Crowdsourcing genepredictions &estimatingpopulation sizesBruno Vieira | bmpvieira.com/seminar14
@bmpvieira
Initially addresstwo issuesScaling up gene prediction
Infer the efective population sizehistory in insects with the PSMCmethod .(Li, 2011)
Citizen Science
James Borrell | |
@James_BorrellCitizen Cyberscience Summit 2014 #ccs14
Science? I don't care...
Cognitive surplus
Shirky, 2010
Useful - Genes In Space
cancerresearchuk.org
Scale up and Gamify anotherOpen Source project →
Anurag Priyam |
gmod/apollo yeban/afra
@yeban
Machine LearningUse data generated by users to improvegene prediction models
Robert Simpson | |
@orbitingfrogCitizen Cyberscience Summit 2014 #ccs14
Effective population size?
Theoretical number ofindividuals thatcontribute gametes tothe next generation
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?
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... untilnow!
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