Approaches to Web Development for Bioinformatics

PHP

In this section:

• Introduction
• Configuring PHP
• Language Basics
• Types
• Variables
• Control Structures
• Object Oriented Programming in PHP 4
• Object Oriented Programming in PHP 5
• Interacting with Browsers and Servers
• HTML Forms
• Authentication and User Sessions
• Working with Files and Text
• PEAR
• PECL
• phpDocumentor
• Sending Email
• Image Generation
• Image Metadata

Introduction

PHP is best known as a template language for creating dynamic web pages.  The name PHP is recursive acronym for "PHP: Hypertext Preprocessor." This section discusses of PHP as a web development platform in the context of bioinformatics applications. The section Accessing a Relational Database with PHP discusses database access with PHP. The section BioPHP discusses the open source bioinformatics project BioPHP.

PHP is freely available, well documented, and multiplatform.  It is especially popular on Linux and, in particular, as the 'P' in LAMP (Linux Apache MySQL PHP) environments. It can be very easily integrated with CGI scripts, including Perl, in a web user interface.  It is lightweight and easy to get started with.  It is also included with most web hosting packages from Internet Service Providers (ISP's). It has a graphical installer that configures Apache, Microsoft Internet Information Server, and other web servers.

PHP has a modern implementation of object oriented types as a basic part of the language. This and other generally well designed language features make it appropriate for implementing large and complex projects. Interested readers can find more detail in the PHP manual ³⁵ and in Sklar and Trachtenberg⁵⁰. A good book is PHP Cookbook by Sklar and Trachtenberg⁶¹.

There is a large open source community for PHP. One rallying point for the PHP community is php.net⁶² At php.net there are mailing lists, the PEAR distribution system for reusable PHP components, the PECL repository for PHP extensions, and more. A number of other useful sites are

• The PHP Knowledge Base⁶³
• The PHP Dev Center⁶⁴
• Planet PHP⁶⁵
• The Zend Developer Zone⁶⁶

There are relatively few commercial products implemented in PHP. This is probably due to its relatively recent nature and the fact that, as it is a scripting language, protection of commercial intellectual capital can be relatively more difficult. However, there are many open source projects implemented in PHP.

Some of the features that I discuss are not available in versions of PHP earlier than PHP. At the time of writing the current version is PHP 5.

Configuring PHP

PHP is configured via a the php.ini file in the PHP home directory. This is a simple text file that you can edit with any text editor. After making changes you can check whether the change has taken effect using the phpinfo() function below. There are a number of categories of things that can be configured, including

• Language options - mostly compatibility options with past releases, ASP style tags, and so on.
• Safe mode - mostly has to do with file permissions, environment variables, and executables
• Error handling and logging - including whether to display errors in the output to the browser or to the web server log file.
• Data handling - use of separators and quotes in URL construction and parsing, treatment of GET, POST, Cookie, and global variables, default charset, and more.
• Paths and pirectories - extension directories and CGI options
• File uploads - temperatry storage and maximum size
• Fopen wrappers - options for opening files from external URL's
• Dynamic extensions - for database drivers, GIMP, LDAP, multibyte string processing, cryptography
• Module settings - configuration settings for individual modules

Extensions are described at the main PHP site and on the PECL site. Installation of an extension usually involves copying a shared object library (.dll on Windows, .so on UNIX), setting the extensions directory (extension_dir in php.ini) and adding a line to php.in like

This example is for the multibyte string extension.

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