Crowdsourcing gene predictions & estimating population sizes

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Information about Crowdsourcing gene predictions & estimating population sizes
Technology

Published on March 3, 2014

Author: bmpvieira

Source: slideshare.net

Description

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 Slides: http://bmpvieira.com/seminar14

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?

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

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  

Previous work

Scale up and Gamify another Open Source project  gmod/apollo →  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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