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Mike Chelen

Creative Commons Attribution Noncommercial ShareAlike Legal Code - 0 views

creativecommons.org/...legalcode

shared by Mike Chelen on 22 May 09 - Snapshot
  • must include a
    copy of, or the Uniform Resource Identifier for, this
    License with every copy
  • Derivative Work
  • the terms of this License
  • ...10 more annotations...
  • distribute
  • may not exercise
  • rights granted to You
    in Section 3 above
  • primarily
  • primarily
    intended for or directed toward commercial advantage or
    private monetary compensation
  • exchange of the Work
    for other copyrighted works by means of digital
    file-sharing or otherwise shall not be considered to be
    intended for or directed toward commercial advantage or
    private monetary compensation
  • provided there is no
    payment of any monetary compensation in connection with
    the exchange of copyrighted works
  • keep intact all
    copyright notices for the Work
  • name of
    the Original Author
  • "Attribution Parties"
Mike Chelen

Science 2.0 - introduction and perspectives for Poland « Freelancing science - 0 views

freelancingscience.com/...on-and-perspectives-for-poland

science2.0 elearning eresearch

shared by Mike Chelen on 20 May 09 - Snapshot
  • transcript of Science 2.0 based on a presentation I gave on conference on open science organized in Warsaw earlier this month
  • prepared for mixed audience and focused on perspectives for Poland
  • new forms of communication between scientists
  • ...44 more annotations...
  • research become meaningful only after confronting results with the scientific community
  • peer-reviewed publication is the best communication channel we had so far
  • new communication channels complement peer-reviewed publication
  • two important attributes in which they differ from traditional models: openness and communication time
  • increased openness and shorter communication time happens already in publishing industry (via Open Access movement and experiments with alternative/shorter ways of peer-review)
  • say few words about experiments that go little or quite a lot beyond publication
  • My Experiment as an example of an important step towards openness
  • least radical idea you can find in modern Science 2.0 world
  • virtual research environment
  • focus is put on sharing scientific workflows
  • use case
  • diagram of the “methods” sections from experimental (including bioinformatics analyses) publications
  • make it easier for others to understand what we did
  • can open towards other scientists we can also open towards non-experts
  • people from all over the world compete in improving structural models of proteins
  • helps in improving protein structure prediction software and in understanding protein folding
  • combine teaching and data annotation
  • metagenome sequences in first case and chemistry spectra in the second
  • interactive visualizations of chemical structures, genomes, proteins or multidimensional data
  • communicate some difficult concepts faster
  • new approaches in conference reporting
  • report in real time from the conference
  • followed by a number of people, including even the ones that were already on the conference
  • “open notebook science” which means conducting research using publicly available, immediately updated laboratory notebook
  • The reason I did a model for Cameron’s grant was that I subscribed to his feed before
  • I didn’t subscribe to Cameron because I knew his professional profile
  • I read his blog, I commented on it and he commented on mine, etc.
  • participation in online communities
  • important part of Science 2.0 is the fact that it has human face
  • PhDs about the same time
  • first was from a major Polish institute, the second from a major European one
  • what a head of a lab both would apply to will see
  • gap we must fill, this is between current research and lectures we give today
  • access to real-time scientific conversation
  • follow current research and decide what is important to learn
  • synthetic biology
  • not all universities in world have synthetic biology courses
  • didn’t stop these students, and they plan to participate in IGEM again
  • community of life scientists
  • not only scientists – there are librarians, science communicators, editors from scientific journals, people working in biotech industry
  • even people without direct connection to science
  • diverse skills and background
  • online conference
  • interact with them and to learn from them
Mike Chelen

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

blog.openwetware.org/...a-licensing-for-public-science

open public science data license

shared by Mike Chelen on 15 May 09 - Snapshot
  • 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
  • don’t tend to be concerned about freeloading
  • 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”
  • providing clear guidance and tools
  • make it easy for researchers to deliver on their obligations
  • 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
Mike Chelen

