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The Automation of Science

The Automation of Science

Konrad Förstner

July 17, 2013
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  1. The automation of science
    A lunch seminar talk
    Konrad U. F¨
    orstner
    Sharma group & Vogel group
    July, 17th, 2013, W¨
    urzburg

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  2. This a subset of slides extracted from a lunch seminar talk given at
    the Institute for Molecular Infection Biology (IMIB).

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  3. Disclaimer
    Yes, this might hurt and I might be wrong.
    http://www.flickr.com/photos/redjar/113823307/ – CC-BY by flickr user redjar

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  4. Problem 1a: Common problem with large scale screenings
    Confirmation via manual, low-throughput methods (e.g. RNA-Seq
    analysis followed by northern blots to confirm candidates)
    http://www.flickr.com/photos/library_of_congress/2179123671/

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  5. Problem 1b: Scaling up experiments
    10 - 100 repetitions possible
    1000 and more repetitions not possible
    http://www.flickr.com/photos/library_of_congress/2179123671/

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  6. Problem 1c: Craft vs. thinking
    Why does somebody who studied several years need to spend most
    of his/her time pipetting one liquid into another?
    http://www.flickr.com/photos/library_of_congress/2179123671/

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  7. Problem 2: Reproducibility/Transparency
    http://www.nature.com/nchembio/journal/v9/n6/full/nchembio.1269.html

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  8. Two ways of running a BLAST query – GUI/web interface

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  9. Two ways of running a BLAST query – command line

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  10. Advantages of having a formal language for actions
    Transparency
    Reproducibility
    Scalability
    https://secure.flickr.com/photos/jurvetson/2018232 – CC-BY by flickr user jurvetson

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  11. Claim
    We need more automation / formalization – especially in the life
    sciences.
    https://secure.flickr.com/photos/jurvetson/2018232 – CC-BY by flickr user jurvetson

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  12. Motos
    ”Work on the business/system not in the business/system.”
    ”Be productive not busy.”
    ”Laziness is a virtue.”
    https://secure.flickr.com/photos/jurvetson/2018232 – CC-BY by flickr user jurvetson

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  13. Microfluid system as one path
    https://secure.flickr.com/photos/schlaus/708447474 – CC-BY by flickr user schlaus

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  14. Challenges
    Price (as long as not coming a commondity)
    Lack of flexibility
    Formalization is hard
    Vendor lock-in ⇒ open standards required
    https://secure.flickr.com/photos/jurvetson/2018232 – CC-BY by flickr user jurvetson

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  15. Example – the language EXACT
    http://bioinformatics.oxfordjournals.org/content/24/13/i295

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  16. Example – the robot scientist ADAM
    http://www.nature.com/nature/journal/v427/n6971/full/nature02236.html

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  17. Example – A small LEGO Mindstorm hardware hack
    http://hackaday.com/2012/04/19/lego-mindstorms-used-to-automate-tedious-laboratory-tasks/

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  18. What is your hack?
    https://secure.flickr.com/photos/konradfoerstner/4168966589/ – CC-BY by flickr user konradfoerstner

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