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Mastering Perl for Bioinformatics

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Spotlight Customer Reviews

Average Customer Rating: 3.5

Customer Rating: 4
Summary: Nice survey of topics, but not too deep on any one thing
Comment: "Mastering Perl for Bioinformatics" is the follow-up to Tisdall's earlier "Beginning Perl for Bioinformatics". Both books are part of O'Reilly's lauded "animal books" series; "Beginning" was graced with tadpoles, while "Mastering" sports a frog.

Naturally, this book picks up where the earlier one left off, diving headfirst into the details of Perl modules. Chapter two is a quick pass over some basic data structures, with discussion of how you'd implement each in Perl. Subsequent chapters cover object-oriented programming in Perl, using Perl with relational databases, using Perl with web services, generating graphics on the fly with Perl, and the use of the Bioperl suite of libraries.

As might be expected, all the coding examples in the book are drawn from reasonably realistic bioinformatics situations. There's a little bit less hand-holding on the biological side in this book, relative to the earlier volume -- which I think is a good idea, as it gives more space to focus on the programming material.

The one weakness of this book is that it covers quite a few topics, which means that it doesn't really go into great depth on any of them. The "survey" approach is well done, and it's very nice to have biologically relevant examples and exercises for the breath of material that is addressed, but I think the book might have been stronger if it forewent the "Perl and the Web" and "Perl and Graphics" chapters in favor of more focus on the Bioperl libraries.

If you're a bioinformatics programmer who enjoyed "Beginning Perl for Bioinformatics", and you want to get a better idea of what more advanced Perl programming looks like and what sorts of things you can do with Perl, this book is a nice place to start. However, if you're looking for more specific information, other more focused books might be a better choice, if you can live without the biologically focused code examples.

Customer Rating: 3
Summary: Not bad
Comment: Basically, this book further develops the author's previous work "Beginning Perl for Bioinformatics" on procedural Perl scripting to object-oriented Perl programming.

You will learn the OOP aspects of Perl in the context of biological problems. For example, this book explains the OOP concepts by developing a Gene class that stores information about a gene. In other books such as Conway's "Object oriented Perl", CD::Music class is given as an example, which I found very boring.

The leap from procedural Perl scripting to object-oriented Perl programming is nontrivial to learn, and I'm sure that this book helps.

Bioperl is the subject of chapter 9 (about 40 pages), and it could have been better if there were more thorough treatment about this module.

Readers may also find useful the chapters 6 (DBI), 7 (CGI), and 8 (GD).

If you are new to Perl, read first "Beginning Perl for Bioinformatics", then this book, because this book assumes that you already have the level of Perl knowledge that can be acquired by that previous book.