Ujorm is an easy-to-use ORM framework based on key-value objects. The framework was designed for rapid Java development with great performance and a small footprint. The key features are type safe queries, relation mapping by Java code, no entity states, and a memory overloading protection cache.
PathVisio is a bioinformatics tool that lets you do everything with biological pathway diagrams. PathVisio helps you organize biological information and lets you present or publish that information easily. You can create and draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl, Entrez or HMDB, and add comments and literature references from pubmed. PathVisio also lets you sort through high-throughput experimental data in pathway context. This is a much more pleasant way to present data than just a large table. You can import microarray, proteomics or metabolomics data. PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods, and new pathway formats. PathVisio is compatible with WikiPathways.
BRAP is a Java remoting protocol that uses native Java object serialization encapsulated in HTTP. It aims to be an alternative to Spring HttpInvoker and Spring Security, especially when you don't need or want the dependencies of Spring in your client, such as when building a rich client application where size might be an issue. The authentication mechanism lets you use your own domain objects as credentials. BRAP gives you "pass by reference" even though the object arguments are serialized and passed to the remote service: changes that happen on the remote side can be applied to the client side automatically. BRAP focuses on being easy to use, small in size, yet powerful and extensible.