Lucane is a free groupware platform written in Java, designed with extensibility in mind. Some applications are bundled with the platform, like a peer to peer quick message service, client/server and peer to peer file sharing, shared drawing, multi-user chat, audioconf, forums, a shared calendar, and more. The platform as a whole provides easy development for your networked applications with an object based network protocol, client/server and peer to peer integration, user and groups management, internationalization, and more.
Dwarf HTTP Server is a full-featured Web server with a Java Servlet API 2.2 implementation and JSP support. Since it is based on the Dwarf framework, it shares its common design principles: powerful security architecture, modularity and extensibility, XML-based configuration, uniform logging, and remote management.
Red-Piranha is a search system that can actually learn what you are looking for. It can be used as a Web page, command line, or XML-WebService, so it will work with most languages, including Java, Perl, C#/.NET, and PHP. It includes learning abilities for the Desktop/Internet search functionality. All feedback from the user is stored in (editable) XML and RDF, and is used by the system to improve the quality of searches.
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.
JChassis TermUI is an API for simple GUI-like user interfaces on ANSI/VT100-compliant terminals and terminal emulators, such as Linux virtual terminals, GNOME Terminal, and KDE Konsole. The intent is similar to that of the ncurses library, but done in pure Java. Several commonly used widgets are available.