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Microbial Genomics, Array Techs Highlight Genome Conference


HILTON HEAD, SC--Approximately 1,000 bioinformaticists and other scientists involved in genetic research are meeting here this week to attend the Ninth International Genome Sequencing and Analysis Conference, sponsored by the Institute for Genomic Research (TIGR) Science Education Foundation. The event is also attracting 55 exhibitors, including most of the major bioinformatics hardware, software, and services companies. Conference cochairmen are Andre Goffeau of the University of Louvain; Leroy Hood of the University of Washington; and Craig Venter, TIGR's president and director.

"The biggest refocusing in the agenda this year is the attention being paid to microbial genomics and related technologies," commented Mike Knapp, the foundation's vice-president of scientific education programs. "We've seen a significant increase in microbial work at TIGR, and also by the US government and the Wellcome Trust. The conference agenda is a reflection of trends that have emerged over the last 12-18 months."

"There will also be significant discussion on new array technologies, that's another trend," Knapp added. "People have talked about it awhile, but now it's finally being utilized." Microbial genomics is the topic of the conference's first plenary session, while arraying technology is the subject of the third. Other plenary sessions focus on eukaryotic genomes, genome biology, sequencing technology, and the human genome. There are also breakout sessions on informatics, genomics, and technology. In addition, 156 poster presentations given during three poster sessions will be an important part of the meeting. Many posters will be electronic, Knapp told BioInform, allowing presenters to demonstrate software such as viewers and analysis tools.

Knapp said the nature of the annual conference has been gradually changing over the years, reflecting the evolution of bioinformatics and genomic activity. "We're seeing somewhat of a shift," he confirmed. "It started as mainly an academic conference, but now it's one of the few places where industry and academia can get together in a scientific environment and throw ideas around, not so much in a marketing sense, but in a real scientific sense."

"The way it's been set up in years past, it's not something where people come and release new data," Knapp continued, "but it brings together the people who are shaping opinions and forcing technologies in different directions. For instance, Fred Blattner, who's publishing the E. coli data in Science this week, he'll be there. People know this is a meeting to come and discuss things. The general flavor of the conference is that everybody's there to share, that's one of the things that makes it really unique. It's very driven by science."

Knapp also acknowledged that the conference is experiencing growing pains as a result of its success. After explosive growth in 1996, attendance was capped at 1,000 this year. Exhibitors are also buying larger spaces, he said. The growth may ultimately force a change in venue, according to Knapp, who noted that after the first conference was held in Wolf Trap, Va., the last eight have been here.

Exhibitors' New Products

The success and stature of what has become widely known as the "Hilton Head conference" have made it a prime opportunity for companies in the bioinformatics marketplace to unveil new products and services. Among the new products that will be shown here this year are the following:

* Paracel (Pasadena, Calif.) is introducing GeneMatcher, a new class of scientific computer for bioinformatics applications that accelerates genetic analysis tasks by as much as 1,000 times over conventional hardware, according to the manufacturer. The result of a two-year engineering effort, GeneMatcher is designed with custom application-specific integrated circuit (ASIC) technology. The product will ship later this year.

GeneMatcher's unique performance characteristics start with the GeneMatcher chip, which has the complexity of over 2.2 million transistors (compared to 3.3 million transistors for an Intel Pentium chip), and is the first custom ASIC designed specifically for genomic analysis, according to Richard Diephuis, Paracel's vice-president of engineering. The GeneMatcher system combines 6,912 of the processors into one package, dramatically increasing the speed at which researchers can analyze genomic data, he contended. The system is a plug-and-play server that can be connected to any network. It comes equipped with Paracel's BioView Tool Kit software that offers users either a web-based or a Unix-command-line interface. Combined with Paracel's Fast Data Finder technology for text analysis, the GeneMatcher system architecture includes the capability for sequence annotation searching.

