Citizen Scientists: harnessing communityintelligence to solve biological problems with

computer games

Paul Gardner

July 17, 2013

Paul Gardner Citizen Scientists: Biolive 2013

Today I will be presenting...

I How to waste a huge amount of time in (possibly) productiveand potentially educational ways.

Paul Gardner Citizen Scientists: Biolive 2013

The Intertubes in 2013...

I NZ’s top websites &ranks∗:

1. Facebook3. YouTube5. Trade Me9. Wikipedia

13. LinkedIn15. Blogspot18. Twitter19. Tumblr22. WordPress27. Pinterest33. PirateBay

User generated content is now the most popular sources ofinformation and entertainment.

*Alexa, July 11th , 2013

Paul Gardner Citizen Scientists: Biolive 2013

Crowdsourcing, citizen science & games with purpose

I CrowdsourcingI E.g. SETI@home & Folding@home

I Citizen scienceI E.g. NZ Garden Bird Survey, Katoa Metagenomics & Galaxy

ZooI Games with purpose

I “We spend 3 billion hours a week as a planet playingvideogames.” – Jane McGonigal

I E.g. Fold.it, Phylo & EteRNA

Paul Gardner Citizen Scientists: Biolive 2013

Phylo: comparative genomics

# STOCKHOLM 1.0#33 unique RNA sequences, 1 peptide sequence#=GR PR1 G..A..D..V..T..H..P..P..A..G..D..#=GR PR3 GlyAlaAspValThrHisProProAlaGlyAspplatypus GGAGCAGACGTCACTCACCCCCCAGCCGGAGATopossum GGAGCAGATGTTACTCACCCTCCTGCTGGAGATsloth GGAGCAGACGTCACACACCCTCCCGCGGGGGATarmadillo GGAGCAGACGTCACGCACCCTCCGGCAGGGGATtenrec GGGGCCGACGTCACGCACCCCCCTGCGGGCGATelephant GGAGCGGATGTCACACACCCGCCTGCGGGGGATshrew GGCGCAGATGTCACGCATCCTCCAGCAGGGGAChedgehog GGAGCAGATGTCACACACCCCCCAGCAGGAGATmegabat GGAGCAGATGTCACACACCCTCCTGCAGGAGATmicrobat GGAGCAGATGTCACCCACCCCCCTGCAGGGGACdog GGAGCGGATGTCACACACCCCCCAGCCGGGGACcat GGAGCCGATGTCACGCACCCCCCAGCAGGGGAThorse GGAGCGGATGTCACACACCCTCCGGCAGGGGATpika GGAGCAGATGTCACTCACCCTCCAGCTGGGGATrabbit GGTGCAGATGTCACACACCCCCCAGCTGGAGATsquirrel GGAGCAGATGTCACTCACCCTCCAGCGGGAGATguinea_pig GGAGCAGATGTCACACACCCACCAGCGGGAGATmouse GGAGCAGATGTCACTCATCCGCCTGCTGGGGACrat GGAGCAGATGTCACTCATCCACCTGCTGGGGATkangaroo_rat GGAGCAGATGTTACACACCCTCCAGCAGGGGATtree_shrew GGCGCAGACGTCACGCACCCCCCGGCCGGGGAThuman GGAGCGGATGTCACACACCCCCCAGCAGGGGATtarsier GGTGCTGATGTCACACACCCCCCTGCAGGGGATmarmoset GGAGCAGATGTCACACACCCACCAGCAGGGGATzebrafinch GGAGCAGATGTCACTCACCCTCCCGCCGGGGATgreen_anole GGGGCAGACGTCACTCACCCGCCAGCCGGGGACxenopus GGAGCAGATGTTACACACCCACCTGCTGGTGATpufferfish GGTGCGGATGTTACTCATCCTCCTGCTGGTGATfugu GGGGCTGATGTTACTCACCCTCCAGCTGGTGATstickleback GGTGCAGACGTCACACATCCTCCAGCGGGTGATmedaka GGTGCCGATGTCACTCATCCTCCTGCCGGGGACzebrafish GGGGCAGATGTTACACACCCGCCGGCTGGTGATlamprey GGTGCCGATGTGACACACCCTCCAGCGGGAGAC//

Zhan et al. (2013) Peregrine and saker falcon genome sequences provide

insights into evolution of a predatory lifestyle. Nature Genetics.

Paul Gardner Citizen Scientists: Biolive 2013

Phylo: re-align human promoters associated with diseaseI http://phylo.cs.mcgill.caI Nucleotides are coloured blocksI Create same coloured columns, minimize gaps & mismatches

Kawrykow et al. (2012) Phylo: A Citizen Science Approach forImproving Multiple Sequence Alignment. PLoS ONE

Paul Gardner Citizen Scientists: Biolive 2013

Play!

I http://phylo.cs.mcgill.ca

Paul Gardner Citizen Scientists: Biolive 2013

Phylo: teaching resource

I http://phylo.cs.mcgill.ca/teaching/

Paul Gardner Citizen Scientists: Biolive 2013

EteRNA: synthetic biology

I http://eterna.cmu.edu

I Energy model: stacked basepairs are favoured, loops aredisfavoured

Paul Gardner Citizen Scientists: Biolive 2013

Thanks!

I Jerome Waldispuhl

PPG is supported by a Rutherford Discovery Fellowship from Government funding, administered by the RoyalSociety of New Zealand.

Paul Gardner Citizen Scientists: Biolive 2013