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).
SNAP Platform is a development toolkit that packages into an easy to install solution the the Jikes Java compiler, the SableVM Java-like virtual machine and the GNU Classpath Java-like API, and the Eclipse universal tools platform, plus sample programs with source code and developer documentation.
XMLImportDB provides an easy-to-use interface that allows developers to create a baseline database environment that can be embedded in their source code for use in jUnit test cases. The database environment can be described in a separate file in the same package as the tests, in a hard coded string in the test case classes, or in any other location for which a java.io.Reader can be created at runtime.
Isobel is a framework to build complex information retrieval and analysis systems. Isobel can be functionally divided in two subsytems, Isobel Gatherer (the crawling and filtering subsystem) and Isobel Analyzer (the analysis subsystem). The two subsytems can also be used separately. Isobel Gatherer offers ready-to-use services like content fetching, scheduling, document format conversion, Hyperlink graph storage and analysis, content storage and indexing. A programmer may easily add new services. Isobel Analyzer uses the IBM UIMA architecture to reuse the analysis components developed for this architecture.