Mastering Perl for Bioinformatics
February 21, 2010 by Bioinformatics Computational Biology
Product 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. 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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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’.
Rating: 4 / 5
Combined with the authors other book, Beginning Perl for Bioinformatics, this book provides a good self-study guide for those interested in understanding bioinformatics. This book is useful for biologist who has some programming experience, as well as programmers with some biology knowledge. It’s written in a style that should suite most readers, as I find it each and smooth to read. Those looking for strict definitions or theory should look elsewhere.
Rating: 5 / 5
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 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.
Rating: 3 / 5
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:
Part I: OBJECT-ORIENTED PROGRAMMING IN PERL
Chapter 1. Modular Programming with Perl – Talks about using modules so that other people can reuse your programs and you can reuse other people’s modules in your own programs.
Chapter 2. Data Structures and String Algorithms – Talks about all of the different data structures available through Perl and how to build up special structures in Perl that you might need to describe complex data. Also mentions various string algorithms that are used in analyzing biological data and implements them in Perl.
Chapter 3. Object-Oriented Programming in Perl – Introduces object-orientation in Perl via a module that includes a class that keeps track of genes.
Chapter 4. Sequence Formats and Inheritance – How to convert sequence files into alternate formats such as FASTA and GCG. The object-oriented concept of inheritance is also introduced.
Chapter 5. A Class for Restriction Enzymes – By writing a more complex class, you get a bigger dose of object-orientated programming in biology.
Part II: PERL AND BIOINFORMATICS
Chapter 6. Perl and Relational Databases – Talks about SQL and the design of relational databases. MySQL is examined specifically.
Chapter 7. Perl and the Web – You learn about web programming in Perl by seeing how to put a laboratory on the Web via Perl and CGI.
Chapter 8. Perl and Graphics – Graphics programming in Perl is demonstrated when you learn to write a program that displays changing data to the Web. The graphical Perl module PD is discussed and demonstrated in a program.
Chapter 9. Introduction to Bioperl – Introduces the reader to Bioperl, which is a group of open source Perl modules used for bioinformatics programming. They provide many basic facilities so you don’t have to worry about them.
Part III: Appendixes
Appendix A. Perl Summary
Appendix B. Installing Perl
I really thought this was a 5-star book. However, it is not obvious from the title that this is really volume two of a two volume set of books on Perl programming for the biologist, so I can see where the lower ratings might have come from.
Rating: 5 / 5
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
Rating: 4 / 5