HILTON HEAD, SC--Significant advances in array technologies that will greatly increase the amount of data requiring bioinformatic analysis; progress in microbial genomics research; and enhanced bioinformatics software packages offering internet-like interfaces were the among the topics and exhibits drawing crowds at the Ninth International Genome Sequencing and Analysis Conference here September 13-16. Attended by over 1,000 bioinformatics, genomics, and other genetic research professionals, the event also included 55 exhibitors, of whom 20 showcased bioinformatics products and services. Many also used the forum to make important new business announcements.
Sponsored by The Institute for Genomic Research (TIGR), the conference has become universally identified with its venue. However, it will be leaving its home of the past eight years in 1998, according to Mike Knapp, TIGR's vice-president of scientific education programs, because the current location can't accommodate the meeting's continual growth in terms of both attendees and exhibits. Next year's conference will be in Miami's Fontainebleau Hotel, a move welcomed by most of the exhibitors, although some long-time attendees worried that, with a new location and larger crowds, the event might lose some of its distinctive character.
"We're very concerned about losing the flavor of the conference," admitted Tony Kerlavage, director of TIGR's Department of Bioinformatics and of the TIGR database. "The hotel in Miami is very similar to this, but bigger." Kerlavage also commented on trends at this year's conference. "The quality of the science is fantastic," he told BioInform. "This year there was an increased presence by the commercial companies in the talks. The whole field has changed. Commercial organizations are now participating in research in software, equipment, and genomics. The field is growing both vertically and horizontally." Kerlavage also chaired the conference's breakout session on informatics.
The main focus of the conference--which was cochaired by Andre Goffeau of the University of Louvain; Leroy Hood of the University of Washington; and Craig Venter, TIGR's president and director--was the strong scientific agenda that included remarks by more than 60 researchers plus 156 poster presentations. However, many companies also used the meeting as a forum for major product and business announcements. Among the news from the conference was the following:
* ApoCom, Oak Ridge, Tenn., http://www.apocom.com, introduced ApoCom GRAIL Personal Edition bioinformatics software, which offers a PC-based platform for the company's original product. The personal edition is a Java-based application that runs on Windows operating systems and is billed as a desktop tool for DNA sequence analysis and gene localization. The interactive program features a batch tool that will run automated analyses of over 30,000 sequences. The commercial version of the US Department of Energy's GRAIL gene characterization software sells for $1,450 to commercial users and $950 to the academic community.
* Compugen, Petach Tikva, Israel, http://www.cgen.com, unveiled two new products: the BioXL sequence analysis system and MouseLEADS, a value-added database. BioXL is a scalable system that consists of both hardware and software modules, designed to accelerate the full range of similarity searches. Its GenCore sequence analysis software allows the construction of multistage search strategies. BioXL's user interface, GenWeb, is Java-based. Other components include a BioXL/P hidden Markov model accelerator, BioXL/G general purpose accelerator, and HMMsearch, a kit that includes GeneWise and other hidden-Markov-model-based algorithms. The system is configurable with two to 32 boards, offering 660-10,600 million matrix cell updates per second, depending upon configuration. It offers either a web or a Unix command-line interface.
MouseLEADS compiles mouse EST and mRNA public databases into a nonredundant, annotated database. Key features include clean data, low redundancy, longer sequences, alternative splicing, protein annotation, simple installation, and viewing through Compugen's proprietary GenWeb Java interface.
* Genetics Computer Group, Madison, Wisc., http://www.gcg.com, previewed its new SeqWeb product, which will be commercially available next spring. SeqWeb makes the bioinformatics software staple Wisconsin Package easier to use, the company claimed, by offering an HTML-based interface. It can be accessed through either Netscape or Internet Explorer. Among the Wisconsin Package programs available in the first release of SeqWeb are database searching, primer selection, protein analysis, mapping, sequence comparison, evolution, sequence translation, RNA secondary structure, and gene finding.
The company also unveiled Version 9.1 of the Wisconsin Package, which shipped September 18. Among the upgrades are new programs in protein analysis, evolutionary analysis, and database searching, as well as new documentation.
* Molecular Dynamics, Sunnyvale, Calif., http://www.mdyn.com, and Amersham Pharmacia Biotech, Uppsala, Sweden, had a joint exhibit reflecting their 1994 collaboration to develop instrumentation, software, and reagent products for genetic analysis. New this year is the MegaBACE 1000 DNA Sequencing System, a sequencer using capillary electrophoresis technology that was specifically designed for high-throughput DNA sequencing and mapping. It runs sequences three to seven times faster than conventional equipment, the companies said.
