SUPERCOMPUTERS TRACK HUMAN GENOME

September 1, 2000

FEATURES & COMMENTARY

Pasadena, CA — Andrew Pollack reports that Kwang-I Yu, president of Paracel Inc., will not say which secretive government agency buys his company’s specialized supercomputers. “We sell to the federal government,” he demurs.

But J. Craig Venter, the president of Celera Genomics, is less circumspect. Paracel’s machines, he said, are used by the National Security Agency, the code-breaking unit that eavesdrops on other nations. And Dr. Venter should know. Celera Genomics, the company that mapped the human genome, acquired Paracel for nearly $250 million in stock in June.

Paracel’s machines are designed to sift documents rapidly for particular words, phrases or strings of letters – an ability of obvious use to those filtering communications for important nuggets.

But what attracted Celera is that Paracel’s technology is also good for breaking another code – the genetic one. The machines are being snapped up to sift the blizzard of data being generated by the Human Genome Project and various private genomics efforts. “They’re all character strings,” said Dr. Yu, comparing the gene sequence to a text message.

The need for Paracel’s machines stems from biology’s shift from a “wet” science performed in test tubes to at least partly a “dry” one, in which much of the crucial analysis is done on computers. This has given rise to a field called bioinformatics, the use of computer science in life science.

And bioinformatics must handle volumes of data so huge they could bring ordinary computers to their knees. The human genome is comprised of three billion chemical units represented by the letters A, C, T, and G – a string that would stretch from Boston to London if written in letters of the size in this article. A scientist studying a particular sequence of DNA might search through the entire human genome, as well as those of other animals and bacteria, to find similar sequences. And genomics companies might want to do thousands of such searches a day.

“There’s a class of algorithms that would take forever on a regular computer,” said Edward Kiruluta, vice president for research and development at DoubleTwist, a bioinformatics company in Oakland, Calif. Even with its Paracel machine, he said, some analyses take weeks. On regular computers, they would take months. And speed is of the essence, especially in analyzing data from the publicly financed Human Genome Project, which makes new sequences available each day to everyone at the same time.

“As the genome data comes out, you want to analyze it as fast as you can, make the discoveries first and protect the intellectual property,” said Martin D. Leach, director for bioinformatics at CuraGen, which uses genomics to develop drugs.

Computers, of course, are doubling in speed for a given cost every 18 months or so, according to Moore’s Law, named after Intel’s co-founder, Gordon Moore. But the volume of genomic data is growing even faster, owing to automated DNA-sequencing machines. GenBank, the government-run public domain database of DNA sequences, more than doubled in size the last six months to more than 8.6 billion chemical units.

I.B.M. estimates that the market for hardware and software for life sciences will grow from $3.5 billion now to more than $9 billion by 2002. Carolyn Kovac, who heads a newly formed life sciences division at I.B.M., said biologists had replaced physicists as the main scientific users of supercomputers.

Sun Microsystems and Compaq Computer are also trying to develop products for the life sciences, with either supercomputers or servers linked together in big clusters. And start-ups like Parabon Computation of Fairfax, Va., and Entropia of San Diego, are trying to harness tens of thousands of home and business computers to work on genomics when they would otherwise be idle by distributing portions of the tasks to these computers over the Internet.

Paracel’s GeneMatcher machine, however, is especially built for genomic searchers. It has 7,000 processors arranged in a way best suited to matching character strings. Dr. Yu likened the process to having each letter of the sequence being studied in a separate processor strung along the inside of a hose. The database to be searched flows over these letters like water through a hose, at the rate of 30 million characters a second, and each processor sees whether it has a match as each letter flows by.

With a list price of $360,000, GeneMatcher would be too much for general-purpose computing. But for the task for which it was designed, it can be up to 1,000 times as fast as a Pentium-based computer, making it cost-effective, Dr. Yu said.

The market for machines like GeneMatcher, which are called genomics accelerators, is tiny. Paracel sells only one or two a month, so few in fact that it assembles its machines by hand in one room of a high-rise office here.

It says it has more than 30 customers, including drug companies like Novartis, Bayer and AstraZeneca, as well as some biotechnology and bioinformatics companies. No customer has more than two machines, other than Celera, which bought four last year.

But sales are growing. Paracel, which was privately held before its acquisition by Celera, had sales of $14.2 million in 1999, up from $5.9 million the year before. Dr. Yu said Paracel was not profitable because of investments but had been in the past.

GeneMatcher accounted for $5.2 million of Paracel’s 1999 sales, and genomics software $1 million. Textfinder machines, used by the government agency and a few other customers to search text databases, accounted for $8 million.

Paracel’s main competitor, TimeLogic, based in Incline Village, Nev., had sales of $3 million in 1999 and was profitable, according to its chief executive, James W. Lindelien. Sales of its DeCypher accelerator rose 350 percent in 1999 and should rise 50 percent this year, he said.

Compugen, an Israeli company that just went public, also sells an accelerator but is de-emphasizing that business.

Some experts think that conventional server farms can do the job less expensively than genomics accelerators can and can also be used for other tasks. The National Center for Biotechnology Information, which runs GenBank, uses about 140 conventional computers that are tied together. It is possible, said one expert, to define the problem so that you don’t have to compare everything with everything else in the entire database.

Indeed, history is not on the side of dedicated hardware. Machines designed for artificial intelligence, computer-aided design, database storage and graphics were all eventually replaced by general-purpose computers, which became fast enough to handle those jobs and cost less because of their huge production volumes. The large sales volumes of general-purpose computers also generate more money for research and development at the companies that produce them, allowing them to improve their machines faster than companies that design specialized computers.

