The Automation of Science

Transcript

1. The automation of science A lunch seminar talk Konrad U. F¨ orstner Sharma group & Vogel group July, 17th, 2013, W¨ urzburg
2. This a subset of slides extracted from a lunch seminar talk given at the Institute for Molecular Infection Biology (IMIB).
3. Disclaimer Yes, this might hurt and I might be wrong. http://www.flickr.com/photos/redjar/113823307/ – CC-BY by flickr user redjar
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/
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/
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/
7. Problem 2: Reproducibility/Transparency http://www.nature.com/nchembio/journal/v9/n6/full/nchembio.1269.html
8. Two ways of running a BLAST query – GUI/web interface
9. Two ways of running a BLAST query – command line
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
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
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
13. Microfluid system as one path https://secure.flickr.com/photos/schlaus/708447474 – CC-BY by flickr user schlaus
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
15. Example – the language EXACT http://bioinformatics.oxfordjournals.org/content/24/13/i295
16. Example – the robot scientist ADAM http://www.nature.com/nature/journal/v427/n6971/full/nature02236.html
17. Example – A small LEGO Mindstorm hardware hack http://hackaday.com/2012/04/19/lego-mindstorms-used-to-automate-tedious-laboratory-tasks/
18. What is your hack? https://secure.flickr.com/photos/konradfoerstner/4168966589/ – CC-BY by flickr user konradfoerstner