplying a new high performance computer to the Max Planck Society, one of Germany's premier research organizations. Comprise Read more…

By Tiffany Trader

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: Read more…

By John Russell

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

In this exclusive interview for HPCwire – sadly not face to face – Steve Conway, senior advisor for Hyperion Research, talks with Dr.-Ing Bastian Koller about the state of HPC and its collaboration with Industry in Europe. Koller is a familiar figure in HPC. He is the managing director at High Performance Computing Center Stuttgart (HLRS) and also serves... Read more…

By Steve Conway, Hyperion

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... 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

Leading Solution Providers

Contributors

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

$100B Plan Submitted for Massive Remake and Expansion of NSF

May 27, 2020

Legislation to reshape, expand - and rename - the National Science Foundation has been submitted in both the U.S. House and Senate. The proposal, which seems to Read more…

By John Russell

John Martinis Reportedly Leaves Google Quantum Effort

April 21, 2020

John Martinis, who led Google’s quantum computing effort since establishing its quantum hardware group in 2014, has left Google after being moved into an advi Read more…

By John Russell

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