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This is a sub-project of the BioMoby project. It aims to develop tools in Java in order: * to access BioMoby registries, allowing all features provided by such registries, including but not limited to registering and deregistering of the BioMoby services and their parts, discovering them, and understanding their data in various formats (such as RDF), * to create Java implementations of BioMoby services, especially to help service providers with creating BioMoby data containers (input and output data) without exposing providers to the complexity of the XML required and produced by BioMoby services, and finally

The main goal of the Ibis project is to create an efficient Java-based platform for grid computing. The Ibis project currently consists of the IPL (a communication library), a variety of programming models, the Java Grid Application Toolkit, and the Zorilla peer-to-peer grid middleware. All components can be deployed on any grid platform, due to the use of Java.

The Java Text Categorizing Library (JTCL) is a pure java 1.5 implementation of libTextCat which in turn is "a library that was primarily developed for language guessing, a task on which it is known to perform with near-perfect accuracy". It's distributed under the LGPL and can also be used in order to categorize text into arbitrary topics by computing appropiate fingerprints which represent the categories.

The Knowledge Annotator is a Java program that allows users to mark-up web pages with SHOE knowledge without having to worry about the HTML-like codes. The Annotator is available as an applet or a stand-alone Java application.

OPS4J stands for Open Participation Software for Java, and this community is trying to build a new, more open model for Open Source development, where not only the usage is Open and Free, but the Participation is Open as well. Removal of barriers, let more people in, have more fun and less politics. I have also seen Open Development as a term to describe this. Think of it as Wiki brought to Coding. Wikipedia is of course the most outstanding example of open collaboration.

Project Wonderland is a 100% Java and open source toolkit for creating collaborative 3D virtual worlds. Within those worlds, users can communicate with high-fidelity, immersive audio, share live desktop applications and documents and conduct real business. Wonderland is completely extensible; developers and graphic artists can extend its functionality to create entire new worlds and new features in existing worlds.

(aka YALE) data mining, machine learning, knowledge discovery, business intelligence in Java. 400+ operators: data mining incl. Weka,learning,preprocessing,validation,visualization. GUI,API,XML,analysis,knowledge discovery,databases,business intelligenc

The Sematic Web Client Library represents the complete Semantic Web as a single RDF graph. The library enables applications to query this global graph using SPARQL- and find(SPO) queries. To answer queries, the library dynamically retrieves information from the Semantic Web by dereferencing HTTP URIs and by following rdfs:seeAlso links. The library is written in Java and is based on the Jena framework.

OntoMat-Annotizer is a user-friendly interactive webpage annotation tool. It supports the user with the task of creating and maintaining ontology-based OWL-markups i.e. creating of OWL-instances, attributes and relationships. It include an ontology browser for the exploration of the ontology and instances and a HTML browser that will display the annotated parts of the text. It is Java-based and provide a plugin interface for extensions. The intended user is the individual annotator i.e., people that want to enrich their web pages with OWL-meta data. Instead of manually annotating the page with a text editor, say, emacs, OntoMat allows the annotator to highlight relevant parts of the web page and create new instances via drag?n?drop interactions. It supports the meta-data creation phase of the lifecycle. It is planned that a future version will contain an information extraction plugin, that offers a wizard which suggest which parts of the text are relevant for annotation. That aspect will help to ease the time-consuming annotation task.

JAX-RS: Java API for RESTful Web Services

This is the "Eclipse of Web Browsers", a secure social web browsing environment that runs off of your own highly personal and private data store. Written primarily in Java, it uses Gecko as its web runtime, and has a back-end driven by MySQL and Lucene See also http://www.suprasphere.com/

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes 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.

LingPipe is a suite of Java libraries for the linguistic analysis of human language.

Taste is a flexible, fast collaborative filtering engine for Java. The engine takes users' preferences for items ("tastes") and returns estimated preferences for other items. For example, a site that sells books or CDs could easily use Taste to figure out, from past purchase data, which CDs a customer might be interested in listening to.

GATE is... * the Eclipse of Natural Language Engineering, the Lucene of Information Extraction, a leading toolkit for Text Mining * used worldwide by thousands of scientists, companies, teachers and students * comprised of an architecture, a free open source framework (or SDK) and graphical development environment * used for all sorts of language processing tasks, including Information Extraction in many languages * funded by the EPSRC, BBSRC, AHRC, the EU and commercial users * 100% Java reference implementation of ISO TC37/SC4 and used with XCES in the ANC * 10 years old in 2005, used in many research projects and compatible with IBM's UIMA * based on MVC, mobile code, continuous integration, and test-driven development, with code hosted on SourceForge

See also: http://lists.w3.org/Archives/Public/semantic-web/2008Apr/0005.html NaturalOWL is an open-source natural language generation engine written in Java. It produces descriptions of individuals (e.g., items for sale, museum exhibits) and classes (e.g., types of exhibits) in English and Greek from OWL DL ontologies. The ontologies must have been annotated in RDF with linguistic and user modeling resources. We demonstrate a plug-in for Protege that can be used to produce these resources and to generate texts by invoking NaturalOWL. We also demonstrate how NaturalOWL can be used by robotic avatars in Second Life to describe the exhibits of virtual museums. NaturalOWL demonstrates the benefits of Natural Language Generation (NLG) on the Semantic Web. Organizations that need to publish information about objects, such as exhibits or products, can publish OWL ontologies instead of texts. NLG engines, embedded in browsers or Web servers, can then render the ontologies in multiple natural languages, whereas computer programs may access the ontologies directly.

Mustru is a desktop search engine written in Java using Lucene, Lingpipe, and the Berkeley DB . Create an index from a set of directories on your local filesystem and use the Web based interface to query the index. Submit questions in natural language or boolean queries using keywords.

Unstructured Information Management applications are software systems that analyze large volumes of unstructured information in order to discover knowledge that is relevant to an end user. UIMA is a framework and SDK for developing such applications. An example UIM application might ingest plain text and identify entities, such as persons, places, organizations; or relations, such as works-for or located-at. UIMA enables such an application to be decomposed into components, for example "language identification" -> "language specific segmentation" -> "sentence boundary detection" -> "entity detection (person/place names etc.)". Each component must implement interfaces defined by the framework and must provide self-describing metadata via XML descriptor files. The framework manages these components and the data flow between them. Components are written in Java or C++; the data that flows between components is designed for efficient mapping between these languages. UIMA additionally provides capabilities to wrap components as network services, and can scale to very large volumes by replicating processing pipelines over a cluster of networked nodes.

IBM (NYSE: IBM) and Sun Microsystems, Inc. (NASDAQ: JAVA) today announced the launch of the OpenDocument Format (ODF) Toolkit Union, a new open-source software community project organized to make document software more innovative, versatile and useful for business.

In my previous article, I introduced the Map/Reduce model as a powerful model for parallelism. However, although Map/Reduce is simple, powerful, and provides a good opportunity to parallelize algorithm, it is based on a rigid procedural structure that requires injection of custom user code and therefore it is not easy to understand the big picture from a high level. You need to drill into the implementation code of the map and reduce functions in order to figure out what is going on.