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.
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.
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.
UIMA SDK is a software architecture and framework for supporting the development, integration, and deployment of search and analysis technologies. It can be used to analyze large volumes of unstructured information (text, audio, video, images, etc.) to discover, organize, and deliver relevant knowledge to the client or application end user.
Hawron is a GUI tool for the Apache XML Web Development Framework Cocoon and pure Java. It mainly supports the "Offline Generation Part" of Cocoon, but an embedded Servlet Container (Jetty) for Cocoon's default environment is included. Hawron tries to help Cocoon users with some extra features like publishing offline generated files (ftp, sftp) and editing content (embedded OpenOffice).