What is the difference between Java SE & Java EE?
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Java SE (standard edition) is just the normal specification of Java. Java EE (enterprise edition) is Java with all sorts of add-ons for enterpris-y things like:
(not an exhaustive list, more detail available on Wikipedia). You generally get Java SE when you download the SDK (for development) or JRE (for running Java applications).
On the other hand, you generally get all the Java EE goodies when you start using IBM Websphere Application Server, or JBoss, or another enterprise-class application server.
You can download the Oracle Java EE 6 SDK here. The JSR for Java EE 6 is here.
Best way to understand is to read the Java EE tutorials:
You can just know this for short: Java SE is for desktop applications and it is the core of Java. Java EE is for web applications which include JSP & Servlet, EJB, Webservice and they are kinda extensions. You can use them when install a Servlet container (Tomcat) or a JPA provider (Oracle Toplink, Hibernate) or an entire Web application which includes servlet container, JPA provider such as JBoss, GlassFish.
Java SE (full name: Java Platform, Standard Edition, old names too many to enumerate) is a specification of a programming platform that consists of:
Confusingly it's also the default name of a specific implementation of the Java SE specification (the proper name being various combinations of the Java SE name with "JDK" or "JRE" attached). You can find out more about Java SE (and most especially the Oracle JDK/JRE implementation) on Oracle's page for it (latest stable version).
Java EE (full name: Java Platform, Enterprise Edition, old names, as above, too many to enumerate) is a specification of another programming platform—a framework, really—that is built up on top of the Java SE platform. This platform is intended to add functionality for modern business applications like web applications, n-tier architectures, etc. There are a myriad of implementations of this specification out there—both open source and proprietary—including Oracle's Glassfish/Java EE SDK, IBM's Websphere, Apache's Geronimo, etc. You can find more information about Java EE (and the Glassfish/Java EE SDK implementation of it) again on Oracle's page.