"With global genomic databases doubling in size every 10 months, high-throughput data analysis is a critical missing link for biotechnology and pharmaceutical companies involved in drug discovery," commented Kwang-I Yu, Paracel's CEO. Mark Adams, director of bioinformatics at the functional genomics company AlphaGene, observed, "The GeneMatcher system will allow AlphaGene to perform what-if bioinformatics scenarios without waiting. We perceive that GeneMatcher will offer us a competitive time-to-market advantage in delivering drug targets to our pharmaceutical partners."

* Molecular Applications Group (Palo Alto, Calif.) is previewing GeneMine Pro, the forthcoming upgrade of the company's flagship Look bioinformatics software. GeneMine Pro is about to be re leased in beta, according to Diane Richardson, MAG's Sales and Marketing Administrator. The software is a Unix-based product that automates the process of gathering data, integrates those data with the appropriate scientific tools, and allows bioinformaticists to communicate findings with others in the organization via hypertext. It offers a number of internet-technology features for sharing and retrieving data, including the ability to operate through a user's resident browser. GeneMine Pro runs on Silicon Graphics workstations.

Myra Williams, MAG's CEO, called GeneMine Pro "essentially an intelligent agent for bioinformatics. It can go out and understand all the vagaries of how information is stored and do that retrieval in an automated fashion, including analysis and validation of the results. There is a major need for intelligent agents that can be customized to the user's preference," she contended.

Stanley Kystek, senior research investigator for Bristol-Myers Squibb, has been alpha-testing GeneMine Pro and commented, "Where they're going is in handling massive amounts of data and in preprocessing the data. They clearly have a very good start in the new tool. Until this last tool they did not handle nucleotide data, so that's one big change over the last version; the last version was focused on protein structure, protein sequence information." GeneMine Pro will run on workstations running IRIX 5.3 or later.

* Oxford Molecular Group (Oxford, UK), along with its recently acquired subsidiary Genetics Computer Group (Madison, Wisc.) is unveiling the initial integration of two bioinformatics software tools originally offered separately by the companies: Oxford's OMIGA and GCG's Wisconsin Package. When the integrated technology is fully evolved into a commercial product, it will combine the ability to perform DNA and protein sequence analysis with easy access to central, shared database resources, through a Windows environment, on an enterprise-wide basis, according to Oxford. This will be achieved by marrying GCG's strengths in analyzing and searching central, shared data with Oxford's ability to deliver user-friendly desktop software that offers enterprise-wide access to powerful bioinformatics tools and a central database source, the company explained.

Oxford will also become the only company to support the four basic platforms for sequence analysis: Windows, Macintosh, Unix, and HTML, the company claimed. "This initial connection of OMIGA and GCG's system is only a start to providing research scientists with integrated tools for discovery research, and shows the strength of our recent acquisition of GCG," said Mark Cortelyou, bioinformatics business development manager. "This demonstration reinforces our commitment to evolve these proven tools into the future using our new CORBA/Java framework."

Also at the conference, Oxford will show MacVector, its Macintosh sequence analysis program, and OMIGA for Windows. In addition to the Wisconsin Package, GCG will show SeqWeb, its Netscape- and Microsoft Internet Explorer-compatible software, and SeqLab, its X-Windows-based interface.

* MDL Information Systems (San Leandro, Calif.) is announcing the availability of new platforms for the Molecular Informatics BioMerge system that it markets. Presently, BioMerge is available for Sun hardware using Sybase as the database system. Soon it will also be available for Oracle on the Sun platform and for both Oracle and Sybase on the Silicon Graphics platform. "One configuration will expand to four because our customers have chosen to buy different hardware and database systems," commented Dennis Smith, MDL's senior vice-president and chief scientist. MDL will also be demonstrating numerous web-based and pipeline tools for BioMerge that provide a base for automatic and end-user annotation, he added.

In addition, MDL will announce a tighter integration of the Bioinformatics Workbench from the University of Illinois at Urbana-Champaign, which MDL also distributes, with BioMerge, Smith continued. This will allow users to "do some of their similarity searching, for example, with BLAST, using the workbench as part of their end user analysis, and putting both results back into the database," he explained, concluding, "it's going to be a particularly exciting show for us."

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