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OYSTER stands for Open sYSTem Entity Resolution, a project to build a configurable, open-source entity resolution engine.

OpenMark is a computer-assisted assessment (CAA) system that has its foundations in computer-assisted learning. It was developed by The Open University, where it has been used by thousands of students, and is now released as open source software under the GNU General Public License

The Distributed Annotation System (DAS) defines a communication protocol used to exchange biological annotations. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities.

By integrating heterogeneous original data with uniform RDF format, creating additional ontology mappings between GO terms, and introducing a set of reasoning rulebases, we proposed a RDF model GORouter.

Protocol buffers are a flexible, efficient, automated mechanism for serializing structured data - think XML, but smaller, faster, and simpler. You define how you want your data to be structured once, then you can use special generated source code to easily write and read your structured data to and from a variety of data streams and using a variety of languages. You can even update your data structure without breaking deployed programs that are compiled against the "old" format.

Businesses are moving beyond marketing in virtual worlds and are exploring other applications of virtual worlds (see a recent BusinessWeek article & slideshow). Enabling collaboration among remote workers is one such application (see our past posts and paper on this topic). A variety of virtual world options or platforms have been available for supporting remote work and these include Second Life, Qwaq, Forterra, and Tixeo. Last week I had the rare opportunity to see an emerging virtual world called Wonderland, the product of an open source project, Project Wonderland, sponsored by Sun Microsystems. During a conference call with our colleague Nicole Yankelovich, Principal Investigator of the Collaborative Environments Project at Sun Microsystems, Becky Jestice and I were lucky enough to get a tour of Wonderland. Nicole graciously spent over an hour to show us some of the impressive features of Wonderland. The tour was so impressive that I want to devote a post to some key aspects of Wonderland: * Virtual meeting participants can use voice to communicate with one another; * If necessary, participants can connect to a Wonderland meeting via telephone; * Private conversations between participants are possible in a virtual meeting; * Participants can share applications; and * Anyone can try out Wonderland (see instructions below).

The GridSphere portal framework provides an open-source portlet based Web portal. GridSphere enables developers to quickly develop and package third-party portlet web applications that can be run and administered within the GridSphere portlet container. Here you will find the GridSphere portal framework available for download and documentation related to the installation and development of portlets using GridSphere.

DynaQ stands for 'Dynamic Queries for document based, personal information spaces'. The goal of the project is to conceptualise and to develop a prototypical inquiry system to explore the personal information space, that supports the user with the help of the searching paradigm orienteering. The document-based, personal information space of the user constitutes by all documents on his computer. Included are documents of several file formats (e.g. *.pdf), but also the users emails. Also included are all available meta informations and existing semantic informations according to the documents. Users that are not aware of the scientific context of the project can just think of DynaQ as an desktop search engine.

Apache Synapse is designed to be a simple, lightweight and high performance Enterprise Service Bus (ESB) from Apache. Based on a small asynchronous core, Apache Synapse has excellent support for XML and Web services - as well as binary and text formats. The Synapse engine is configured with a simple XML format and comes with a set of ready-to-use transports and mediators. We recommend you start by reading the QuickStart and then trying out the samples.

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

The Bio2RDF project is a tool to convert bioinformatics data and knowledge bases to RDF format. It is a kind of generalized rdfizer for bioinformatics applications, and it is a place for the semantic web life science community to develop and grow.

Apache ODE (Orchestration Director Engine) executes business processes written following the WS-BPEL standard. It talks to web services, sending and receiving messages, handling data manipulation and error recovery as described by your process definition. It supports both long and short living process executions to orchestrate all the services that are part of your application.

Jersey is the open source (under dual CDDL+GPL license) JAX-RS (JSR 311) Reference Implementation for building RESTful Web services. But, it is also more than the Reference Implementation. Jersey provides additional APIs and extension points (SPIs) so that developers may extend Jersey to suite their needs.

The Disco - Hyperdata Browser is a simple browser for navigating the Semantic Web as an unbound set of data sources. The browser renders all information, that it can find on the Semantic Web about a specific resource, as an HTML page. This resource description contains hyperlinks that allow you to navigate between resources. While you move from resource to resource, the browser dynamically retrieves information by dereferencing HTTP URIs and by following rdfs:seeAlso links.

All conferences and research events have much informal related content spread around the Internet, including abstracts, papers, presentations and audio/visual material. Locating this content can be difficult and time-consuming. Using semantic web tools, IUGO is investigating how to organise and provide access to this valuable information.

Felix is a community effort to implement the OSGi R4 Service Platform, which includes the OSGi framework and standard services, as well as providing and supporting other interesting OSGi-related technologies. The ultimate goal is to provide a completely compliant implementation of the OSGi framework and standard services and to support a community around this technology. Felix currently implements a large portion of the OSGi release 4 specification, but additional work is necessary for full compliance. Despite this fact, the OSGi framework functionality provided by Felix is very stable.

Apache ActiveMQ is the most popular and powerful open source Message Broker and Enterprise Integration Patterns provider.

SWOOP is a tool for creating, editing, and debugging OWL ontologies. It was produced by the MIND lab at University of Maryland, College Park, but is now an open source project with contributers from all over.