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Crowdsourcing gene predictions & estimating population sizes

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Bruno Vieira
Bruno Vieira

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 ºÝºÝߣs: http://bmpvieira.com/seminar14

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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).
Gene?prediction?
Crowdsourcing gene predictions & estimating population sizes
Why?is?this?important?
Why?is?this?important? Genes?are?the?basic?building block?of?organisms
How? Gene?prediction?models?(Sleator,?2010)
Crowdsourcing gene predictions & estimating population sizes
Crowdsourcing gene predictions & estimating population sizes
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 ?
Crowdsourcing gene predictions & estimating population sizes
Crowdsourcing gene predictions & estimating population sizes
Crowdsourcing gene predictions & estimating population sizes
Previous?work
Scale?up?and?Gamify?another Open?Source?project ??gmod/apollo?¡ú???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?Cyberscience?Summit?2014?|???#ccs14
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) 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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