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"Mastering Perl for Bioinformatics": Advanced Perl Programming Techniques for Biological Research

October 13, 2003

Sebastopol, CA--Historically, programming hasn't been considered a critical skill for biologists, but now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. As author James Tisdall explains in Mastering Perl for Bioinformatics (O'Reilly, US $39.95), the history of biological research is filled with examples of new laboratory techniques, which, at first, are suitable topics for doctoral theses but eventually become so widely used that they are learned by most undergraduates. Says Tisdall, "As active sciences evolve, unifying principles and techniques developed in one field are often found to be useful in other areas. As a result, the established boundaries between disciplines are sometimes blurred, and the new principles and techniques may result in new ways of seeing the science as a whole."

Tisdall broadly defines "bioinformatics" as the use of computers in biological research and maintains that it is becoming a foundational science for a broad range of biological studies. "Just as it's now commonplace to find a geneticist or a field biologist using the techniques of molecular biology as a routine part of her research, so you can frequently find the same researcher applying the techniques of bioinformatics," he says. "Molecular biology or bioinformatics may not be the researcher's main area of interest, but the tools from molecular biology and bioinformatics have become standard in searching for the answers to the questions of interest. The Perl programming language plays no small part in that search for answers."

And, in fact, among the many computer languages available to biologists, Perl--with its highly developed capacities in string handling, text processing, networking, and rapid prototyping--has emerged as the programming language of choice for biological data analysis. "Mastering Perl for Bioinformatics" covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with "Beginning Perl for Bioinformatics," forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics.

"Mastering Perl for Bioinformatics" covers advanced Perl programming topics such as:

  • Modular and object-oriented programming in Perl
  • Complex data structures for biological applications
  • Using Perl to present data graphically and online
  • The Bioperl library of modules

Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.

Additional Resources:

Mastering Perl for Bioinformatics
James D. Tisdall
ISBN 0-596-00307-2, 377 pages, $39.95 US, $61.95 CA, 28.50 UK
1-800-998-9938; 1-707-827-7000

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