Crowdsourcing gene
predictions &
estimating
population sizes
bmpvieira.com/seminar14
Bruno Vieira |  @bmpvieira
Bioinformatics
& Population
Genomics
Initially address
two issues
Initially address
two issues
Scaling up gene prediction
Initially address
two issues
Scaling up gene prediction
Infer the efective population size
history in insects with the PSM...
Gene prediction?
Why is this important?
Why is this important?
Genes are the basic building
block of organisms
How?

Gene prediction models (Sleator, 2010)
Web application
to crowdsource
gene prediction
 github.com/yeban/afra
Crowdsource?

?
Crowd + Outsource
Citizen Science

James Borrell |  @James_Borrell 
Citizen Cyberscience Summit 2014 |  #ccs14
Self-reward helping Science
Zooniverse success
Science? I don't care...
Cognitive surplus

Shirky, 2010
Gamification
Gamification

A way to engage
users into solving
a problem by
adding game
mechanics to it
Useless game - Flappy bird
50 milion downloads

 flappybird.io
Useful - Genes In Space

 cancerresearchuk.org

 
Previous work
Scale up and Gamify another
Open Source project
 gmod/apollo →  yeban/afra

 Anurag Priyam |  @yeban
Current work
Scale up
Move most of the logic to the browser
Scale up
Biology logic on the browser

 github.com/bionode/bionode
Gamification
Dashboad mockup
Machine Learning
Use data generated by users to improve
gene prediction models

Robert Simpson |  @orbitingfrog 
Citizen ...
PSMC
Effective population size?
Theoretical number of
individuals that
contribute gametes to
the next generation
Why is this important?
Why is this important?
Measure of genetic diversity
Why is this important?
Measure of genetic diversity
Affects selection efficiency
Used
Effect of historical climate
changes (Miller, 2012)
Measure the impact of
anthropogenic activity (Zhao, 2013)
Discove...
How to measure?
How to measure?
Previously hard to do
How to measure?
Previously hard to do

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

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

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

Highly stochastic nature of inbreeding and
genetic drift
Other confounding factors
...
PSMC

Li, 2011
Hasn't been used in
insects a lot...
Hasn't been used in
insects a lot... until
now!
Use PSMC to answer some
evolutionary questions
Is the effective
population size in
solitary insects >
social?

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

 
Reproducing published
results to master PSMC

Li, 2011
Freedman, 2014
Thank you!
 Bruno Vieira |  @bmpvieira
 Anurag Priyam |  @yeban
 Yannick Wurm |  @yannick__
bmpvieira.com/seminar14
© 2...
Crowdsource gene prediction
Address data "deluge" in gene prediction
Scale up by moving logics to browser
Gamify to tap in...
Crowdsourcing gene predictions & estimating population sizes
Crowdsourcing gene predictions & estimating population sizes
Crowdsourcing gene predictions & estimating population sizes
Crowdsourcing gene predictions & estimating population sizes
Crowdsourcing gene predictions & estimating population sizes
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.

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

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Crowdsourcing gene predictions & estimating population sizes

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

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