Approaches to Web Development for Bioinformatics

In this section:

• Application Development Languages
  • Perl
    • Language Basics
    • Perl Modules
    • Object Oriented Programming in Perl
    • Tools for Perl Development
    • Perl Documentation (POD)
    • Perl Compared with Other Languages

Application Development Languages

There are many different programming platforms and tools available to solve bioinformatics problems.  It can be bewildering at first, but it makes more sense to build on top of some of these tools rather than build from scratch.  Some the problems with using these tools for a bioinformatics portal are

1. Many tools are written in different programming languages and on different platforms.
2. Some tools have particular prerequisites to operate, most often databases with particular schemas.
3. Many may not be in a form that is usable by the people using your software or portal.  For example, you want to present a web page but the utility is a command line program.
4. The context that gives meaning to users of the software may be missing.  For example, users may have to get data from a database somewhere else in order to input data into web forms.

Standardization on a particular platform can help manageability but for most organizations a compromise between standardization and adoption of several different platforms will allow many people to develop software in platforms that they are already comfortable with and allow the reuse of a large amount of freely available software.  In the sections that follow I will give a brief description of a few development platforms important to bioinformatics and some of the pros and cons or their use within a bioinformatics web portal.

Perl

This section gives a brief introduction to Perl with a bioinformatics flavor. The section Perl and CGI describes developing a web user application in Perl. The section BioPerl describes the BioPerl open source project.

Practical Execution and Report Language (Perl) dates back to the 1980's when it was developed as a language to aid in automating practical UNIX system administration tasks.  It became very popular in the 1990's when it was the language of choice for many web sites in the early development of the Web.  It has also been used extensively to create bioinformatics utilities because of its power in processing text data.  A good place to start with Perl is the book Learning Perl by Schwartz, Phoenix, and foy¹².  Moving past the basics you might look at Intermediate Perl by Schartz , foy, and Phoenix²⁹ or the Comprehensive Perl Archive Network (CPAN) web site cpan.org¹³.

There are links to download Perl at perl.com¹⁴. It is freely available on many different platforms.

Perl's main strengths are

1. It is easy to get started on some useful tasks.  Biologists need not become software engineers to get some useful work done.
2. It is powerful for text processing, which is very common in bioinformatics.
3. Perl is good for creating simple web pages, especially providing web interfaces for command line utilities.
4. Perl is freely available on many different platforms and is pre-installed on many Linux distributions, including Red Hat.

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