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Collaborative platforms for streamlining workflows in Open Science

Collaborative platforms for streamlining workflows in Open Science

Konrad Förstner

July 30, 2011
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  1. Collaborative platforms for streamlining
    workflows in Open Science
    Konrad U. F¨
    orstner, Gregor Hagedorn, Claudia Koltzenburg,
    M. Fabiana Kubke, Daniel Mietchen
    July 30th, 2011 – OKCon 2011, Berlin

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  2. About this work
    Wiki base version of the manuscript:
    http://is.gd/openworkflows

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  3. Problem: There are many gaps in the scientific process
    Time consuming and often annoying
    Loss of information
    http://www.flickr.com/photos/eirikref/403363597 – CC-BY by flick user eirikref

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  4. A proposal for improved scientific workflow
    Seamless transition from bench to publication
    Based on Virtual Research Environments (VRE)
    Transparency, reproducibility & reusability
    Formalization
    Reputation system included
    http://commons.wikimedia.org/wiki/File:Future73nb.jpg – PD

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  5. Conception and project planning
    Utilizing collective intelligence
    Management tools can help to handle complex projects
    http://www.flickr.com/photos/marksurman/3604105727/ – CC-BY by flick user marksurman

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  6. Experiments and data generation
    More automation needed (ideally via Open Hardware)
    Formal language to design/program experiments
    http://www.flickr.com/photos/kaibara/2072160194/ – CC-BY by flick user kaibara

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  7. Data storage = data release
    Publish data immediately in a machine-readable form
    Every entity gets an unique identifiers (⇒ referable)
    http://www.flickr.com/photos/wilhei/109404222/ – CC-BY by flick user wilhei

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  8. Data analysis
    Scripting / programming or recording of GUI-tool actions
    Good examples: Taverna or Galaxy
    Grid computing if needed / possible
    http://commons.wikimedia.org/wiki/File:Plastic_tape_measure.jpg – CC-BY by Wimedia Commons user Pastorius

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  9. Knowledge generation
    Again: Collaborative - increase the number of brains involved
    Again: Formalization - e.g. argument maps which link to
    results and literature
    http://www.flickr.com/photos/diana_blackwell/2597258115/ – CC-BY by flick user diana blackwell

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  10. Final publication
    Little effort: linking to the major outcomes and putting them
    into the scientific context
    http://www.flickr.com/photos/yorkjason/3265889476/ – CC-BY by flickr user yorkjason

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  11. Implementation - Technology
    Most needed building blocks are available (as FLOSS) –
    “just” need to be connected
    Open standards needed
    Domain specific solutions should be created by the
    communities
    http://www.flickr.com/photos/tallkev/256810217/ – CC-BY by flickr user tallkev

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  12. Implementation - Reputation
    Microcontribution ⇒ Microattribution (e.g. ORCID based)
    http://www.flickr.com/photos/tallkev/256810217/ – CC-BY by flickr user tallkev

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  13. Implementation - Licenses
    Ideally: Public domain / CC0 (see Panton Principle)
    http://www.flickr.com/photos/subcircle/500995147 – CC-BY by flickr user subcircel

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  14. Implementation - Funding
    Long term aim: Funding agencies require the usage of such
    Open Science workflows (worked for OA)
    – CC-BY by flickr user therichbrooks

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  15. Dealing with the cultural clash via a gradual approach
    Proposed infrastructure but with fine granular access control and a
    smaller number of participants.
    http://www.everystockphoto.com/photo.php?imageId=1761122 – source: The Library of Congress

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  16. Take home messages in a nut shell
    All steps of the research process can be represented in /
    connected to VREs
    Gaps between the steps are minimized
    Gain of transparency, reproducibility & reusability
    Main problems are not technical but cultural/political
    http://www.flickr.com/photos/marcoarment/3129076932 – CC-BY by flickr user marcoarment

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  17. http://www.flickr.com/photos/nateone/3768979925/ – CC-BY by flick user nateone

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