OpenEJB is a simple, lightweight Enterprise JavaBeans (EJB) container and server. You can embed OpenEJB in your own applications, or in a Web application server like Tomcat, or run it as a standalone EJB server. It supports EJB 3.0, 2.1, 2.0, and 1.1, and has partial support for EJB 3.1.
OpenJPA is a 100% compliant feature-rich implementation of the persistence part of Enterprise Java Beans 3.0, also known as the Java Persistence API (JPA). It can be used as a stand-alone POJO persistence layer, or it can be integrated into any EJB3.0 compliant container and many lightweight frameworks.
The OpenUDDI project is focused on creating a high performance, easy to use UDDI v3 compliant server and client library. The server and client is built using Java, version 5 for the server and version 1.4 for the client. The server uses Hibernate, and supports a wide variety of SQL databases for data storage.
Poor Man's Imaging Wrapper a clean and simple API wrapper over JAI, Java2D, ImageIO, and AWT. It supports a set of imaging operations (read, write, scale/resize, crop, grayscale, add transparency, rotate, add border, flip/mirror, add text, overlay, blur, sharpen, etc.) with simple direct calls to the API. If you want to switch from Java2D to JAI, all you need to do is add JAI jars to the classpath. It supports GIF encoding if PJA tools jars are available in the classpath.
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.