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Mastering Perl for Bioinformatics
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Binding: Paperback
Dewey Decimal Number: 005.133
EAN: 9780596003074
Edition: 1st
ISBN: 0596003072
Label: O'Reilly Media, Inc.
Manufacturer: O'Reilly Media, Inc.
Number Of Items: 1
Number Of Pages: 377
Publication Date: 2003-06
Publisher: O'Reilly Media, Inc.
Studio: O'Reilly Media, Inc.
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Editorial Review:
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 languagewill 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.
Customer Reviews
Average Rating: 
Rating: - Only chapters 4, 5 and 9 make it a worthwhile "Masters" book
This book is definitely written for the biologist that knows some perl and not the experienced perl programmer. To the biologists who have some experience, this book will open up many new possibilities, but to a person with a few years of perl experience, many sections are skimpy and wasteful on topics better covered by other Perl books.
For example, for anyone with truely massive datasets, it might have been worth the mention of the performance cost/benefits of using BerkleyDBs and ... Read More
Rating:  - A good follow-on to Tisdall's other Perl book
This book is a continuation of Tisdall's "Beginning Perl for Bioinformatics" and thus illustrates more advanced Perl programming techniques. This book not only talks about Perl programming, but it goes into some detail on the subject of bioinformatics itself. It is assumed that the CS-type reader has a good understanding of biology and the goals of bioinformatic programming. Otherwise, the examples and projects within the book will not make sense. The following is a description of the book's contents: ... Read More
Rating:  - Perhaps the CGI could have been omitted?
This is the sequel to his earlier beginner's book on Perl. Now, he goes further into usages of Perl. While experienced programmers will not find these terribly challenging, they are not the intended audience.
Of the topics, the most important is where he shows you how to interface with a SQL database. Given the sheer mass of sequence data generated these days, it is inevitable that efficient database usage be done. So he gives a quick tour of relational database design. With examples of how ... Read More
Rating: - Good Companion text
This first half of the book focuses entirely on Object-Oriented(OO) Perl. The second half follows up with a general survey of various perl implementations of particular programming issues involving databasing, cgi, graphics, modules, etc, and BioPerl.
This book does a good job of applying Perl in OO for Biology in the first half of the book. In the second half he overviews a few broad topics in bioinformatics; he doesn't go super specific, but its a sufficient overview and for me sparked more ... Read More
Rating: - Great book, leads to others for true mastery
Published in late 2003, this clearly-written book picks up where "Beginning Perl for Bioinformatics" leaves off. Perl is very commonly used in the field of bioinformatics, and this book does a good job of surveying the more advanced topics in perl from the bioinformatics point-of-view. For a more thorough treatment of each of these topics though, the student will need to explore more specialized titles.
While Tisdall's first volume teaches the core of procedural programming in Perl, this one ... Read More
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