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