Beginning Perl for Bioinformatics

Chapter 13. Further Topics

This book’s goal has been to help you learn basic Perl programming. In this chapter, I will point the way to further learning in Perl.

The Art of Program Design

My emphasis on the art of program design has determined the way in which the programs were presented. They’ve generally progressed from a discussion of problems and ideas, to pseudocode, to small groups of small, cooperating subroutines, and finally to a close-up discussion of the code. At several points you’ve seen more than one way to do the same task. This is an important part of a programmer’s mindset: the knowledge of, and willingness to try, alternatives.

The other recurrent theme has been to explain the problem-solving strategies programmers rely on. These include knowing how to use such sources of information as searchable newsgroup archives, books, and language documentation; having a good working knowledge of debugging tools; and understanding basic algorithm and data structure design and analysis.

As your skills improve, and your programs become more complex, you’ll find that these strategies take on a much more important role. Designing and coding programs to solve complex problems or crunch lots of complex data requires advanced problem-solving strategies. So it’s worth your while to learn to think like a computer scientist as well as a biologist.

Web Programming

The Internet is the most important source of bioinformatics data. From FTP sites to web-enabled programs, the Perl-literate ...