Mastering Perl for Bioinformatics: Perl Programming for Bioinformatics


About this book

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:. 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.

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Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and. Mastering Perl for Bioinformatics [James D. Tisdall] on grapplingindo.com *FREE* shipping on qualifying offers. Historically, programming hasn't been considered a .

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. Odoo 11 Development Cookbook - Second Edition. Core Objective-C in 24 Hours.

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Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. 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. This book is a very good way for someone who has been doing bioinformatics with traditional declarative programming to get started with object-oriented Perl, and with the development and use of OO module libraries. At the end of the chapter, Tisdall explains the use of an invaluable debugging function of the bptutorial. It also gives a good first-hack approach to web programming and RDBMS programming, although any bioinformaticist needing to do more extensive work in these areas should seek further information elsewhere.

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Mastering Perl for Bioinformatics

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The examples all use MySQL. Perl's DBI modules are explained and their use demonstrated. The web-programming chapter explains the benefits of web-based user interfaces which are extremely widespread among bioinformatics applications and then introduces the CGI module. Tisdall again extends the Rebase system, equipping it with a web-driven front end. The chapter on graphics programming introduces the GD. It is disappointing that none of the graphics of restriction maps produced by this code are illustrated in the book, although some ordinary spreadsheet-type graphs produced by the GD-based code are reproduced.

For bioinformatics, which language should I learn first?

Finally, we get a very detailed look at the process of installing and testing the Bioperl modules from CPAN. This final chapter shows all the warts of working with new open-source code, which may often have bugs in the documentation and inadequate tutorials.

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Tisdall does an excellent job of detailing the process of debugging a new installation, correcting bugs in tutorial code, and identifying missing pieces that you can get by without. At the end of the chapter, Tisdall explains the use of an invaluable debugging function of the bptutorial. This chapter on Bioperl will be very helpful for anyone who has ever been stymied in attempting to use CPAN to install a large and complex set of modules, as several of the most common problems are given detailed examples, along with a thorough account of how to work through to the solution of each one.

The book concludes with two appendices, a summary of Perl and a guide to installing Perl on various platforms.

The summary is excellent, using bioinformatics-motivated examples throughout. It often gives examples that work together well and concisely illustrates aspects of Perl that I hadn't noticed as clearly before. The book is marred by a few typographical errors of the sort that might be especially confusing for beginners e.