Crowdsourcing gene predictions & estimating population sizes
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Crowdsourcing gene predictions & estimating population sizes

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Talk presented on the 28 February 2014, at the Queen Mary, University of London for a seminar of the School of Biological and Chemical Sciences. ...

Talk presented on the 28 February 2014, at the Queen Mary, University of London for a seminar of the School of Biological and Chemical Sciences.

HTML5 Slides: http://bmpvieira.com/seminar14

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  • 1. Crowdsourcing gene predictions & estimating population sizes bmpvieira.com/seminar14 Bruno Vieira |  @bmpvieira
  • 2. Bioinformatics & Population Genomics
  • 3. Initially address two issues
  • 4. Initially address two issues Scaling up gene prediction
  • 5. Initially address two issues Scaling up gene prediction Infer the efective population size history in insects with the PSMC method (Li, 2011).
  • 6. Gene prediction?
  • 7. Why is this important?
  • 8. Why is this important? Genes are the basic building block of organisms
  • 9. How? Gene prediction models (Sleator, 2010)
  • 10. Web application to crowdsource gene prediction  github.com/yeban/afra
  • 11. Crowdsource? ?
  • 12. Crowd + Outsource
  • 13. Citizen Science James Borrell |  @James_Borrell  Citizen Cyberscience Summit 2014 |  #ccs14
  • 14. Self-reward helping Science Zooniverse success
  • 15. Science? I don't care...
  • 16. Cognitive surplus Shirky, 2010
  • 17. Gamification
  • 18. Gamification A way to engage users into solving a problem by adding game mechanics to it
  • 19. Useless game - Flappy bird 50 milion downloads  flappybird.io
  • 20. Useful - Genes In Space  cancerresearchuk.org  
  • 21. Previous work
  • 22. Scale up and Gamify another Open Source project  gmod/apollo →  yeban/afra  Anurag Priyam |  @yeban
  • 23. Current work
  • 24. Scale up Move most of the logic to the browser
  • 25. Scale up Biology logic on the browser  github.com/bionode/bionode
  • 26. Gamification Dashboad mockup
  • 27. Machine Learning Use data generated by users to improve gene prediction models Robert Simpson |  @orbitingfrog  Citizen Cyberscience Summit 2014 |  #ccs14
  • 28. PSMC
  • 29. Effective population size? Theoretical number of individuals that contribute gametes to the next generation
  • 30. Why is this important?
  • 31. Why is this important? Measure of genetic diversity
  • 32. Why is this important? Measure of genetic diversity Affects selection efficiency
  • 33. Used Effect of historical climate changes (Miller, 2012) Measure the impact of anthropogenic activity (Zhao, 2013) Discover unexpected population bottlenecks (Freedman, 2014) Detect the time of divergence between populations (Li, 2011)
  • 34. How to measure?
  • 35. How to measure? Previously hard to do
  • 36. How to measure? Previously hard to do Highly stochastic nature of inbreeding and genetic drift
  • 37. How to measure? Previously hard to do Highly stochastic nature of inbreeding and genetic drift Other confounding factors
  • 38. How to measure? Previously hard to do Highly stochastic nature of inbreeding and genetic drift Other confounding factors Needs a lot of specific data
  • 39. How to measure? Previously hard to do Highly stochastic nature of inbreeding and genetic drift Other confounding factors Needs a lot of specific data Now from a diploid genome
  • 40. PSMC Li, 2011
  • 41. Hasn't been used in insects a lot...
  • 42. Hasn't been used in insects a lot... until now!
  • 43. Use PSMC to answer some evolutionary questions
  • 44. Is the effective population size in solitary insects > social? ?
  • 45. Experimental design Run PSMC across a wide range of social insects and their solitary relatives    
  • 46. Reproducing published results to master PSMC Li, 2011 Freedman, 2014
  • 47. Thank you!  Bruno Vieira |  @bmpvieira  Anurag Priyam |  @yeban  Yannick Wurm |  @yannick__ bmpvieira.com/seminar14 © 2014 Bruno Vieira CC-BY 4.0
  • 48. Crowdsource gene prediction Address data "deluge" in gene prediction Scale up by moving logics to browser Gamify to tap into Cognitive Surplus Effective pop. size history in insects Deploy the PSMC on the servers Master PSMC by reproducing results Effective pop. size solitary insects > social?