Chapter 7. Perl and the Web

One of the basic skills of a programmer is designing and putting up an interactive web site. This is as true for bioinformaticians as it is for other programmers.

Not every bioinformatician will need to implement a web site. Your work in bioinformatics may specialize early; perhaps you work in analyzing algorithms for representing gene cascades, while web programming is someone else's responsibility.

However, the Web has become the principal way to provide programs to users. This is certainly true in biology, where it is typical for laboratories to provide programs and access to data via the Web. Collaborations can be promoted between research groups, the need for publication of results can be addressed ( witness the many peer-reviewed journal articles that invite readers to visit web sites for supporting information), and valuable research tools can be widely disseminated.

This chapter provides a quick introduction to the way web pages and the Internet work, followed by a closer look at some important parts of web programming. You'll see these techniques applied to create an interactive web page that accepts a sequence and enzyme names and returns a restriction map.

Along with the remarkable growth in use of the Web and the Internet have come an equal proliferation of languages, systems, and tools for web programming. There are now a variety of choices in how a programmer can create interactive web pages.

We will use one such system that employs the Perl language. To make the web pages interactive ”to enable users to type in queries and get responses ”we'll use the popular CGI.pm Perl module that's shipped with all recent versions of Perl. CGI stands for the Common Gateway Interface, a protocol that provides dynamic web content ”web pages that change for various reasons (such as a user asking for a restriction map) ”as opposed to static, unchanging web pages. Perl and CGI were an early success story in programming the Web and remain widely available as a standard web programming technique. They constitute a basic skill set in web programming, despite the many alternatives now available.

Because bioinformatics programmers need at least a basic working knowledge of web programming, I'll teach you the skills necessary to put an interactive web page on the Web; the example is based on a continuation of the restriction map example from previous chapters.

To begin, I'll give a brief run down of the chief components of web technology to give you the basic overview and terminology you'll need to do web programming and to read further in the field. If you're already familiar with servers, browsers, HTML, and the other components of web programming, feel free to skip ahead.