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SWAN (Semantic Web Applications in Neuromedicine) is a Web-based collaborative program that aims to organize and annotate scientific knowledge about Alzheimer disease (AD) and other neurodegenerative disorders. Its goal is to facilitate the formation, development and testing of hypotheses about the disease. The ultimate goal of this project is to create tools and resources to manage the evolving universe of data and information about AD in such a way that researchers can easily comprehend their larger context ("what hypothesis does this support or contradict?"), compare and contrast hypotheses ("where do these two hypotheses agree and disagree?"), identify unanswered questions and synthesize concepts and data into ever more comprehensive and useful hypotheses and treatment targets for this disease. The SWAN project is designed to allow the community of AD researchers to author, curate and connect a diversity of data and ideas about AD via secure personal and public SWAN workspaces, using the emerging Semantic Web paradigm for deep interconnection of data, information and knowledge. We are initially focusing on developing a fully public Web resource deployed as part of the Alzheimer Research Forum web site (www.alzforum.org). After the public resource has been launched, we will also develop secure personal workspaces (MySWAN) and semi-private lab workspaces (LabSWAN). An essential component of this project is development of an initial, core knowledge base within SWAN, which will provide immediate value to researchers at the time of deployment. This is a critically important part of our strategy to ensure that the SWAN system gains wide adoption and active participation by the AD research community. As part of our development strategy, we are also recruiting a "beta test" community of AD researchers to enter their own hypotheses, add commentaries and citations, and provide feedback on the technology and content. SWAN is being developed by a collaborative team from

The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics. The foundation grew out of the volunteer projects BioPerl, BioJava and BioPython and was formally incorporated in order to handle our modest requirements of hardware ownership, domain name management and funding for conferences and workshops.The Foundation does not participate directly in the development or structure of the open source work, but as the members of the foundation are drawn from the member projects, there is clear commonality of direction and purpose. Occasionally the O|B|F directors may make announcements about our direction or purpose (a recent one was on the licensing of academic software) when the board feels there is a need to clarify matters, but in general we prefer to remain simply the administrative support organization for our member projects. Our main activities are: * Underwriting and supporting the BOSC conferences * Organizing and supporting developer-centric "hackathon" events * Managing our servers, colocation facilities, bank account & other assets We are incorporated in the state of Delaware, USA as a not-for-profit company.

Open Journal Systems (OJS) is a journal management and publishing system that has been developed by the Public Knowledge Project through its federally funded efforts to expand and improve access to research.

The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods allowing scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our visionis that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that they are semantically interoperable and useful for improving biomedical science and clinical care. Our resources include the Open Biomedical Ontologies (OBO) library, the Open Biomedical Data (OBD) repositories, and tools for accessing and using this information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects to enable outside research and stimulate technology development in the Center. The Center undertakes outreach and educational activities (Biomedical Informatics Program) to train future researchers to use biomedical ontologies and related tools with the goal of enhancing scientific discovery.

The advent of the World Wide Web has led to an explosion in the number of diverse resources available to neuroscientists. Despite the availability of powerful search engines, locating these diverse resources has become increasingly difficult and time consuming. The NIF project utilizes both advanced machine-based search technologies and old-fashioned human legwork to provide access to neuroscience-relevant resources on the Web. Resources include research materials, Web pages, software tools, data sets, literature and general information. The NIF has developed technologies that allow a user to search across these different types of resources, all from a single interface. A unique feature of the NIF is the ability to issue direct queries against multiple databases simultaneously, retrieving content that is largely hidden from traditional search engines. A second unique feature is an extensive vocabulary covering major neuroscience domains for describing and searching these resources. The NIF takes advantage of advances in knowledge engineering to broaden and refine searches based on related concepts. The NIF beta test site was developed to gain feedback on the NIF search interface and content. Users will be asked to search the NIF, explore the vocabularies, and answer a questionnaire about their experience.

bioconductor.org Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.

This package of tools encompasses many of the common pieces of software required for the analysis of short read sequences produced by the Second Generation DNA sequencing machines. (eg. Illumina/Solexa sequencers, ABI SOLiD and 454). The focus of this project is on post-alignment analysis, thus the input for this process should be the files produced by sequence aligners such as MAQ, Eland or Exonerate. The output should be provided in several formats, including BED and WIG files which are readable by the UCSC Genome Browser.

To establish a method of measuring the solubility of some compounds in organic solvents. For a justification of this project see here.

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

The myGrid team produce and use a suite of tools designed to "help e-Scientists get on with science and get on with scientists". The tools support the creation of e-laboratories and have been used in domains as diverse as biology, social science, music, astronomy, text mining and chemistry. The tools have been adopted by a large number of projects and institutions. The team has developed tools and infrastructure to allow: * the design, editing and execution of workflows in Taverna * the sharing of workflows and related data by myExperiment * the cataloguing and annotation of services in BioCatalogue and Feta * the creation of user-friendly rich clients such as UTOPIA

A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.