Open Science and Information - 0 views

opensciinfo.referata.com/...Main_Page

opensci mediawiki semantic

shared by Mike Chelen on 01 May 09 - Snapshot
  • Mike Chelen
    Mike Chelen on 01 May 09
     
    semantic mediawiki for testing and development
Mike Chelen

Edge of Space Found | LiveScience - 0 views

www.livescience.com/...090409-edge-space.html

space solar_wind

shared by Mike Chelen on 10 Apr 09 - Snapshot
  • boundary between Earth's atmosphere and outer
    space
  • instrument developed by scientists at the University of Calgary
  • 73 miles (118 kilometers) above Earth's
    surface
  • ...21 more annotations...
  • astronauts can say they've
    been to space     after only passing the 50-mile (80-kilometer) mark
  • space industry is also a somewhat
    arbitrary 62 miles (100 kilometers)
  • United States, however, has never officially adopted a set boundary standard
  • overflight rights of satellites and other
    orbiting bodies
  • NASA's
    mission control uses 76 miles (122 kilometers) as their re-entry altitude
  • shuttle switches from steering with thrusters to
    maneuvering with air surfaces
  • 13 million miles (21
    million kilometers)
  • the boundary
    where Earth's gravity is no longer dominant
  • Supra-Thermal Ion Imager
  • tracking the relatively gentle winds of Earth's
    atmosphere     and the more violent flows of charged particles in space
  • difficult to make
    measurements in this region, which is too high for balloons and too low for
    satellites
  • second time that direct measurements of charged particle flows have
    been made in this region
  • first time all the ingredients – such as the
    upper atmospheric winds – have been included
  • David Knudsen of the University of Calgary
  • carried by the JOULE-II rocket on Jan. 19, 2007
  • an altitude of about 124 miles (200 kilometers) above sea level and collected
    data for the five minutes it was moving through the "edge of space."
  • Journal of Geophysical Research on April 7
  • space weather and its impacts
    on Earth
  • calculate energy flows into the Earth's atmosphere that
    ultimately may be able to help us understand the interaction between space and
    our environment
  • link between sunspots and the warming and cooling of the
    Earth's climate
  • how space weather impacts satellites, communications,
    navigation, and power systems
Mike Chelen

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

code.google.com/...eclipse.html

google appengine java eclipse plugin

shared by Mike Chelen on 08 Apr 09 - Snapshot
  • Eclipse 3.4 (Ganymede)
  • Help menu > Software Updates...
  • Add Site...
  • ...18 more annotations...
  • http://dl.google.com/eclipse/plugin/3.4
  • Google Plugin for Eclipse 3.4
  • Google App Engine Java SDK
  • Google Web Toolkit SDK
  • Install...
  • restart
  • File menu > New > Web Application Project
  • Guestbook
  • Project name
  • guestbook
  • Package
  • 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: The App Engine deploy button.
  • 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

EclipsePlugin - GitWiki - 0 views

git.or.cz/EclipsePlugin

git eclipse

shared by Mike Chelen on 06 Mar 09 - Snapshot
Mike Chelen

Main Page - Open Bioinformatics Foundation - 0 views

www.open-bio.org/Main_Page

open biology informatics

shared by Mike Chelen on 22 Sep 08 - Snapshot
  • Mike Chelen
    Mike Chelen on 22 Sep 08
     
    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

Home :::Academic Journals - 0 views

www.academicjournals.org

journals academic open access article science research

shared by Mike Chelen on 01 Mar 09 - Snapshot
  • Mike Chelen
    Mike Chelen on 01 Mar 09
     
    ACADEMIC JOURNALS provides free access to research information to the international community without financial, legal or technical barriers. All the journals from this organization will be freely distributed and available from multiple websites.....ACADEMIC JOURNALS, breaking new frontiers in the world of journals.
Mike Chelen

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

blog.okfn.org/...-implementing-open-access-data

open access data okfn science commons

shared by Mike Chelen on 01 Mar 09 - Snapshot
  • Science Commons Protocol for Implementing Open Access Data
  • Protocol gives 3 basic reasons for preferring the ‘PD’ approach
  • I am not really convinced by any of these points that attribution or share-alike provisions should not be included in open data licenses
  • ...7 more annotations...
  • the protocol does not discuss any of the possible attractions of allowing such provisions
  • 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
  • interpretative problems
  • selective waiving of intellectual property rights
Mike Chelen

