Crowdsourcing gene predictions & estimating population sizes
Crowdsourcing gene predictions & estimating population sizes
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seminar14
Talk given in a seminar at the Queen Mary, University of London.On Github bmpvieira / seminar14
Crowdsourcing gene predictions & estimating population sizes
Bruno Vieira | @bmpvieira
Bioinformatics & Population Genomics
Initially address two issues
Scaling up gene prediction
Infer the efective population size history in insects with the PSMC method (Li, 2011).
Gene prediction?
Why is this important?
Genes are the basic building block of organisms
How?
Gene prediction models (Sleator, 2010)Web application to crowdsource gene prediction
Crowdsource?
Crowd + Outsource
Citizen Science
James Borrell | @James_Borrell Citizen Cyberscience Summit 2014 | #ccs14
Self-reward helping Science
Science? I don't care...
Cognitive surplus
Gamification
Gamification
A way to engage users into solving a problem by adding game mechanics to it
Useless game - Flappy bird
50 milion downloads
Useful - Genes In Space
Previous work
Scale up and Gamify another Open Source project
Anurag Priyam | @yeban
Current work
Scale up
Move most of the logic to the browser
Scale up
Biology logic on the browser
Gamification
Dashboad mockup
Machine Learning
Use data generated by users to improve gene prediction models
Robert Simpson | @orbitingfrog Citizen Cyberscience Summit 2014 | #ccs14
PSMC
Effective population size?
Theoretical number of individuals that contribute gametes to the next generation
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)
Discover unexpected population bottlenecks (Freedman, 2014)
Detect the time of divergence between populations (Li, 2011)
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
PSMC
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
Current work
Reproducing published results to master PSMC
Thank you!
Bruno Vieira | @bmpvieira
Anurag Priyam | @yeban
Yannick Wurm | @yannick__
© 2014 Bruno Vieira CC-BY 4.0
- Address data "deluge" in gene prediction
- Scale up by moving logics to browser
- Gamify to tap into Cognitive Surplus
- Deploy the PSMC on the servers
- Master PSMC by reproducing results
- Effective pop. size solitary insects > social?