November 21, 2001

"Beginning Perl for Bioinformatics" released by O'Reilly

Author: JT Smith

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

The O'Reilly Bioinformatics Technology Conference, Practical Tools for
Innovation, will take place January 28-31, 2002 in Tucson, AZ. For more
information, go to:

An article by the author, "Why Biologists Want to Program Computers"
can be found at:

Another article by the author, "Parsing Protein Domains with Perl" can
be found

Chapter 10, "GenBank," is available free online at:

For more information about the book, including Table of Contents,
index, author bio, and samples, see:

For a cover graphic in jpeg format, go to: 

Beginning Perl for Bioinformatics
By James Tisdall
November 2001
ISBN 0-596-00080-4, 368 pages, $39.95 (US)

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