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Mastering Perl for Bioinformatics [Paperback]

James Tisdall
3.7 out of 5 stars  See all reviews (3 customer reviews)
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Book Description

Oct. 5 2003 0596003072 978-0596003074 1

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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About the Author

James Tisdall has worked as a musician, a programmer at Bell Labs (where he programmed for speech research and discovered a formal language for musical rhythm), and as a bioinformaticist at Mercator Genetics in Menlo Park, California, and at Fox Chase Cancer Center in Philadelphia. He has a B.A. in mathematics from the City College of New York and an M.S. in computer science from Columbia University; he is working towards a Ph.D. in computer science at the University of Pennsylvania. In his spare time, Jim teaches computer music at the Settlement Music School in Philadelphia. He is also the author of O'Reilly's Beginning Perl for Bioinformatics.


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Customer Reviews

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3.7 out of 5 stars
3.7 out of 5 stars
Most helpful customer reviews
Format:Paperback
"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.
Was this review helpful to you?
3.0 out of 5 stars Not bad Feb. 13 2004
Format:Paperback
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.
Was this review helpful to you?
4.0 out of 5 stars as the title implies, it is for bioinformatician Dec 16 2003
Format:Paperback
Just browsing through this, I can see this book will be very useful for me (as a student majoring in bioinformatics).
A very book explaining area most used in bioinformatics, and the price is ok for a 'starving student'.
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Most Helpful Customer Reviews on Amazon.com (beta)
Amazon.com: 4.2 out of 5 stars  10 reviews
18 of 18 people found the following review helpful
4.0 out of 5 stars Great book, leads to others for true mastery Aug. 29 2004
By Joshua Orvis - Published on Amazon.com
Format:Paperback
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 takes you into the world of object-oriented (OO) programming. The first two chapters explore namespaces, modules, packages, references and data structures, all of which are prerequisites to OO programming. Common bioinformatics algorithms are introduced such as dynamic programming and approximate string matching.

The next three chapters, 3-5, are the meat of this title. Here objects, methods and classes are introduced. Rather than just throwing out independent examples, these topics are developed by starting and building upon a Gene class, the first of several through which Tisdall guides the reader. Due to the practicality of these examples, they can even be used and improved by the reader for use in their own work.

After this decent treatment of OO programming the book takes a turn into other realms of perl, each of which seems to have been written as a short introduction and for which other O'Reilly titles offer more complete coverage. These topics include the use of Perl to access relational databases, CGI programming and graphics generation using GD. If interested in any of these the reader should check out "Programming the Perl DBI", "CGI Programming with Perl" and "Perl Graphics Programming", respectively.

Tisdall wraps up with a much-needed coverage of Bioperl, a large collection of Perl modules for common bioinformatics operations. I looked forward to this section most of all and was fairly disappointed with its brief, 28-page coverage. The entire chapter can currently be downloaded for free from O'Reilly's website as a PDF, but the Bioperl website has better examples and even a contributed course, though good documentation is still lacking in some areas.

In all, I like this book because it does a good review of introducing object-oriented programming in Perl using relevant bioinformatics examples and introduces the reader to other topics including the DBI, CGI, and GD modules. While I believe this makes the book very useful, the coverage of each of the topics in this book will certainly not give the reader a mastery of any of them. For that, one will need to check out the three previously mentioned titles, along with "Learning Perl Objects, References & Modules." This book does a fine job of introducing these four titles from the bioinformatician's perspective.
7 of 7 people found the following review helpful
4.0 out of 5 stars Nice survey of topics, but not too deep on any one thing April 28 2004
By John S. J. Anderson - Published on Amazon.com
Format:Paperback
"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.
5 of 5 people found the following review helpful
4.0 out of 5 stars Good Companion text June 23 2005
By Elliot Kleiman - Published on Amazon.com
Format:Paperback|Verified Purchase
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 interest in understanding how I can use perl to handle my informatics issues.

In the first half, the author does an excellent job on detailing the ins and outs of perl references and how to construct complex data structures. Indeed they are a bit strange looking at first, but the author breaks it down really good so pretty much anyone can understand it.

For me the most intriguing part of the book was in the second half, which included relational databases, graphics, and bioperl. In particular, the chapter that covers Perl DBI and DBD::mysql was really cool. That secion was very helpful for me because I am familiar with php/mysql, but have not ever used Perl to interact with Mysql before.

I especially liked the gif draw aka GD chapter. I had no idea how cool GD is. But moreover how it can be integrated with Perl to generate really cool looking plots. Before this book I always used gnuplot. But Tisdall shows you how to get to work with GD pretty good using basic practical examples.

The chapter on BioPerl was especially helpful as well. In particular, he shows you what he did to install the beast. He shows you how to use the CPAN shell and again its really beneficial to read through. It motivated me to pursue other topics in bioperl and how I can use it to query different ncbi databases for example.

Overall, the text provided a good overview on OO Perl and on various other topics involving Perl for Bioinformatics in general. I am glad I bought it. It was really very practical/useful - I refer to it all the time actually!
5 of 6 people found the following review helpful
3.0 out of 5 stars Not bad Feb. 13 2004
By Seungwoo Hwang - Published on Amazon.com
Format:Paperback
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.
2 of 2 people found the following review helpful
4.0 out of 5 stars Only chapters 4, 5 and 9 make it a worthwhile "Masters" book March 10 2007
By William Leizerowicz - Published on Amazon.com
Format:Paperback
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 hash joins (180-3500 times). With improvements of 2-3 orders of magnitude for large sets, it would have been worth a complementary example in chapter 6 so that readers can weigh the alternatives for certain situations.

The book, however, is well worth the price just for chapters 4, 5 and 9.

4) Sequence Formats and Inheritance

5) A Class for Restriction Enzymes

9) Introduction to Bioperl
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