SAN DIEGO--Bioinformaticists from around the world have gathered to discuss new genomics research technologies at two major professional meetings in the US this month. The fourth Pacific Symposium on Biocomputing drew 250 specialists to Hawaii January 4-9, and plant and animal genome researchers will attend a series of bioinformatics presentations January 17-21 at the seventh annual Plant and Animal Genome Conference here.
Agricultural genomes share technology
The plant and animal genomics event, considered the premier international meeting in the field of agricultural genomics, will feature a series of plenary sessions, more than 35 workshops and vendor presentations, and 537 poster sessions. Overall, 700 abstracts will be presented and 45 companies will exhibit to a crowd of at least 1,200 attendees, whom one cochair described as "a healthy mix of academics and industry scientists." Sponsors include four separate divisions of the US Department of Agriculture (USDA), six nonprofit organizations, and seven companies.
Max Rothschild, the US Pig Genome Project coordinator at Iowa State University and a conference cochair, observed that the technology used for genomics research is of equal interest to both plant and animal researchers. "DNA is DNA. And the numbers, the sequences, and challenges about how to handle the data are concerns that apply to both groups," he told BioInform.
Several bioinformatics workshops will be held during the week, including a session on databases, gene systematics, and nomenclature; a workshop on large insert DNA libraries and their applications; and a bioinformatics strategy workshop conducted by the International Rice Research Institute. Specific bioinformatics presentations include: "Internet Access to Analytical Tools and Molecular Data"; "Curatools: An Integrated Approach to Sequence Analysis"; "Bioinformatic Sequence Markup Language and BSML Browser for Communication and Interactive Visualization of Bioinformatic Data"; "Analysis, Display and Management of Large Datasets"; "New FlyBase Graphical Query and Browsing Tools for Accessing Genetic Data by Map and by Fly"; "Scriptable Access to the C. Elegans Genome Sequence and other ACEDB Databases"; "UK CropNet and CORBA"; and "Bioinformatics for Comparative Genomics in Farmed and Domestic Animals."
Michael Gale, a conference cochair from the UK's John Innes Center, told BioInform that he expected several technology topics to generate interest. "This year the big story will be single-nucleotide polymorphism analysis of one sort or another," he predicted.
"Daniel Cohen of Genset in Paris will be talking about linkage disequilibrium mapping work, where on a single chip you can map entire genomes," he added.
A presentation of a new laboratory-on-a-chip technology by Anthony de Mello of Imperial College in the UK will also be of interest, predicted Gale. "This is a fantastic miniaturization of our technology. De Mello can carry out 30 PCR reactions on something no bigger than a microscope slide," he explained.
Gale said the conference's policy for accepting presentations generates an agenda that includes some of the latest breaking research available in a field that changes rapidly. "One of the great things about this conference is there are no proceedings," Gale remarked. "There are only abstracts. Speakers don't have to agree to provide a chapter in order to present their research, so if you want to hear it you have to be there."
The fact that many separate genome projects have adopted this meeting as the venue for their annual workshops also contributes to its reputation for breaking the latest technology, Gale added.
Among the genomic topics that will be discussed at workshops here are: Arabidopsis, aquaculture, barley, cattle, cotton, Compositae, fluorescence, forest trees, horses, legumes, maize, poultry, rice, sheep, Solanaceae, sugar beets, sugar cane, and swine.
Proceedings are available at http://www.intl-pag.org.
Automated literature analysis gains attention
Organizers pronounced the Pacific Symposium on Biocomputing, held January 4-9, a success. They called the meeting, which grew 25 percent in attendance from last year, a leading forum for the publication and discussion of emerging issues in computational biology.
The meeting drew top researchers from the US, Asian-Pacific nations, and the rest of the world to exchange research results and address issues in all aspects of computational biology. Presentations included work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as it applied to biological problems.
Sessions addressed eight subject areas: gene expression and genetic networks; datamining and knowledge discovery in molecular databases; computer modeling in physiology: from cell to tissue; information theoretic approaches to biology; molecules to maps: tools for visualization and interaction; computer-aided drug design; protein structure prediction; and disorder in protein structure and function.
Larry Hunter, head of the International Society for Computational Biology, the event's sponsor, commented on some of the meeting highlights.
"David Haussler introduced a new sequence analysis method based on Fischer discriminators that he claimed was better than HMMs for discrimination tasks--quite a statement from the originator of biological HMMs," Hunter said.
He added, "A lot of the talk in the hallways concerned automated literature analysis systems." He predicted the meeting next year would feature a session on natural language processing for bioinformatics.
Hunter also observed what could be a sign that the profession is maturing: "The rush for new recruits seemed to be slowing a bit." Most companies that were looking to recruit new hires at this year's conference were young startups or new ventures, he said.
In addition to sponsorship by the society, the symposium also received support from the US Department of Energy and corporate sponsors including Amgen, Axys, Cisco, Compaq, Genome Therapeutics, Merck, Silicon Graphics, and Zymogenetics.
Proceedings of the meeting are available at http://www.cgl. ucsf.edu/psb/.