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Curtis Jamison's innovative text introduces basic elements of computer science and software engineering in an abbreviated format, building up to a bioinformatics users' guide for Perl. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. Jamison incorporates real-life examples throughout to illustrate how Perl is used to solve biological problems, offering valuable code fragments that the current practitioner can recycle into his or her own program. Divided into sections on basic-, intermediate-, and advanced-level Perl, the book includes chapters on:
- Variables and data types
- Arrays and hashes
- Control structures
- String manipulation
- Object-orientated programming
Upon completing the book, readers will be able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurence of an EcoRI site, adapting other writers scripts to one's own purposes, and most important, wriing reusable and maintainable scripts that will spare the rote repetition of code.
PART I: THE BASICS.Introduction. Chapter 1. An Introduction to Perl.Chapter 2. Variables and Data Types.Chapter 3. Arrays and Hashes.Chapter 4. Control Structures.PART II: INTERMEDIATE PERL.Chapter 5. Subroutines.Chapter 6. String Manipulation.Chapter 7. Input and Output.Chapter 8. Perl Modules and Packages.PART III: ADVANCED PERL.Chapter 9. References.Chapter 10. Object-Oriented Programming.Chapter 11. Bioperl.Appendix A. Partial Perl Reference.Appendix B. Bioinformatics File Formats.Index.
This well written book illustrates PERL with examples...Those with less or no programming skills should read this book before attempting the practice of bioinformatics ideas. (Journal of Statistical Computation & Simulation, January 2005) "...the book is useful to biologists who already use languages like C+ or Visual Basic and want to learn Perl." (Biomolecular Engineering, November 2004) "...written in a pleasant chatty style with obvious enthusiasm for the topic" (Robotica, Vol. 22, 2004) "...unique and I highly recommend it as a first book on programming for biology-oriented professionals interested in using perl...excellent for self-study...can also be a great resource as classroom material..." (Clinical Chemistry, Vol. 50, No. 2, 2004) "...not be surprised to see [it] finding a space on the bookshelves in many biological laboratories in the near future." (Briefings in Bioinformatics, Vol 5(1), March 2004)