DATABASES OF GENETIC CODE ARE MOVING TO THE WEB

September 24, 1999

SCIENCE AND ENGINEERING NEWS

San Francisco. CA — As Lawrence M. Fisher reported for the New York TImes, Pangea Systems Inc. is a small company in “bioinformatics,” a new field that combines the two keystone technologies of the 1990s computing and biotechnology. But its products are expensive and difficult for mortals to use, which limits Pangea’s potential market and reduces the prospects for a public stock offering.

What to do? This being 1999, the answer, if you are Pangea, is to dot-com yourself.

Pangea, which is based in Oakland, Calif., intends to begin a shakedown test of DoubleTwist.com, a new Web site intended to make online genetic and biological research fast, easy and available to any amateur or professional biologist. While the test phase is available only to faculty and students at Stanford University, the site is scheduled to go live for general use in December.

The DoubleTwist site, whose name is a play on the double-helix structure of DNA, holds the near-term promise of lifting Pangea above the pack of competitors chasing the business opportunities in bioinformatics. But other companies may not be far behind. And the implications go beyond the interests of professional biologists and biotechnology executives.

As more of the arcane secrets of genetics and molecular biology become available to the modemed masses, some industry executives foresee the day when an educated consumer might take a CD-ROM containing a laboratory’s rendering of his or her genetic profile, and combine it with a Web surf through gene libraries to determine the person’s predisposition toward adverse drug reactions, for example, or for Alzheimer’s disease, colon cancer or other afflictions that might eventually be treatable through gene therapy.

To promote its name and capabilities, Pangea plans to let individuals who make only casual use of the site have access to its software and data base at no charge. Heavy users and corporations may obtain licenses to pay for access on a sliding fee scale, which could run tens of thousands of dollars a year, but would still be significantly less than the $500,000 or more that Pangea now charges big pharmaceutical companies to buy its software outright.

“The power of bioinformatics has been somewhat limited to those who could afford it,” said John Couch, Pangea’s president and chief executive, who was an executive at Apple Computer in the late 1970s and early 1980s. “I’ve been trying to figure out how to empower the scientist the way we did computer users at Apple in the early days,” Couch said. “We saw the opportunity to be the first Web portal that enabled scientists to do molecular research.”

Celera Genomics Group is another company that has said it will offer its bioinformatics tools from its Web site, although it has not specified a launch date.

“This is an Internet company,” said Craig Venter, president and chief executive of Celera, a unit of the PE Corp., which is based in Rockville, Md. Scientists and nonscientists alike, he said, will be able to use Celera’s tools to gain insights into their genetic makeup. And as catalogs of common mutations correlated with disease become broadly available, he said, individuals will be able to make appropriate lifestyle changes or health-care decisions. “You’ll be able to log on to our data base and get information about yourself,” Venter said. “Our ultimate customer on the Internet is individuals.”

Bioinformatics is a field that emerged from the Human Genome Project, the international quest, which began in 1988 and is expected to be concluded in the next two years, to spell out the precise sequence of the three billion letters in the human genetic code. The first industry spawned by the genome project was genomics companies, which sell data bases of individual genes whose sequences have already been identified or are developing drugs aimed at gene targets. As these efforts began to produce vast amounts of biological information, they needed powerful software to keep track and make sense of it all. And so, in the early 1990s, bioinformatics was born as a tool of genomics.

While the software created by the government-funded labs like the Whitehead Institute at the Massachusetts Institute of Technology is in the public domain, with intriguing names like Blast and Fasta, the genomics companies, like Human Genome Sciences Inc. and Incyte Pharmaceuticals Inc., have kept their tools for use by themselves or their licensed partners. That is Celera’s primary business as well, despite Venter’s intent to offer bioinformatics services on the Web.

It was not long before a few entrepreneurs and venture capitalists saw an opportunity in a pure-play bioinformatics company, which would sell not genes or data, but software. As private companies, none of the bioinformatics players publish revenue figures, but most say they are between $5 million and $10 million in annual sales, and growing. Indeed, some analysts predict a multibillion-dollar bioinformatics market within the next 10 years.

“Bioinformatics is not necessarily the next wave, but the glue that holds everything together,” said Tim Wilson, an analyst with S.G. Cowen. “If you don’t get that part right, it’s hard to realize the value of genomics,” he said. “The opportunity is something obvious to anyone who speaks to pharmaceutical companies.”

With the DoubleTwist site, according to Pangea, a researcher would have many of the same capabilities previously available only to the company’s big corporate customers, which include drug companies like Bristol-Myers Squibb and Hoechst Marion Roussel.

After logging on to the DoubleTwist site, a visitor could enter a partial sequence of a gene, some combination of the letters A, C, T and G, which make up the genetic alphabet, and then search for contiguous sequences that might lead to a full-length gene. Or if the code of a full-length gene were known, the researcher could ask in which tissues of the body that gene is found or found only when in the presence of cancer. To the extent the answer is available in the scientific literature, including patent filings, the software would retrieve it and highlight relevant passages. Other cross-referenced data might include notations on what biochemical materials are required for working with a given gene in the laboratory.

Such are the capabilities of the computational biology that underlies bioinformatics, a field that Francis Collins, director of the Human Genome Project for the National Institutes of Health, says he now often counsels promising graduate students to look to for career opportunities. “I just think it is going to hit us like a freight train and we really have too small a supply of expertise in that area,” he said.

But there has been a dichotomy between the opportunity and the market reality for Pangea and competitors like Netgenics Inc. of Cleveland; Informax Inc. of Rockville, Md.; Lion Bioscience AG of Heidelberg, Germany; Compugen Ltd. of Tel Aviv; the Genomica Corp. of Boulder, Colo.; and Molecular Applications Group of Palo Alto, Calif. Most of these companies are five years old or more, yet few are profitable.

