In this section:
Web application development in Java can be an excellent option. This section gives an introduction to development of web applications using the Java 2 Enterprise Edition (J2EE) platform. The section Java gives an overview of the Java programming language with a bioinformatics flavor. The section BioJava gives an overview of the BioJava open source project.
Web development with Java is a great option if you are hosting the application within your own enterprise or if you have the resources to host your own server on the Internet. ISP solutions for Java are more expensive and more limited than both Linux Apache MySQL PHP (LAMP) and .NET solutions. Creation of a web interface in Java is usually done using the J2EE platform. The tools for developing with the J2EE platform are quite comprehensive, relatively easy to get started with, and freely available.
There are a number of popular J2EE implementations, both open source and commercial. One very good open source platform that contains the essentials for delivering web based content is Apache Tomcat23. Commercial implementations include Caucho Resin44 and BEA WebLogic53. The Eclipse Web Tools Platform (WTP) Project53 includes APIs and templates for J2EE and Web-centric application development. The J2EE API and the Java Server Pages Specification are available at Sun Microsystems web site39. The book Java Servlet Programming by Jason Hunter40 is also a good reference on the topic.
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