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. For more
information, go to: http://conferences.oreilly.com/biocon/cfp.html
An article by the author, "Why Biologists Want to Program Computers"
can be found at: http://www.oreilly.com/news/perlbio_1001.html
Another article by the author, "Parsing Protein Domains with Perl" can
be found http://www.perl.com/pub/a/2001/11/16/perlbio2.html
Chapter 10, "GenBank," is available free online at:
http://www.oreilly.com/catalog/begperlbio/chapter/ch10.html
For more information about the book, including Table of Contents,
index, author bio, and samples, see:
http://www.oreilly.com/catalog/begperlbio/
For a cover graphic in jpeg format, go to:
ftp://ftp.ora.com/pub/graphics/book_covers/hi-res/0596000804.jpg
Beginning Perl for Bioinformatics
By James Tisdall
November 2001
ISBN 0-596-00080-4, 368 pages, $39.95 (US)
order@oreilly.com
1-800-998-9938
http://www.oreilly.com
About O'Reilly
O'Reilly & Associates is the premier information source for
leading-edge computer technologies. We communicate the knowledge of
experts through our books, conferences, and web sites. Our books, known
for their animals on the covers, occupy a treasured place on the
shelves of the developers building the next generation of software. Our
conferences and summits bring innovators together to shape the
revolutionary ideas that spark new industries. From the Internet to the
Web, Linux, open source, peer-to-peer networking, and now
bioinformatics, we put technologies on the map. For more information:
http://www.oreilly.com
# # #
O'Reilly is a registered trademark of O'Reilly & Associates, Inc. All
other trademarks are property of their respective owners.
