Perl Programming for Biologists

Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. 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. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusable and maintainable scripts that 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)

Curtis Jamison received his B.A. (Molecular, Cellular and Developmental Biology) from the University of Colorado, Boulder in 1985, and his Ph.D. (Biological Sciences) from the University of Denver in 1991. He held an NSF CISE postdoctoral fellowship while at National Center for Supercomputing Applications, University of Illinois, Champaign-Urbana, where he received a patent for his work on distributed application gateways and database federation. Dr. Jamison continued his work on database federation with plant genome databases for the USDA Agricultural Genome Information Service, and then later evolved to work on higher organisms at the National Institutes of Health where he created computational tools for genome mapping for the Human Genome Project. He is currently an Associate Professor of Bioinformatics at George Mason University, and is director of the Bioinformatics Ph.D. program. With a loose structure that allows for fast and easy coding, the Perl programming language is the most widely used scripting language in bioinformatics. Working on the assumption that the reader has never had any formal training in programming, and using examples geared toward real problems faced by biologists, Perl Programming for Biologists serves as an accessible, introductory reference for teaching Perl programming.

Curtis Jamison’s innovative text introduces basi c elements of computer science and software engineering in an abbreviated format, building toward a bioinformatics users’s 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 numerous 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
• Subroutines
• String manipulation
• Object-oriented 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 occurrence of an EcoRI site, adapting other writers’ scripts to one’s own purposes, and most important, writing reusable and maintainable scripts that will spare the rote repetition of code. Upper-level undergraduates, graduate students, biologists, and other life scientists will find Perl Programming for Biologists to be an essential resource.