Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

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 interactiveto enable users to type in queries
and get responseswe'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 contentweb 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.