Published on March 3, 2014
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 PSMC method (Li, 2011).
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
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 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
Scale up and Gamify another Open Source project gmod/apollo → yeban/afra Anurag Priyam | @yeban
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 Cyberscience Summit 2014 | #ccs14
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) Discover unexpected population bottlenecks (Freedman, 2014) Detect the time of divergence between populations (Li, 2011)
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 Needs a lot of specific data
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 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 © 2014 Bruno Vieira CC-BY 4.0
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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