ProteomeCommons.org Java Analysis Framework is a framework for referencing common mass spectrometry data such as atoms and residues. This framework provides a programmer with an easy-to-use library for writing programs that rely on common mass spectrometry data. The framework also contains utilities such as an isotope calculator and a reference for residue abbreviations.
ApacheDS is an LDAP and X.500 experimentation platform. Its backend subsystem and frontend are separable and independently embeddable. It provides a server side JNDI LDAP provider that directly interacts with the backend storage. It is powered by SEDA (Staged Event-Driven Architecture), which can handle large amounts of concurrency.
Morph is a Java framework that eases the internal interoperability of an application. As information flows through an application, it undergoes multiple transformations. Morph provides a standard way to implement these transformations. In addition to providing a framework for performing transformations, Morph provides implementations of many common transformations. It has been built from the ground up for flexibility and extensibility, and it integrates seamlessly with dependency injection frameworks such as Spring, PicoContainer, and Hivemind.
OpenArm is an implementation of the Open Group's Application Response Measurement (ARM) standard. It provides a complete implementation of the ARM 4.0 Java interfaces, as well as ARM agent functionality that allows you to record your transaction events as log4J logging events, JMS messages, SNMP traps, JMX notifications, or as records in a relational database.