VRaptor3 is a fully-fledged Java Web framework focused on fast development and maintainable code. It intends to make RESTful application development easy. A resource corresponds to a business logic annotated with its path and HTTP method. It runs inside DI Containers (Spring or Pico out of the box) and, therefore, enables full integration with them. Also, using Hibernate is easier: its session is automatically injected by VRaptor, so you just have to use it. VRaptor3 is refactor-friendly, especially in its redirecting configuration. It is also nicely extensible.
The Generic Repository (grepo) is a framework for Java which allows you to access (database) repositories in a generic and consistent manner. Using grepo, it is generally no longer required to provide all the boilerplate code which is necessary in order to access (database) repositories from Java. All you have to do is write appropriate database code (queries, procedures, functions, etc.), an appropriately annotated Java interface, and very little Spring configuration.
HornetQ is a multi-protocol, embeddable, high performance, clustered, asynchronous messaging system. HornetQ is an example of Message Oriented Middleware. It includes an extensive, easy-to-understand user-manual and quick-start guide and over 65 ready-to-run examples out of the box, demonstrating everything from simple JMS usage to complex clusters of servers and more exotic functionality. Its elegant POJO based design has minimal third party dependencies. You can run HornetQ as a stand-alone messaging broker, run it in integrated in your favorite JEE application server, or run it embedded inside your own application. Its journal provides high persistent messaging performance. Automatically switching into native mode when running on Linux, it uses asynchronous IO to provide persistent messaging rates that can saturate the write throughput of a disk. Its pluggable transport system uses JBoss Netty out of the box to provide high performance and scalability on the wire.
RelEx is an English-language semantic dependency relationship extractor, built on the Carnegie-Mellon Link Grammar parser. It can identify subject, object, indirect object, and many other syntactic dependency relationships between words in a sentence; it generates dependency trees, resembling those of dependency grammars, and specifically, those of Dekang Lin's MiniPar and the Stanford parser. It accomplishes this by applying a sequence of rules, based on the local context, and thus resembles constraint grammar in its implementation. In this sense, it implements some of the ideas of Hudson's Word Grammar. However, unlike other dependency parsers, RelEx attempts a greater degree of semantic normalization.
Thread Weaver is a framework for writing multithreaded unit tests for Java classes. It lets you create breakpoints inside your code and to stop individual threads when they reach a breakpoint. This allows you to produce controlled repeatable tests that can help to verify thread safety and detect race conditions.
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.
Niocchi is a Java crawler library implementing synchronous I/O multiplexing. This specific type of implementation allows crawling tens of thousands of hosts in parallel on a single low end server. Niocchi has been designed for big search engines that need to crawl massive amount of data, but can also be used to write no-frills crawlers.
lambdaj is a Java library that allows you to manipulate collections in a pseudo-functional and statically typed way. The main purpose of lambdaj is to partially eliminate the burden of writing (often nested and poorly readable) loops while iterating over collections. In particular, it allows you to iterate a collection in order to filter its items on a given condition, convert each item with a given rule, extract a given property from each item, sort the items on the values of one of their properties, group or index the items on the value of one or more properties, invoke a method on each item, or aggregate the items or the values of one of their properties. It allows all this without having to write a single explicit loop.
SlimWeb aims to replace Struts or JSF in your J2EE application, but is closer to Rails or TurboGears in its heavy use of convention-over-configuration, simplicity, and power. It aims to reduce (and most of the time completely eliminate) all boilerplate code, XML configuration files, and even deployment times.