Mastering Perl for Bioinformatics

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Mastering Perl for Bioinformatics

By James Tisdall
First Edition September 2003
Pages: 396
ISBN 10: 0-596-00307-2 | ISBN 13: 9780596003074
(Average of 4 Customer Reviews)

Book description

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.
Full Description

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. 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. The range of topics covered in Mastering Perl for Bioinformatics prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as:

Gene finding
String alignment
Methods of data storage and retrieval (SML and databases)
Modeling of networks (graphs and Petri nets)
Graphics (Tk)
Parallelization
Interfacing with other programming languages
Statistics (PDL)
Protein structure determination
Biological models of computation (DNA Computers)

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.

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Featured customer reviews

Excelent, February 23 2006

Rating:

Submitted by ende [Respond | View]

This is an easy to read, very clever description of the very meshed Perl topics that many (non professional programmers) can understand.

It's worth to read it yet if you are not Bio-researcher.

I only lack a more detailed description of BioPerl and comparisons to the others (BioPython, BioRuby, BioTcl, etc..). Specially will be wellcome examples of use.

Mastering Perl for Bioinformatics Review, February 07 2004

Rating:

Submitted by Jon S [Respond | View]

It is a great second book to beginning perl for bioinformatics. I have only scanned the parts that were interesting to me, but I found mostly what I was looking for. This book goes into practical applications like perl/mysql. perl/web and perl/bioperl and it spends quite a bit of time on object oriented perl. There are very few books out there that explore all these topics. (If Oreilly is reading this. I would like the solution to exercise 7.7 pg 270 chapter 7.) An object oriented database using perl on the web is a personal goal of mine. Also, Oreilly should put up the answers to all the excercises, just like in beginning perl. They were very helpful in learning the material.

Mastering Perl for Bioinformatics Review, December 06 2003

Rating:

Submitted by Bela Tiwari [Respond | View]

The only reason I gave this a Very Good instead of Definitive is that I bought the book this afternoon and have only made it through the first 70 pages - so I can't say what my opinion on later chapters will be...but so far, so excellent! This is a great book. It contains the information key to being able to use Perl well for bioinformatics, and has really good listings for further reading and documentation. The only negative is that I can't seem to find any sample answers for the exercises. If sample answers were easily available, this book would have had "Definitive" even after only 70 pages.

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Mastering Perl for Bioinformatics Review, October 17 2003

Rating:

Submitted by Pat [Respond | View]

A good biologist's version of the 2nd volume of Learning Perl.

Where's the example code and solutions on the website though?

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