BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit....

Hazelcast is a clustering and highly scalable data distribution platform for Java.

Features:

Distributed implementations of java.util.{Queue, Set, List, Map} Distributed implementation of java.util.concurrency.locks.Lock Distributed implementation of java.util.concurrent.ExecutorService Distributed MultiMap for one-to-many relationships Distributed Topic for publish/subscribe messaging Transaction support and J2EE container integration via JCA Socket level encryption support for secure clusters Synchronous (write-through) and asynchronous (write-behind) persistence Second level cache provider for Hibernate Monitoring and management of the cluster via JMX Dynamic HTTP session clustering Support for cluster info and membership events Dynamic discovery Dynamic scaling Dynamic partitioning with backups Dynamic fail-over ...

uPortal is a free, opensource portal under development by institutions of higher-education. This group sees an institutional portal as a "pocket-sized" version of the campus Web and a services delivery platform. Portal technology adds "customization" and "community" to the campus Web presence. uPortal is standards-embracing, including XML, JSR-168 and JSR-286, and XSLT....

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs.

The Web Services Description Language for Java Toolkit (WSDL4J) allows the creation, representation, and manipulation of WSDL documents. Is the reference implementation for JSR110 'JWSDL' (jcp.org).

OpenMRS is an application which enables design of a customized medical records system with no programming knowledge (although medical and systems analysis knowledge is required). It is a common framework upon which medical informatics efforts in developing countries can be built. The system is based on a conceptual table structure which is not dependent on the actual types of medical information required to be collected or on particular data collection forms and so can be customized for different uses....

Encog is an advanced neural network and machine learning framework for Java, C# and C/C++. Encog contains classes to create a wide variety of networks, as well as support classes to normalize and process data for these neural networks. Encog trains using multithreaded resilient propagation. Encog can also make use of a GPU to further speed processing time. A GUI based workbench is also provided to help model and train neural networks. Encog has been in active development since 2008....

AXIOM stands for AXis Object Model (also known as OM - Object Model) and refers to the XML infoset model that was initially developed for Apache Axis2. XML infoset refers to the information included inside the XML and for programmatical manipulation it is convenient to have a representation of this XML infoset in a language specific manner. For an object oriented language the obvious choice is a model made up of objects. DOM and JDOM are two such XML models. OM is conceptually similar to such an XML model by its external behavior but deep down it is very much different....

Mondrian is an OLAP (online analytical processing) engine written in Java. It reads from JDBC data sources, aggregates data in a memory cache, and implements the MDX language and the olap4j and XML/A APIs.

Ever wanted to get rid of Outlook ? DavMail is a POP/IMAP/SMTP/Caldav/LDAP gateway allowing users to use any mail/calendar client with Exchange, even from the internet through Outlook Web Access on any platform, tested on MacOSX, Linux and Windows