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Crowdsourcing genepredictions &estimatingpopulation sizesBruno Vieira | bmpvieira.com/seminar14
@bmpvieira
Bioinformatics& PopulationGenomics
Initially addresstwo issues
Initially addresstwo issuesScaling up gene prediction
Initially addresstwo issuesScaling up gene prediction
Infer the efective population sizehistory in insects with the PSMCmethod .(Li, 2011)
?Gene prediction?
Why is this important?
Why is this important?Genes are the basic buildingblock of organisms
Crowdsource?
?
Citizen Science
James Borrell | |
@James_BorrellCitizen Cyberscience Summit 2014 #ccs14
Science? I don't care...
Cognitive surplus
Shirky, 2010
Gamification
Gamification
A way to engageusers into solvinga problem byadding gamemechanics to it
Useful - Genes In Space
cancerresearchuk.org
Previous work
Scale up and Gamify anotherOpen Source project →
Anurag Priyam |
gmod/apollo yeban/afra
@yeban
Current work
Scale upMove most of the logic to the browser
GamificationDashboad mockup
Machine LearningUse data generated by users to improvegene prediction models
Robert Simpson | |
@orbitingfrogCitizen Cyberscience Summit 2014 #ccs14
PSMC
Effective population size?
Theoretical number ofindividuals thatcontribute gametes tothe 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
UsedEffect of historical climatechanges
Measure the impact ofanthropogenic activity
Discover unexpected populationbottlenecks
Detect the time of divergencebetween populations
(Miller, 2012)
(Zhao, 2013)
(Freedman, 2014)
(Li, 2011)
How to measure?
How to measure?
Previously hard to do
How to measure?
Previously hard to doHighly stochastic nature of inbreeding andgenetic drift
How to measure?
Previously hard to doHighly stochastic nature of inbreeding andgenetic driftOther confounding factors
How to measure?
Previously hard to doHighly stochastic nature of inbreeding andgenetic driftOther confounding factorsNeeds a lot of specific data
How to measure?
Previously hard to doHighly stochastic nature of inbreeding andgenetic driftOther confounding factorsNeeds a lot of specific data
Now from a diploid genome
Hasn't been used ininsects a lot...
Hasn't been used ininsects a lot... untilnow!
Use PSMC to answer someevolutionary questions
Is the effectivepopulation size insolitary insects >social? ?
Experimental designRun PSMC across a wide range of socialinsects and their solitary relatives
Reproducing publishedresults to master PSMC
Li, 2011Freedman, 2014
Thank you!
Bruno Vieira |
Anurag Priyam |
Yannick Wurm |
© 2014
@bmpvieira
@yeban
@yannick__bmpvieira.com/seminar14
Bruno Vieira CC-BY 4.0
Crowdsource gene predictionAddress data "deluge" in gene predictionScale up by moving logics to browserGamify to tap into Cognitive Surplus
Effective pop. size history in insectsDeploy the PSMC on the serversMaster PSMC by reproducing resultsEffective pop. size solitary insects > social?
