Mastering Perl for Bioinformatics

Foreword

If you can’t do bioinformatics, you can’t do biology, and Perl is the biologist’s favorite language for doing bioinformatics. The genomics revolution has so altered the landscape of biology that almost anyone who works at the bench now spends much of his time at the computer as well, browsing through the large online databases of genes, proteins, interactions and published papers. For example, the availability of an (almost) complete catalog of all the genes in human has fundamentally changed how anyone involved in genetic research works. Traditionally, a biologist would spend days thinking out the strategy for identifying a gene and months working in the lab cloning and screening to get his hands on it. Now he spends days thinking out the appropriate strategy for mining the gene from a genome database, seconds executing the query, and another few minutes ordering the appropriate clone from the resource center. The availability of genomes from many species and phyla makes it possible to apply comparative genomics techniques to the problems of identifying functionally significant portions of proteins or finding the genes responsible for a species’ or strains distinguishing traits.

Parallel revolutions are occurring in neurobiology, in which new imaging techniques allow functional changes in the nervous systems of higher organisms to be observed in situ; in clinical research, where the computer database is rapidly replacing the paper chart; and even in botany, where herbaria are being digitized and cataloged for online access.

Biology is undergoing a sea change, evolving into an information-driven science in which the acquisition of large-scale data sets followed by pattern recognition and data mining plays just as prominent a role as traditional hypothesis testing. The two approaches are complementary: the patterns discovered in large-scale data sets suggest hypotheses to test, while hypotheses can be tested directly on the data sets stored in online databases.

To take advantage of the new biology, biologists must be as comfortable with the computer as they now are with thermocyclers and electrophoresis units. Web-based access to biological databases and the various collections of prepackaged data analysis tools are wonderful, but often they are not quite enough. To really make the most of the information revolution in biology, biologists must be able to manage and analyze large amounts of data obtained from many different sources. This means writing software. The ability to create a Perl script to automate information management is a great advantage: whether the task is as simple as checking a remote web page for updates or as complex as knitting together a large number of third-party software packages into an analytic pipeline.

In his first bioinformatics book, Beginning Perl for Bioinformatics, Jim introduced the fundamentals of programming in the language most widely used in the field. This book goes the next step, showing how Perl can be used to create large software projects that are scalable and reusable. If you are programming in Perl now and have experienced that wave of panic when you go back to some code you wrote six months ago and can’t understand how the code works, then you know why you need this book. If you are an accomplished programmer who has heard about bioinformatics and wants to learn more, this book is also for you. Finally, if you are a biologist who wants to ride the crest of the information wave rather than being washed underneath it, then buy both this book along with Beginning Perl for Bioinformatics. I promise you won’t be disappointed.

—Lincoln SteinCold Spring Harbor, NYSeptember 2003