While biologists haven't been historically expected to know how to program, it's fast becoming a critical skill. We now have access to enormous amounts of biological data in the public databases. That means that in biology research and development, the demand for programming skills is growing fast.
Perl is the perfect choice for this application, since it has well developed string handling capacities, text processing, networking, and rapid prototyping processes, and is the programming language of choice when it comes to analysis of biological data. "Mastering Perl for Bioinformatics" gives you information on the core language as well as many extensions, and puts them in the right context - not something that most conventional Perl books can manage, since they're intended for use by computer scientists and students in that field.
The range of topics covered by this book prepare readers for developments in critical bioinformatics programming areas, including string alignment, gene finding, data storage and retrieval methods (including both databases and SML), network modeling, graphics uses, interfacing with other languages, statistics, parallelization, biological models of computation (or DNA computers), protein structure determination and other topics.
All biologists and others who have mastery of Perl basics and are ready to learn more about this useful, versatile language, will appreciate the volume's balanced approach. The analytical capabilities of Perl are applied to the bioinformatics field, and many practical examples, including real-world solving of biological problems, are included.
This book is vital for readers who want to use Perl in bioinformatics beyond the beginner level. Here's a brief summary of the content to help you discover what Mastering Perl for Bioinformatics has to offer you.
Chapter one, Modular Programming with Perl, explains what a module is and why use of Perl modules is desirable. Namespaces and packages are also discussed, in addition to how to define and store a module, and writing Perl modules on your own. Use of modules is included, as well as CPAN modules and exercises to help you master the content in this chapter.
Chapter two, Data Structures and String Algorithms, covers the basic Perl data types, matrices, references, and complex data structures. Printing complex data structures is explained. Other topics covered in this chapter include data structures in action, dynamic programming and approximate string matching.
Chapter three, Object Oriented Programming in Perl, discusses the definition of this term and how to use Perl classes without writing them on your own. It also talks about objects, methods and classes in relation to Perl and the use of arrow notation. It gives a few examples of Perl classes, and explains how AUTOLOAD works. Also covered are how to clean up objects that haven't been used with DESTROY and how to document a Perl class with POD. Practice these skills in the exercises that accompany this chapter.
Chapter four is Sequence Formats and Inheritance. Sections in this chapter include Inheritance, FileIO.pm, and SeqFileIO.pm, covering reading and writing files and sequence file formats. Resources and exercises are included, as usual.
In chapter five, A Class for Restriction Enzymes, topics include Envisioning an Object, Rebase.pm, Restriction.pm, and drawing restriction maps. Exercises and resources are included to help deepen understanding of the topics that make up this chapter.
Chapter six, called Perl and Relational databases, covers the fact that Perl can use many databases, and talks about some of the most popular. It then covers relational database definitions and structured query language, relational database design, and includes a rebase database implementation. Also covered in this chapter are Perl DBI and DBD interface modules.
In chapter seven, Perl and the Web, the way the web functions is discussed, including web server and browser function and the common gateway interface. A discussion on building dynamic web pages is also included, and the usual exercises.
Chapter eight, Perl and Graphics, covers computer graphics in general, GD, and addition of GD graphics to Restrictionmap.pm. Making graphs is also covered by this chapter.
Introduction to Bioperl is chapter nine, the last in the book, and discusses the growth of Bioperl, installation and testing, and problems that might be encountered with Bioperl. An overview of objects and discussion of using Bioperl modules are also included in this chapter.
Appendix A acts as a Perl summary, including command interpretation, comments, scalar variables and values, assignment, arrays, hashes, statements and blocks, complex data structures, operators and much more. Appendix B contains information on how to install Perl, including informations on the various versions, how to download this program and how to run Perl programs. In addition, you'll receive instructions on how to find help with your Perl projects.
If you've got a good grasp on the basics of Perl, it's time to take your skills further and learn to master the language. Using "Mastering Perl for Bioinformatics" is an excellent way for biologists and others who have a good basic command of Perl to advance their skills in a way that's well suited for the field.
This book is an important follow-up to its earlier companion volume, and users looking for a full Perl course should check it out to see what it can offer. Anyone wanting to move beyond the basic level will benefit heavily from "Mastering Perl for Bioinformatics".
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Mastering Perl for Bioinformatics
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