The device is optimized for data generation, Jay Flatley, Molecular Dynamics' president, told BioInform, with a database-oriented architecture designed to collect information. "It ties into bioinformatics because it produces so much data," he explained. The system comes with its own software, but can also be easily interfaced with other vendors' products, Flatley claimed, noting, "We don't want to lock people into anything restrictive." MegaBACE 1000 will become commercially available sometime next year.
* Molecular Simulations, San Diego, Calif., http://www.msi.com, released the PC version of its new WebLab Gene Explorer bioinformatics software that analyzes DNA and protein sequences and protein structures in a browser environment. A Macintosh version is scheduled for release November 15. Among the modules available with the new software are restriction analysis, DNA similarity search, protein similarity search, 3-D structure prediction, and virtual mutagenesis. 3-D visualization is provided by the free WebLab Viewer.
* Neomorphic Software, Berkeley, Calif., http://www.neomorphic.com, a software company that focuses on Java-based bioinformatics tools that don't require a high level of computer science expertise, previewed several products being developed for commercial release. Expression is the company's suite of Java tools that provides a library for the display of sequence data, annotations, and collaborative data. It can be customized for individual users. Labtrack, a sequence production and analysis system, provides support for high-throughput sequencing and annotation projects. It allows either bar-code or manual entry of laboratory reagents and processes. Sequences are automatically annotated and can be viewed using Expression. Genie is a gene identification system that uses a generalized hidden Markov model that models gene structure in DNA sequences by estimating transitions and state probabilities. It will soon be available for human and Drosophila genes, with training sets for other species available by special order.
* Pangea Systems, Oakland, Calif., http://www.pangeasystems.com, introduced GeneWorld 2.5, a sequence database application for high-throughput sequence annotation and analysis, and Gene Thesaurus 1.0, which Pangea called the first bioinformatics environment to integrate major sequence and annotation databases through a single point of access. Both products are open-platform, and they can be purchased either individually or bundled. They allow users to analyze and annotate new se quences automatically, then combine the enriched data with existing databases for cross-referencing and annotation-based analysis, according to Pangea.
Ralph Snodgrass, vice-president of research and chief scientific officer of the genomics company Progenitor, commented, "Our partnership with Pangea has given us the opportunity to beta-test GeneWorld 2.5. Though the earlier version has given us a lot of mileage, we're excited about the additional tools and workflow advantages that this new version affords." Joel Bellenson, Pangea's founder, added, "GeneWorld can be used to automatically analyze and annotate new sequences before the results are added and compared to the data residing in GeneThesaurus. Conversely, one can filter information using GeneThesaurus and create a database of sequences related to your work in GeneWorld."
* ThoughtWare, Arlington, Texas, is a new bioinformatics software company that was unveiled at the conference. ThoughtWare also announced its first product, Transition, a Smith-Waterman software tool that searches for se quence homology between a query sequence and a BLAST database, and also accelerates the computation of Smith-Waterman scores. Transition is built on the BLAST 1.4.9 source tree, according to the company, and as a result includes many BLAST features, such as full parallel execution on Unix servers; memory-mapped input/output; database screening based on BLAST word criteria; nucleic acid translation support; run methodology and output format; and source-code availability for customization purposes.
* Time Logic, Incline Village, Nev., http://www.timelogic.com, released its DeCypher II Sequence Similarity Search System high-performance enterprise server. The scalable, reconfigurable, accelerated bioinformatics computational system runs several existing bioinformatics algorithms plus Time Logic's proprietary Symmetric Frame Independent (SFI) algorithm. Upgrades to support new and improved algorithms are free. Standard DeCypher II configurations range from 480 million to 80 billion SW cells per second, or 50-100 times faster than standard equipment, the company claimed. The server integrates seamlessly with such basic bioinformatics software tools as Gene Explorer, GeneWorld, the Wisconsin Package, and GAIS, among others, and can easily be adapted to proprietary systems.
The first DeCypher II was delivered this month to Teijin Systems Technologies, a leading supplier of bioinformatics software in Japan. The company "selected DeCypher II because of its unique benefits, performance, and scalability," observed Toshiaki Murai, manager of the Lifescience Section of Teijin's Science Systems Department. "The configurable design delivers supercomputer speed, is simple to administer, and can be updated easily as advances in bioinformatics occur. That it can be extended with SFI and other new developments over time is a clear long-term benefit to our customers."
In addition to the news noted above, four other companies introduced new products at the conference that were described in detail in the September 15 BioInform. Those companies were:
* MDL Information Systems, San Leandro, Calif., http://www.mdli.com
* Molecular Applications Group, Palo Alto, Calif., http://www.mag.com
* Oxford Molecular Group, Oxford, UK, http://www.oxmol.com
* Paracel, Pasadena, Calif., http://www.paracel.com