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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.
List of contents
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.
About the author
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.
Summary
Working on the assumption that the reader has no formal training in programming, this book 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.
Report
"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)