Protocol for Implementing Open Access Data - 0 views

sciencecommons.org/...open-access-data-protocol

science commons open access data public domain

shared by Mike Chelen on 07 Sep 08 - Snapshot
  • information for the Internet community
  • distributing data or databases
  • “open” and “open access”
  • ...47 more annotations...
  • requirements for gaining and using the Science Commons Open Access Data Mark and metadata
  • interoperability of scientific data
  • terms and conditions around data make integration difficult to legally perform
  • single license
  • data with this license can be integrated with any other data under this license
  • too many databases under too many terms already
  • unlikely that any one license or suite of licenses will have the correct mix of terms
  • principles for open access data and a protocol for implementing those principles
  • Open Access Data Mark and metadata
  • databases and data
  • the foundation to legally integrate a database or data product
  • another database or data product
  • no mechanisms to manage transfer or negotiations of rights unrelated to integration
  • submitted to Science Commons for certification as a conforming implementation
  • Open Access Data trademarks (icons and phrases) and metadata on databases
  • protocol must promote legal predictability and certainty
  • easy to use and understand
  • lowest possible transaction costs on users
  • Science Commons’ experience in distributing a database licensing Frequently Asked Questions (FAQ) file
  • hard to apply the distinction between what is copyrightable and what is not copyrightable
  • lack of simplicity restricts usage
  • reducing or eliminating the need to make the distinction between copyrightable and non-copyrightable elements
  • satisfy the norms and expectations of the disciplines providing the database
  • norms for citation will differ
  • norms must be attached
  • Converge on the public domain by waiving all rights based on intellectual property
  • reconstruction of the public domain
  • scientific norms to express the wishes of the data provider
  • public domain
  • waiving the relevant rights on data and asserting that the provider makes no claims on the data
  • Requesting behavior, such as citation, through norms rather than as a legal requirement based on copyright or contracts, allows for different scientific disciplines to develop different norms for citation.
  • waive all rights necessary for data extraction and re-use
  • sui generis database rights
  • copyright
  • claims of unfair competition
  • implied contracts
  • and other legal rights
  • any obligations on the user of the data or database such as “copyleft” or “share alike”, or even the legal requirement to provide attribution
  • non-legally binding set of citation norms
  • waiving other statutory or intellectual property rights
  • there are other rights, in addition to copyright, that may apply
  • sui generis rights apply in the European Union
  • uncopyrightable databases may be protected in some countries
  • waivers of sui generis and other legal grounds for database protection
  • no contractual controls
  • using contract, rather than intellectual property or statutory rights, to apply terms to databases
  • affirmatively declare that contractual constraints do not apply to the database
Mike Chelen

The Control Fallacy: Why OA Out-Innovates the Alternative : Nature Precedings - 0 views

precedings.nature.com/...1

open science data license

shared by Mike Chelen on 11 Feb 09 - Snapshot
  • Mike Chelen
    Mike Chelen on 11 Feb 09
     
    This article examines the relationship between Open Access to the scholarly literature and innovation. It traces the ideas of "end to end" network principles in the Internet and the World Wide Web and applies them to the scholarly biomedical literature. And the article argues for the importance of relieving not just price barriers but permission barriers.
Mike Chelen

Open Knowledge Foundation Blog » Blog Archive » Open Data: Openness and Licensing - 0 views

blog.okfn.org/...en-data-openness-and-licensing

okfn blog open data science license

shared by Mike Chelen on 11 Feb 09 - Snapshot
  • Why bother about openness and licensing for data
  • It’s crucial because open data is so much easier to break-up and recombine, to use and reuse.
  • want people to have incentives to make their data open and for open data to be easily usable and reusable
  • ...8 more annotations...
  • good definition of openness acts as a standard that ensures different open datasets are ‘interoperable’
  • Licensing is important because it reduces uncertainty. Without a license you don’t know where you, as a user, stand: when are you allowed to use this data? Are you allowed to give to others? To distribute your own changes, etc?
  • licensing and definitions are important even though they are only a small part of the overall picture
  • If we get them wrong they will keep on getting in the way of everything else.
  • Everyone agrees that requiring attribution is OK
    • Mike Chelen
      Mike Chelen on 11 Feb 09
       