Paracel’s acquisition by Celera will give the company more financial resources to help it keep up. But some experts were shocked that Celera would spend so much money for such a tiny, niche company.

But Dr. Venter of Celera said the Paracel machines would be important. “There’s no university or pharmaceutical company that has the compute capability they need to deal with our data or anyone else’s genomic data,” he said.

Celera must persuade companies to pay for its genomic data when GenBank offers much of the same human genome data free. One way to compete is to offer more and better data. But another, Dr. Venter said, is to use the Paracel machines to offer Celera customers faster searches than they could get using GenBank.

Paracel technology can also be used to compare the sequence of amino acids that make up a protein and could become part of a protein analysis machine that is being designed by Applied Biosystems, Celera’s sister company. Both Celera and Applied Bio, formerly known as PE Biosystems, are subsidiaries of the PE Corporation. Celera has one of the largest computer centers in the world, costing more than $50 million, and made up mainly of Compaq servers. By May, Celera had bought only $1.9 million of Paracel machines. But Dr. Venter said that while the Compaq machines were used to assemble the genome sequence in the correct order, the Paracel machines would be used to search the database.

PE and Paracel have long been partners. In 1996 PE bought a 14 percent stake in Paracel for $4.5 million. Dr. Yu himself owned about 17 percent of Paracel, giving him Celera stock worth about $35 million when the the acquisition closed in June.

Dr. Yu, 50, grew up in Hong Kong, Taiwan and Malaysia and came to the United States for college. After earning his doctorate in computer science from the California Institute of Technology, he joined TRW, the defense contractor, where he worked on development of the text-searching chip. In 1992 TRW spun out Paracel to commercialize the technology and before the buyout held 13 percent of the company.

The acquisition by Celera will benefit Paracel, but it could also cause genomics companies that compete with Celera to avoid buying from Paracel. TimeLogic is already playing up this factor in its sales pitch. And to counter Paracel’s alliance with Celera, TimeLogic is expected to announce soon that its machines will be distributed by Sun Microsystems.

Dr. Yu said he did not think customers would desert Paracel. And Paracel will obtain information from Celera that could help it design better machines.

“I really want to be part of something that’s the definitive provider of tools to mine that information,” he said. “I can get there faster by merging with Celera.”

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

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!

At SC19: What Is UrgentHPC and Why Is It Needed?

November 14, 2019

The UrgentHPC workshop, taking place Sunday (Nov. 17) at SC19, is focused on using HPC and real-time data for urgent decision making in response to disasters such as wildfires, flooding, health emergencies, and accidents. We chat with organizer Nick Brown, research fellow at EPCC, University of Edinburgh, to learn more. Read more…

By Tiffany Trader

China’s Tencent Server Design Will Use AMD Rome

November 13, 2019

Tencent, the Chinese cloud giant, said it would use AMD’s newest Epyc processor in its internally-designed server. The design win adds further momentum to AMD’s bid to erode rival Intel Corp.’s dominance of the glo Read more…

By George Leopold

NCSA Industry Conference Recap – Part 1

November 13, 2019

Industry Program Director Brendan McGinty welcomed guests to the annual National Center for Supercomputing Applications (NCSA) Industry Conference, October 8-10, on the University of Illinois campus in Urbana (UIUC). One hundred seventy from 40 organizations attended the invitation-only, two-day event. Read more…

By Elizabeth Leake, STEM-Trek

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing components with Intel Xeon, AMD Epyc, IBM Power, and Arm server ch Read more…

By Tiffany Trader

Intel AI Summit: New ‘Keem Bay’ Edge VPU, AI Product Roadmap

November 12, 2019

At its AI Summit today in San Francisco, Intel touted a raft of AI training and inference hardware for deployments ranging from cloud to edge and designed to support organizations at various points of their AI journeys. The company revealed its Movidius Myriad Vision Processing Unit (VPU)... Read more…

By Doug Black

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

Help HPC Work Smarter and Accelerate Time to Insight

 

[Attend the IBM LSF & HPC User Group Meeting at SC19 in Denver on November 19]

To recklessly misquote Jane Austen, it is a truth, universally acknowledged, that a company in possession of a highly complex problem must be in want of a massive technical computing cluster. Read more…

SIA Recognizes Robert Dennard with 2019 Noyce Award

November 12, 2019

If you don’t know what Dennard Scaling is, the chances are strong you don’t labor in electronics. Robert Dennard, longtime IBM researcher, inventor of the DRAM and the fellow for whom Dennard Scaling was named, is th Read more…

By John Russell

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

Intel AI Summit: New ‘Keem Bay’ Edge VPU, AI Product Roadmap

November 12, 2019

At its AI Summit today in San Francisco, Intel touted a raft of AI training and inference hardware for deployments ranging from cloud to edge and designed to support organizations at various points of their AI journeys. The company revealed its Movidius Myriad Vision Processing Unit (VPU)... Read more…

By Doug Black

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. That’s the conclusion drawn by the scientists and researchers of Europe’s NEXTGenIO project, an initiative funded by the European Commission’s Horizon 2020 program to explore this new... 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 instances for storage workloads. The fourth-generation Azure D-series and E-series virtual machines previewed at the Rome launch in August are now generally available. 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

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

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

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

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

Cerebras to Supply DOE with Wafer-Scale AI Supercomputing Technology

September 17, 2019

Cerebras Systems, which debuted its wafer-scale AI silicon at Hot Chips last month, has entered into a multi-year partnership with Argonne National Laboratory and Lawrence Livermore National Laboratory as part of a larger collaboration with the U.S. Department of Energy... 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