Beginning Perl for Bioinformatics

Chapter 3. The Art of Programming

This chapter provides an overview of how programmers accomplish their jobs. If you already have Perl installed, and you want to get started writing programs for bioinformatics, feel free to skip ahead to Chapter 4.

Just as visitors to a biology lab tend to have a clueless awe of “all those test tubes,” so the newcomer to programming may regard the world of the programmer as a kind of arcane black box full of weird terminology and abstruse skills. So, to make the whole enterprise a little more congenial, let’s take a short tour of some important realities that affect all programmers. Two of the most important are practical strategies that good programmers use and where to go to find answers to questions that arise while you are programming. Using a couple of brief narrative case studies, we’ll look at how programmers find solutions to problems. Appendix A lists some of the best Perl and bioinformatics resources to help you solve your particular problems.

Individual Approaches to Programming

What’s the best way to learn programming? The answer depends on what you hope to accomplish. There are several ways to get started. You can:

• Take classes of many different kinds

• Read a tutorial book like this one

• Get the programming manuals and plunge in

• Be tutored by a programmer

• Identify a program you need

• Try any and all of the above until you’ve managed to write the program

The answer also depends on how you choose to learn. Some people prefer classes, because the information ...