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.
While the author of BSAX-J has not yet come to a final conclusion about the need for a binary XML format, BSAX is his idea of one possible encoding that leverages other XML prior art (SAX events and UTF-8, in particular). It is complete in that it can be used to perform round-trip conversions from textual XML to SAX events to BSAX binary streams, and back to SAX events and textual XML. The test code in the distribution does exactly that for a simple example XML file, and measures the difference in file size (the file is slightly smaller for the BSAX encoding of the sample file) and the difference in read time (the read time is significantly faster for the sample file).
JAM (JavaGen Ant Modules) allows Java/J2EE developers to create robust, test-driven build environments with just a few lines of Ant script. Builds are simplified with a standard set of commands that you customize for your project. The Maven-to-Ant bridge manages classpaths, dependencies, versioning, and resource downloads automatically. JAM modules support JBoss, Tomcat 5, Resin, Oracle OC4J, JUnit, Cactus, XDoclet, CVS, Axis, Castor, JMX EJBs, and Hibernate.