Apache Tomcat, http://jakarta.apache.org/tomcat
version 5.0.25

Tomcat is our java servlet container. We use it because it's free, we know how to use it, and we've had no significant problems with it.

Oracle, www.oracle.com
Oracle Database 10g Enterprise Edition Release 10.2.0.4.0 - 64bit Production With the Partitioning, OLAP, Data Mining and Real Application Testing options

Oracle is the database standard within the Northwestern Bioinformatics Core.

Spring, java/j2ee Application Framework, www.springframework.org

We use Spring as a Dependency Injection/Inversion of Control lightweight container, as a unit testable and simpler alternative to EJBs. We also have begun using Spring MVC for our web layer, and we use Spring's Hibernate and JDBC wrappers to simplify our database access code.

Hibernate, Object/Relational Mapping and Transparent Object Persistence for Java and SQL Databases, www.hibernate.org
version 2.1.6

Hibernate is our object/relational mapping (ORM) tool, for mapping between java business objects and the database tables that store them.

Quartz, www.opensymphony.org/quartz
version 1.4.2

Part of the OpenSymphony project, "Quartz is an open source job scheduling system that can be integrated with, or used along side virtually any J2EE or J2SE application." We use Quartz to run various scheduled jobs associated with the site (nightly data imports, etc.).

ANTLR, www.antlr.org

We use ANTLR to define and parse a grammar for mutant line searches.

JUnit, www.junit.org

Automated unit testing with JUnit is an integral part of our development process.

FitNesse, www.fitnesse.org

We have recently begun using FitNesse to write and run automated acceptance/functional/integration tests for the site.

Others

Velocity: for formatting automated email messages

iText: for PDF invoice generation

<display:*> tag library, Log4J, Other Jakarta: Commons, Taglibs (Input), ORO

Struts, http://jakarta.apache.org/struts

Because we find it easier to unit test code developed using Spring MVC than Struts, all new web layer code uses Spring MVC, and we are slowly porting existing web layer code from Struts to Spring.