Beginning Perl for Bioinformatics

Developing Bioinformatics Computer Skills

Perl Books

Mastering Perl for Bioinformatics

Format: Paperback
Author: James D. Tisdall
ReleaseDate: June, 2003
Publisher: O'Reilly Media
Rating:

Perhaps the CGI could have been omitted?
Now, he goes further into usages of Perl. This is the sequel to his earlier beginner's book on 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 Perl has modules to submit and query the database. The treatment is somewhat cursory, since he has other, non-database topics to cover.

Of those, he includes CGI programming. This might be questionable. CGI code has proved incredibly hard to scale. Maybe he felt the necessity to include code for handling web servers. Unfortunately, a typical reader won't have enough experience to be aware of CGI's problems. The danger is that she actually starts coding CGI Perl. The true debugging and maintenance costs will not show up till later.

Good Companion text
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 first half of the book focuses entirely on Object-Oriented(OO) Perl.

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!.

Great book, leads to others for true mastery
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. Published in late 2003, this clearly-written book picks up where "Beginning Perl for Bioinformatics" leaves off. 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.