Sebastopol, CA--Bioinformatics is the rapidly evolving discipline of using computational tools and techniques to find answers to biological questions. With the advent of the Internet and World Wide Web, biologists have access to vast amounts of biological data contained in public databases such as GenBank (the Genetic Sequence Data Bank) and the Protein Data Bank. As a consequence, computer-based tools now play a critical role in biological research. Because of its capacity for detecting patterns in data, Perl has become one of the most popular programming languages for biological data analysis. In his new book, Beginning Perl for Bioinformatics (O'Reilly, US $39.95), author James Tisdall provides a practical introduction to Perl for biologists with little or no programming experience, approaching programming as an important new laboratory skill.
"Bioinformatics is an important component of a lot of modern biology research," says Tisdall. "Perl is the most popular computer language in bioinformatics because it is very easy to represent data like long DNA sequences or manipulate biological data like GenBank records or BLAST reports, and especially because it makes the writing of biologically useful programs relatively straightforward."
Programming skills are now in strong demand in biology research and development. Although historically programming has not been viewed as a critical skill for biologists, recent trends have made computer analysis of massive amounts of data central to many research programs.
"This is the golden era of biology research," Tisdall explains. "All the genes of several organisms, including humans, are now known, and more are on the way. As we use this information to unravel the mechanisms by which genes and their products interact and are controlled, programming skills will be a very important part of the discovery process. Bioinformatics programming is a part of the endeavor to cure diseases, to improve agriculture, and ultimately to learn the secrets of life (hopefully for the benefit of all)."
Beginning Perl for Bioinformatics is intended as a hands-on, one-volume course for busy biologists. It begins with an introduction to the "art" of programming in general, walking the reader through the approaches to programming and programming strategy, then focuses on Perl specifically. Tisdall's goal is to teach researchers how to write useful and practical bioinformatics programs as quickly and as painlessly as possible. The book presents a programming tutorial that includes a collection of "protocols" or programming techniques that can be immediately applied in the lab. Exercises and examples are based on real biological problems.
"Many scientists start out writing small programs and find that they really like programming," Tisdall says. "As programmers, they never need to worry about finding the right tools for their needs: they can write programs themselves. This book will get them started."
Beginning Perl for Bioinformatics is the second release in O'Reilly's highly acclaimed new series of books on the field of bioinformatics. It provides a good introduction to the most common bioinformatic programming problems and the most common computer-based biological data.
The O'Reilly Bioinformatics Technology Conference, Practical Tools for Innovation, will take place January 28-31, 2002 in Tucson, AZ.
An article by the author, "Why Biologists Want to Program Computers."
Another article by the author, "Parsing Protein Domains with Perl."
Chapter 10, "GenBank," is available free online.
More information about the book, including Table of Contents, index, author bio, and samples.
A cover graphic in jpeg format.
Beginning Perl for Bioinformatics
By James Tisdall
ISBN 0-596-00080-4, 368 pages, $39.95 (US)
O'Reilly Media spreads the knowledge of innovators through its books, online services, magazines, and conferences. Since 1978, O'Reilly Media has been a chronicler and catalyst of cutting-edge development, homing in on the technology trends that really matter and spurring their adoption by amplifying "faint signals" from the alpha geeks who are creating the future. An active participant in the technology community, the company has a long history of advocacy, meme-making, and evangelism.
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