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

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?

8. Why is this important?

9. Why is this important?
Genes are the basic building
block of organisms

10. How?
Gene prediction models (Sleator, 2010)

13. Web application
to crowdsource
gene prediction
 github.com/yeban/afra

14. Crowdsource?
?

15. Crowd + Outsource

16. Citizen Science
James Borrell |  @James_Borrell
Citizen Cyberscience Summit 2014 |  #ccs14

17. Self-reward helping Science
Zooniverse success

18. Science? I don't care...

19. Cognitive surplus
Shirky, 2010

20. Gamification

21. Gamification
A way to engage
users into solving
a problem by
adding game
mechanics to it

22. Useless game - Flappy bird
50 milion downloads
 flappybird.io

23. Useful - Genes In Space
 cancerresearchuk.org

27. Previous work

28. Scale up and Gamify another
Open Source project
 gmod/apollo →  yeban/afra
Anurag Priyam |  @yeban

29. Current work

30. Scale up
Move most of the logic to the browser

31. Scale up
Biology logic on the browser
 github.com/bionode/bionode

32. Gamification
Dashboad mockup

33. Machine Learning
Use data generated by users to improve
gene prediction models
Robert Simpson |  @orbitingfrog
Citizen Cyberscience Summit 2014 |  #ccs14

34. PSMC

35. Effective population size?
Theoretical number of
individuals that
contribute gametes to
the next generation

36. Why is this important?

37. Why is this important?
Measure of genetic diversity

38. Why is this important?
Measure of genetic diversity
Affects selection efficiency

39. 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)

40. How to measure?

41. How to measure?
Previously hard to do

42. How to measure?
Previously hard to do
Highly stochastic nature of inbreeding and
genetic drift

43. How to measure?
Previously hard to do
Highly stochastic nature of inbreeding and
genetic drift
Other confounding factors

44. How to measure?
Previously hard to do
Highly stochastic nature of inbreeding and
genetic drift
Other confounding factors
Needs a lot of specific data

45. 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

46. PSMC
Li, 2011

47. Hasn't been used in
insects a lot...

48. Hasn't been used in
insects a lot... until
now!

49. Use PSMC to answer some
evolutionary questions

50. Is the effective
population size in
solitary insects >
social?
?

51. Experimental design
Run PSMC across a wide range of social
insects and their solitary relatives

52. Reproducing published
results to master PSMC
Li, 2011
Freedman, 2014

53. Thank you!
Bruno Vieira |  @bmpvieira
Anurag Priyam |  @yeban
Yannick Wurm |  @yannick__
bmpvieira.com/seminar14
© 2014 Bruno Vieira CC-BY 4.0

54. 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?