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Mike Chelen

SWAN (Semantic Web Applications in Neuromedicine) Project - 0 views

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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
Mike Chelen

opentextbooks - Open Knowledge Foundation Wiki - 0 views

  • Rick_GTP Rick Watson, Global Text Project and University of Georgia
  • ameeg Amee Godwin, ISKME, OER Commons, Calif
  • jwyg jwyg = Jonathan Gray, The Open Knowledge Foundation + Open Text Book
  • ...12 more annotations...
  • karen_at_k12opened Karen Fasimpaur from K12 Opened and the Kids Open Dictionary (http://dictionary.k12opened.com)
  • JudyBaker Judy Baker, Director of Community College Open Textbook and Dean of Foothill Global Access, Foothill College, California
  • jonathan_Connexions Jonathan Emmons, community development specialist for the Connexions Project
  • Don Don McCubbrey, University of Denver, Co-Project leader if Global Text (http://globaltext.org) with Rick Watson
  • emerika Brad Emerson K12 Opened.com and the Kids Open Dictionary
  • JudyBaker Community College Consortium for Open Educational Resources (http://cccoer.wordpress.org)
  • mikechelen Mike Chelen, OpenSci.Info
  • Andrew Andrew Whitworth, English Wikibooks
  • sub Sub, (french) admin and main contributor to http://fr.wikibooks.org/
  • mib_9pubxh Sanford Forte, Senior Research and Project Consultant, Community College Open Textbook Project; and, Founder/Director, California open Source Textbook Project
  • mpal Yes, this is Murugan
  • mpal from CK-12 Foundation
Mike Chelen

Main Page - Open Bioinformatics Foundation - 0 views

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    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.
Mike Chelen

Open Journal Systems | Public Knowledge Project - 0 views

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    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.
Mike Chelen

The National Center for Biomedical Ontology - 0 views

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    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.
Mike Chelen

Neuroscience Information Framework (Main.WebHome) - Neuroscience Information Framework ... - 0 views

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    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.
Mike Chelen

Welcome to BioConductor - bioconductor.org - 0 views

shared by Mike Chelen on 12 Dec 08 - Cached
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    bioconductor.org Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
Mike Chelen

http://vancouvershortr.sourceforge.net/ - 0 views

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    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.
Mike Chelen

UsefulChem » Exp207 - 0 views

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

Bioclipse - Home - 0 views

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    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.
Mike Chelen

myGrid » Home - 0 views

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    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
Mike Chelen

Using the Google Plugin for Eclipse - Google App Engine - Google Code - 0 views

  • Eclipse 3.4 (Ganymede)
  • Help menu > Software Updates...
  • Guestbook
  • ...18 more annotations...
  • http://dl.google.com/eclipse/plugin/3.4
  • Google Plugin for Eclipse 3.4
  • Google Web Toolkit SDK
  • Google App Engine Java SDK
  • Install...
  • restart
  • File menu > New > Web Application Project
  • Add Site...
  • Project name
  • Package
  • guestbook
  • Verify that "Use Google App Engine" is checked.
  • Finish
  • Run menu, Debug As > Web Application
  • App Engine deploy button uploads your application to App Engine:
  • register an application ID with App Engine using the Admin Console
  • edit the appengine-web.xml file and change the <application>...</application> element to contain the new ID
  • administrator account username (your email address) and password
Mike Chelen

Open Knowledge Foundation Blog » Blog Archive » Comments on the Science Commo... - 0 views

  • the protocol does not discuss any of the possible attractions of allowing such provisions
  • Protocol gives 3 basic reasons for preferring the ‘PD’ approach
  • Science Commons Protocol for Implementing Open Access Data
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  • I am not really convinced by any of these points that attribution or share-alike provisions should not be included in open data licenses
  • application of obligations based on copyright in situations where it is not necessary
  • non-copyrightable elements extends to the entire database and inadvertently infringe
  • If intellectual property rights are involved
  • requirements carrying a stiff penalty for failure
  • selective waiving of intellectual property rights
  • interpretative problems
Mike Chelen

SourceForge.net: Staden Package - 0 views

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