Issue #38
Last Update April 18, 2005
Technology Bioinformatics by David Katz Over the past 20 years, the distinctions between formerly distinct scientific and technological disciplines have been breaking down, to the benefit of the scientists involved and the world. Reversing the trend to narrower and narrower specialization that was prevalent for most of the 19th and 20th century, scientists from diverse fields are talking to each other and discovering that seemingly intractable problems in one field were long ago solved in another.
Biology was one of the last sciences to benefit from this trend. Long intertwined with chemistry, biology lately has formed profitable alliances with physics and, most recently, computer science. Known variously as computational biology and bioinformatics, this new field is making an impact in areas as diverse as drug discovery, genomics, evolutionary biology and cladistics.
At a conference on bioinformatics in San Diego this month, sponsored by O'Reilly, a leading publisher of computer books and other technical publications, recent developments in the field were shared with colleagues. As might be expected, the sessions and tutorials were divided between biological techniques and concerns and computer techniques and concerns.
The thrust of all of these sessions, however, was making sense of the floods of data that are being generated by new techniques for teasing out the detailed composition and structure of genes and proteins. The objective in all of this is twofold: understanding how the structure and composition of these molecules define their function, and understanding their origins and evolutionary development.
Three sets of tools have been developed to deal with this: public and private databases to store the molecular information; pattern recognition software to parse the data in these databases and match similar structures from different sources; and graphical tools to display molecular relationships in two or three dimensions. The major effort taking place today is the creation of software that will the allow use of proprietary information in conjunction with existing databases, and that will allow scripting as part of the database handling tools; that is, the ability to extend the utility of database information by being able to append Perl, Python, C or other computer language extensions to the database programs. In parallel with these developments is the drive to agree on data representation standards so that information from multiple databases can be used together.
At this point the tension between the desire for openness to allow science to happen freely and efficiently, and the desire to maintain proprietary techniques and data to protect potential profits (especially in the pharmaceutical area) is unresolved. How this tension is resolved will be an important determinant of the rate of scientific progress in this vital and promising field.
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New York Stringer is published by NYStringer.com. For all communications, contact David Katz, Editor and Publisher, at david@nystringer.com
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