      My opinion is that there should be no requirements, including attribution, and that standards should be community-based instead of legal.
  • Even if a basic license is used it can be argued that any ‘requirements’ for attribution or share-alike should not be in a license but in ‘community norms’.
    • Mike Chelen
      Mike Chelen on 11 Feb 09
       
      Licenses and community norms are not exclusive. It's recommended to adopt a Public Domain license, and encourage attribution through community standards.
  • A license is likely to elicit at least as much, and almost certainly more, conformity with its provisions than community norms.
    • Mike Chelen
      Mike Chelen on 11 Feb 09
       
      Ease of access and should be the goal, not conformity.
  • (even to a user it is easy to comply with the open license)
    • Mike Chelen
      Mike Chelen on 11 Feb 09
       
      It is important to specifically publish using a Public Domain dedication.
  • Mike Chelen
    Mike Chelen on 11 Feb 09
     
    Why bother about openness and licensing for data? After all they don't matter in themselves: what we really care about are things like the progress of human knowledge or the freedom to understand and share.
Mike Chelen

Main Page - OpenResearch.org - 0 views

openresearch.org/Main_Page

semantic wiki open research science

shared by Mike Chelen on 06 Feb 09 - Snapshot
  • Mike Chelen
    Mike Chelen on 06 Feb 09
     
    This semantic wiki at OpenResearch.org aims at making the world of science more visible and accessible. Everybody can add his favorite events (e.g. conferences and workshops), co-workers, tools / datasets, community fora or journals. Pooled together these pieces of information constitute a vast knowledge base about who and what moves science forward.
Mike Chelen

SourceForge.net: Staden Package - 0 views

sourceforge.net/staden

dna open source gap4 spin

shared by Mike Chelen on 04 Feb 09 - Snapshot
  • Mike Chelen
    Mike Chelen on 04 Feb 09
     
    A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
Mike Chelen

Portal:Gene Wiki - Wikipedia, the free encyclopedia - 0 views

en.wikipedia.org/...Portal:Gene_Wiki

genetics wiki wikipedia gene science biology

shared by Mike Chelen on 29 Jan 09 - Snapshot
  • Mike Chelen
    Mike Chelen on 29 Jan 09
     
    Welcome to the Gene Wiki portal. This portal is dedicated to the goal of applying community intelligence to the annotation of gene and protein function. The Gene Wiki is an informal collection of pages on human genes and proteins, and this effort to develop these pages is tightly coordinated with the Molecular and Cellular Biology Wikiproject. Our specific aims are summarized as follows:

    * To provide a well written and informative Wikipedia article for every notable human gene
    * To invite participation by interested lay editors, students, professionals, and academics from around the world
    * To integrate Gene Wiki articles with existing Wikipedia content through the use of internal wiki links increasing the value of both

    Please browse around the Gene Wiki, make an edit to your favorite gene page, and feel free to ask questions!
Mike Chelen

Wikipedia:WikiProject NIH - Wikipedia, the free encyclopedia - 0 views

en.wikipedia.org/...Wikipedia:WikiProject_NIH

wiki nih research science wikipedia

shared by Mike Chelen on 29 Jan 09 - Snapshot
  • Mike Chelen
    Mike Chelen on 29 Jan 09
     
    Welcome to the NIH WikiProject, a collaboration area and group of editors dedicated to improving Wikipedia's coverage of National Institutes of Health. This is a new WikiProject, so please join!!

    (For more information on WikiProjects, please see Wikipedia:WikiProject and the Guide to WikiProjects).


    Goals

    * Improve Wikipedia's current coverage of the NIH and deepen the coverage with more pages.

    Scope

    * Cover all of the Institutes all the way down to individual laboratories/units.

Mike Chelen

#opensciinfo - Twitter Search - 0 views

search.twitter.com/search

opensciinfo twitter

shared by Mike Chelen on 29 Jan 09 - Snapshot
  • Mike Chelen
    Mike Chelen on 29 Jan 09
     
    search for #opensciinfo hashtag used in twitter "room"
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