mod_auth_useragent2 is an Apache module that can be used to limit access to documents by means of the User-Agent. As an authentication method, this is really unsafe because it is easy to change the User-Agent in most browsers, but it could be used to prevent stupid bots and spiders from accessing your Web sites.
ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
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.