IT FIRMS COMPETE TO COMPUTE THE GENOME

December 1, 2000

COMMERCIAL NEWS

Hinxton, ENGLAND — Ben Hirschler reports that the gene machines at the Sanger Centre near Cambridge, responsible for mapping a third of the human genome, are still whirring night and day. Never mind that a working draft of the 3.1 billion letters in the “book of life” was completed on June 26. That is just the start of a coming tidal wave of genetic information.

Managing and interpreting the trillions of bits of data, or terabytes, generated by the genomics revolution is now the biggest task facing biologists – and a major business opportunity for computer companies.

“Informatics is going to be the key challenge in the future,” said Richard Durbin, Sanger deputy head and the man in charge of making the number-crunching work.

Sequencing the repeats of the four letters, A, C, T and G, representing the nucleotides that make up DNA in humans and other species, has already piled up more than 22 terabytes of data on the Sanger Centre’s hard disk drives. That is equivalent to more than twice the entire contents of the U.S. Library of Congress.

Durbin expects it to rise to 50-100 terabytes within two or three years as researchers investigate how the three-billion-piece “parts list” embedded in our chromosomes determines the way we develop, age and fall victim to disease.

Both hardware and software companies are queuing to service this exploding market, which is providing business opportunities well beyond academic institutions like the Sanger Centre, which is backed by the Wellcome Trust medical charity.

Biotechnology, pharmaceutical and agrochemical companies share the same requirement for supercomputing power, data storage and specialized software programs as they strive to apply genomic discoveries to new products.

That makes life science an increasingly enticing prospect for information technology (IT) companies – especially when sales of computers to other businesses are showing signs of slowing down.

International Business Machines Corp estimates the IT market for life sciences will surge from $3.5 billion this year to more than $9 billion by 2003, as the volume of life science data doubles every six months.

“Big Blue” is designing products specifically for this new market, including a $100 million investment in a supercomputer known as “Blue Gene,” designed to simulate protein folding.

Calculating the way a single human protein folds – a key determinant in its interaction with other molecules – is a deceptively simple task.

But the possible permutations are so vast that it will take the monster computer a year to do the calculation, even though it will be 1,000 times more powerful than “Deep Blue,” the IBM machine that beat world chess champion Gary Kasparov in 1997.

Other computer firms have also woken up to the potential of the market unleashed by the genome.

IBM’s arch-rival Compaq Computer Corp, the world’s biggest personal computer maker, is already a big supplier of servers to the life science sector – including the Sanger Centre.

In a bid to cultivate a new generation of clients, Compaq plans to invest $100 million in start-up biotech companies.

Martin Walker, head of high performance computing for Compaq in Europe, sees a huge opportunity in this field for his firm’s top-of-the-range servers, which sell at substantially higher margins than PCs.

Close to 10 percent of the aggregate research and development budget of the world’s 12 biggest life science companies is already being spent on IT, and the figure is set to rise exponentially, he predicts. “Biology is going to become the dominant application in all of computational science,” Walker told Reuters.

Alongside the computer industry’s big guns are a growing number of specialist bioinformatics companies, springing up to service the booming market with customized software.

They include Germany’s Lion Bioscience AG whose SRS, or Sequence Retrieval System, is starting to establish itself as a new industry standard. Shares in Lion have surged 50 percent since their August debut.

“It’s incredible how fast data is being put out in the public domain alone, and on top of that companies have proprietary databases which are also producing an incredible amount of data each day,” said Jan Mous, Lion’s chief scientific officer.

“The big challenge is to speed up analysis of that data so that you don’t have to wait half an hour to get the result back from a query.”

Other bioinformatics boutiques include U.S. firms Doubletwist, Genomica, Synomics and Inpharmatica, while integrated genomics companies like Incyte Genomics, Celera Genomics and Genaissance all offer differing levels of capability in the field.

============================================================

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!

Mira Supercomputer Enables Cancer Research Breakthrough

November 11, 2019

Dynamic partial-wave spectroscopic (PWS) microscopy allows researchers to observe intracellular structures as small as 20 nanometers – smaller than those visible by optical microscopes – in three dimensions at a mill Read more…

By Staff report

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quantum annealing) – ion trap technology is edging into the QC Read more…

By John Russell

Tackling HPC’s Memory and I/O Bottlenecks with On-Node, Non-Volatile RAM

November 8, 2019

On-node, non-volatile memory (NVRAM) is a game-changing technology that can remove many I/O and memory bottlenecks and provide a key enabler for exascale. That’s the conclusion drawn by the scientists and researcher Read more…

By Jan Rowell

What’s New in HPC Research: Cosmic Magnetism, Cryptanalysis, Car Navigation & More

November 8, 2019

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

Machine Learning Fuels a Booming HPC Market

November 7, 2019

Enterprise infrastructure investments for training machine learning models have grown more than 50 percent annually over the past two years, and are expected to shortly surpass $10 billion, according to a new market fore Read more…

By George Leopold

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

IBM Accelerated Insights

Atom by Atom, Supercomputers Shed Light on Alloys

November 7, 2019

Alloys are at the heart of human civilization, but developing alloys in the Information Age is much different than it was in the Bronze Age. Trial-by-error smelting has given way to the use of high-performance computing Read more…

By Oliver Peckham

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quant Read more…

By John Russell

Tackling HPC’s Memory and I/O Bottlenecks with On-Node, Non-Volatile RAM

November 8, 2019

On-node, non-volatile memory (NVRAM) is a game-changing technology that can remove many I/O and memory bottlenecks and provide a key enabler for exascale. Th Read more…

By Jan Rowell

MLPerf Releases First Inference Benchmark Results; Nvidia Touts its Showing

November 6, 2019

MLPerf.org, the young AI-benchmarking consortium, today issued the first round of results for its inference test suite. Among organizations with submissions wer Read more…

By John Russell

Azure Cloud First with AMD Epyc Rome Processors

November 6, 2019

At Ignite 2019 this week, Microsoft's Azure cloud team and AMD announced an expansion of their partnership that began in 2017 when Azure debuted Epyc-backed ins Read more…

By Tiffany Trader

Nvidia Launches Credit Card-Sized 21 TOPS Jetson System for Edge Devices

November 6, 2019

Nvidia has launched a new addition to its Jetson product line: a credit card-sized (70x45mm) form factor delivering up to 21 trillion operations/second (TOPS) o Read more…

By Doug Black

In Memoriam: Steve Tuecke, Globus Co-founder

November 4, 2019

HPCwire is deeply saddened to report that Steve Tuecke, longtime scientist at Argonne National Lab and University of Chicago, has passed away at age 52. Tuecke Read more…

By Tiffany Trader

Spending Spree: Hyperscalers Bought $57B of IT in 2018, $10B+ by Google – But Is Cloud on Horizon?

October 31, 2019

Hyperscalers are the masters of the IT universe, gravitational centers of increasing pull in the emerging age of data-driven compute and AI.  In the high-stake Read more…

By Doug Black

Cray Debuts ClusterStor E1000 Finishing Remake of Portfolio for ‘Exascale Era’

October 30, 2019

Cray, now owned by HPE, today introduced the ClusterStor E1000 storage platform, which leverages Cray software and mixes hard disk drives (HDD) and flash memory Read more…

By John Russell

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a Read more…

By John Russell

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated mo Read more…

By John Russell

Rise of NIH’s Biowulf Mirrors the Rise of Computational Biology

July 29, 2019

The story of NIH’s supercomputer Biowulf is fascinating, important, and in many ways representative of the transformation of life sciences and biomedical res Read more…

By John Russell

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

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