db4o is an object database for Java and all .NET environments. Its features include ACID transactions, automatic class schema recognition, query-by-example, a S.O.D.A. object querying API, native queries, LINQ support on .NET, callback methods, memory files, cascade-on-delete, multi-threaded access, and Java Webstart and servlet support.
The Internet Document And Report Server (IDRS) is a full Web development platform. All pages are built using an XML like dialect called the Reporting Markup Language (RML), can be generated using data from any JDBC complient database, and mostly require no programming logic. For reports that do require programming logic, RML pages can also use external Java classes and embedded JPython and BeanShell scripts for a higher level of control. Features of the IDRS include user-based security, data connection pooling for use by both the central IDRS system and by individual reports, and multiple databases to be used for each report and JSP.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
jMusic provides a library of classes for generating and manipulating music, and is a solid framework for computer assisted composition in Java. jMusic supports composers by providing a music data structure based upon note/sound events, and methods for working with that musical data. jMusic can read and write MIDI files, audio files, and its own .jm files. jMusic is designed to be extendible, encouraging you to build upon the functionality of jMusic by programming in Java to create your own music composition tools.
MUSCLE (Multi User Server Client Linking Environment) is an N-way messaging server and networking API. It includes client-side networking APIs for various languages, including C, C++, C#, Delphi, Java, and Python. MUSCLE lets programs communicate over a network via streams of serialized Message objects. The included server program ("muscled") lets its clients message each other and store information in its server-side hierarchical database. The database supports flexible queries via hierarchical wildcarding, and "live" updates via a subscription mechanism.
The Extended Universal Resource Locator library provides a complete virtualization of file-like objects. How data is stored is completely transparent to the client, since the library is meant to replace java.io.File. It provides implementations for handling local files, Jar/Zip archives, and XML documents. (Implementations for CVS and FTP are available seperately.) Other storage providers can be written and plugged in. It also provides a merged filesystem implementation that allows multiple hierarchies to appear as one and to override each other in a controlled way. Other features include notification of changes to files, and support for attaching (dynamically updatable) actions to file objects.
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
JGraph is a free, mature, and robust Java diagramming library. It contains all the graph visualization, layout, and interaction functionality you might expect in a graph library, including multiple views, layering, zoom, drag and drop, undo, automatic expanding and collapsing, routing, and layouts. You can create workflow editors, BPMN, CAD tools, network diagrams, database visualization tools, and more. It is fully documented, including examples, and has an active support community.