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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

open science blog - 0 views

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    The Network for Open Scientific Innovation is founded upon the belief, no, the unshakeable certainty, that creativity, love, and intelligence can solve any problem. Recent years have seen technological revolutions in informatics, communications, and the life sciences. Sadly, this rapid progress has not been matched by a revolution in the democratization of scientific problem solving.
Mike Chelen

UCSF Chimera Home Page - 0 views

shared by Mike Chelen on 11 Dec 08 - Cached
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    UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics and funded by the NIH National Center for Research Resources (grant P41-RR01081).
Mike Chelen

Main Page - GenBioWiki - 0 views

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    GenBioWiki is the student home page for the Genetics, Bioinformatics, and Computational Biology (GBCB) program at Virginia Tech. Bioinformatics and computational biology provide a research platform to acquire, manage, analyze, and display large amounts of data, which in turn catalyze a systems approach to understanding biological organisms, as well as making useful predictions about their behavior in response to environmental and other perturbations. Moreover, bioinformatics is the study of biological systems and large biological data sets using analytical methods borrowed from computer science, mathematics, statistics, and the physical sciences. This transdisciplinary approach to research requires graduates with extensive cross-cultural professional and technical training and provides ample employment opportunities for Ph.D. graduates. [1]
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

Science in the open » A breakthrough on data licensing for public science? - 0 views

  • Peter Murray-Rust and others at the Unilever Centre for Molecular Informatics at Cambridge
  • conversation we had over lunch with Peter, Jim Downing, Nico Adams, Nick Day and Rufus Pollock
  • appropriate way to license published scientific data
  • ...27 more annotations...
  • value of share-alike or copyleft provisions of GPL and similar licenses
  • spreading the message and use of Open Content
  • prevent “freeloaders” from being able to use Open material and not contribute back to the open community
  • presumption in this view is that a license is a good, or at least acceptable, way of achieving both these goals
  • allow people the freedom to address their concerns through copyleft approaches
  • Rufus
  • concerned more centrally with enabling re-use and re-purposing of data as far as is possible
  • make it easy for researchers to deliver on their obligations
  • worried by the potential for licensing to make it harder to re-use and re-mix disparate sets of data and content into new digital objects
  • “license”, will have scientists running screaming in the opposite direction
  • we focused on what we could agree on
  • common position statement
  • area of best practice for the publication of data that arises from public science
  • there is a window of opportunity to influence funder positions
  • data sharing policies
  • “following best practice”
  • don’t tend to be concerned about freeloading
  • providing clear guidance and tools
  • if it is widely accepted by their research communities
  • “best practice is X”
  • enable re-use and re-purposing of that data
  • share-alike approaches as a community expectation
  • Explicit statements of the status of data are required and we need effective technical and legal infrastructure to make this easy for researchers.
  • “Where a decision has been taken to publish data deriving from public science research, best practice to enable the re-use and re-purposing of that data, is to place it explicitly in the public domain via {one of a small set of protocols e.g. cc0 or PDDL}.”
  • focuses purely on what should be done once a decision to publish has been made
  • data generated by public science
  • describing this as best practice it also allows deviations that may, for whatever reason, be justified by specific people in specific circumstances
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