Who This Book Is For

This books is a practical introduction to programming for biologists.

Programming skills are now in strong demand in biology research and development. Historically, programming has not often been viewed as a critical skill for biologists at the bench. However, recent trends in biology have made computer analysis of large amounts of data central to many research programs. This book is intended as a hands-on, one-volume course for the busy biologist to acquire practical bioinformatics programming abilities. So, if you are a biologist who needs to learn programming, this book is for you. Its goal is to teach you how to write useful and practical bioinformatics programs as quickly and as painlessly as possible.

This book introduces programming as an important new laboratory skill; it presents a programming tutorial that includes a collection of "protocols," or programming techniques, that can be immediately useful in the lab. But its primary purpose is to teach programming, not to build a comprehensive toolkit.

There is a real blending of skills and approaches between the laboratory bench and the computer program. Many people do indeed find themselves shifting from running gels to writing Perl in the course of a day—or a career—in biology research. Of course, programming is its own discipline with its own methods and terminology, and so must be approached on its own terms. But there is cross-fertilization going on (if you'll pardon the metaphor between the two disciplines).

This book's exercises are of varying difficulty for those using it as a class textbook or for self study. (Almost) all examples and exercises are based on real biological problems, and this book will give you a good introduction to the most common bioinformatics programming problems and the most common computer-based biological data.

This book's web site, http://www.oreilly.com/catalog/begperlbio, includes all the program code in the book for convenient download, including the exercises and solutions, plus errata and other information.^[1]

^[1] Program code, or simply code, means a computer program—the actual Perl language commands a programmer writes in a file.