Collaborative platforms for streamlining workflows in Open Science

Transcript

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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