Couch, Pangea’s president, said the two hurdles to expanding the market have been complexity and cost. Besides the $500,000 price for Pangea’s suite of software programs, a suite customer must make a comparable investment in hardware. And even though they have a point-and-click graphical user interface, like any Windows application, their sophistication has tended to restrict their use to bioinformatics specialists within large pharmaceutical or biotechnology companies, not to individual research scientists without special training.

In moving to the Web, Pangea will find neighbors with some similar-sounding offerings. This week, HySeq Inc., a genomics company in Sunnyvale, Calif., will launch GeneSolutions.com, which will sell genes and genetic information over the Web. And there are various Web sites, for example, that freely offer public-domain algorithms, or mathematical formulas, that can perform the basic tasks of bioinformatics. These include a technique called clustering and alignment, which pieces together full-length genes from the fragments spewed out by so-called automated sequencing machines that derive their data from DNA samples.

But these public-domain tools tend to be difficult to use, and limited in their application to specific gene data bases. Pangea’s DoubleTwist, by contrast, will aggregate data from multiple sources, and then make it available using software agents, small automated software programs that will scan the Web at a user’s request and return answers to complex biological queries via e-mail. Theses agents can update information as it becomes available, suggest necessary laboratory supplies and provide links to vendors.

DoubleTwist is intended to complement rather than supplant Pangea’s established software suites. But Couch said it was possible that a growing portion of the company’s revenues would come from the Web rather than packaged programs. Rather than buy Pangea’s software suite for $500,000, companies or academic institutions could spend $10,000 a year to provide each user access to these programs over the Web.

Pangea’s competition in this arena is companies very much like itself: small, financed with venture capital and possessing more programming prowess than marketing skills.

All of these companies are looking for ways to differentiate themselves, and while an Internet presence is one way to do that, it is by no means the only one.

For example, Netgenics’ programs run on corporate intranets, rather than the World Wide Web. But they are built using Internet technology like the Java programming language so that they can be easily adapted to the specific needs of different customers. “Pangea decided they would come up with the perfect schema for all types of drug discovery and put a nice graphic user interface on it,” said Manuel J. Glynias, president and chief executive of Netgenics, which was founded in 1996. “We decided there was no perfect schema because every pharmaceutical company is different.”

Netgenics did consider a Web-based electronic commerce business model, but decided a faster route to growth was to bundle consulting services with custom bioinformatics software. So far, customers include Abbott Laboratories and Pfizer. “We’ve very much targeted big pharma and biotech,” Glynias said. “They’re the only ones who can afford it, and really the only ones it makes sense for. At the end of the day you’ve got 50 big pharma and biotech companies and 100 medium-sized ones. It’s not a big market.”

If the market is small, creating a big company requires that each sale be large, and Netgenics bases its goals on finding at least 20 customers willing to pay $5 million annually for its services.

Another player, Lion Bioscience, takes that model a step further. It recently announced a deal in which it would develop new bioinformatics systems and identify target genes for drug development by Bayer A.G. for an investment estimated at $100 million. The figure includes an up-front equity stake in Lion as well as fees for use of Lion’s existing information systems, research and set-up costs for a new subsidiary to be based in Cambridge, Mass., and royalties on drugs developed from the gene targets identified at the subsidiary.

Lion calls its concept iBiology, and like Netgenics’ approach, it uses intranets rather than the Internet. “It goes far beyond the usual gene sequence analysis software,” said Claus Kermoser, Lion’s vice president for corporate development. “We crawl further up the value chain to include the chemical side, and also pharmacological and toxicology data. It’s not just a software package, tools and data; it’s a solution for pharmaceuticals research data management.”

In fact, Lion is actually a hybrid of pure-play bioinformatics and genomics, because it sells gene targets along with information-processing capabilities. Similarly, Compugen, after building a successful business selling bioinformatics tools, has recently added a genomics thrust, selling novel gene variants the Compugen researchers have identified with the company’s tools.

Compared with these other companies, which have aimed for a corporate clientele, Informax has taken a vastly different tack. For six years it has sold a program for individual scientists, Vector NTI, which is almost to biology what desktop publishing software was to print publications. At $3,500 a user, for the Windows or Macintosh versions, Vector NTI is not inexpensive. But because it is a purchase that typically can be authorized at the department level, it is the most widely used bioinformatics program in the industry. It is used at 60 pharmaceuticals companies, 250 biotechnology concerns and 500 academic institutions.

“We’ve built our franchise by meeting the needs of the bench biologist,” said Timothy Sullivan, Informax’s senior vice president for marketing and sales. “Informax took a bottom-up approach and did it well, versus Pangea and Netgenics, who started out at the enterprise level,” he said. Informax recently introduced its own enterprise product, Software Solution for Bioscience, and hopes to use the leverage of its existing customer base to win sales at large companies.

One hurdle for all of these competitors is that the large companies that are their obvious customers often have substantial bioinformatics capabilities of their own — expertise that the company may even view as a proprietary advantage.

“You’re trying to do cutting-edge research, and if you’re on the leading edge of the curve that means you also have to develop the software to do it,” said Paul Godowski, director of molecular biology at Genentech Inc., the pioneering biotech company. “On the other hand, there are products out there from these third-party vendors we can import for our programs,” Godowski. “It’s a mixture, and I don’t see that going away, certainly not at a place like Genentech.”

No wonder Pangea is looking to cyberspace to expand its potential audience.

“Only a few select pharmas can afford the tools, and if they can, then in some cases they can also afford to produce their own software,” Couch said. “Why not take the infrastructure we’ve created, add a graphic interface that makes it easier, and offer it directly to the scientist? We are taking the Internet, which was originally developed to do research, and giving it back to the researchers.”

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

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