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

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

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

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Two ways of running a BLAST query – command line

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

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

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

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