harnessing community intelligence to solve biological problems with computer games

1. Citizen Scientists: harnessing community
intelligence to solve biological problems with
computer games
Paul Gardner
July 17, 2013
Paul Gardner Citizen Scientists: Biolive 2013

2. Today I will be presenting...
How to waste a huge amount of time in (possibly) productive
and potentially educational ways.
Paul Gardner Citizen Scientists: Biolive 2013

3. The Intertubes in 2013...
NZ’s top websites &
ranks∗:
1. Facebook
3. YouTube
5. Trade Me
9. Wikipedia
13. LinkedIn
15. Blogspot
18. Twitter
19. Tumblr
22. WordPress
27. Pinterest
33. PirateBay
User generated content is now the most popular sources of
information and entertainment.
*Alexa, July 11th
, 2013
Paul Gardner Citizen Scientists: Biolive 2013

4. Crowdsourcing, citizen science & games with purpose
Crowdsourcing
E.g. SETI@home & Folding@home
Citizen science
E.g. NZ Garden Bird Survey, Katoa Metagenomics & Galaxy
Zoo
Games with purpose
“We spend 3 billion hours a week as a planet playing
videogames.” – Jane McGonigal
E.g. Fold.it, Phylo & EteRNA
Paul Gardner Citizen Scientists: Biolive 2013

5. 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 GlyAlaAspValThrHisProProAlaGlyAsp
platypus GGAGCAGACGTCACTCACCCCCCAGCCGGAGAT
opossum GGAGCAGATGTTACTCACCCTCCTGCTGGAGAT
sloth GGAGCAGACGTCACACACCCTCCCGCGGGGGAT
armadillo GGAGCAGACGTCACGCACCCTCCGGCAGGGGAT
tenrec GGGGCCGACGTCACGCACCCCCCTGCGGGCGAT
elephant GGAGCGGATGTCACACACCCGCCTGCGGGGGAT
shrew GGCGCAGATGTCACGCATCCTCCAGCAGGGGAC
hedgehog GGAGCAGATGTCACACACCCCCCAGCAGGAGAT
megabat GGAGCAGATGTCACACACCCTCCTGCAGGAGAT
microbat GGAGCAGATGTCACCCACCCCCCTGCAGGGGAC
dog GGAGCGGATGTCACACACCCCCCAGCCGGGGAC
cat GGAGCCGATGTCACGCACCCCCCAGCAGGGGAT
horse GGAGCGGATGTCACACACCCTCCGGCAGGGGAT
pika GGAGCAGATGTCACTCACCCTCCAGCTGGGGAT
rabbit GGTGCAGATGTCACACACCCCCCAGCTGGAGAT
squirrel GGAGCAGATGTCACTCACCCTCCAGCGGGAGAT
guinea_pig GGAGCAGATGTCACACACCCACCAGCGGGAGAT
mouse GGAGCAGATGTCACTCATCCGCCTGCTGGGGAC
rat GGAGCAGATGTCACTCATCCACCTGCTGGGGAT
kangaroo_rat GGAGCAGATGTTACACACCCTCCAGCAGGGGAT
tree_shrew GGCGCAGACGTCACGCACCCCCCGGCCGGGGAT
human GGAGCGGATGTCACACACCCCCCAGCAGGGGAT
tarsier GGTGCTGATGTCACACACCCCCCTGCAGGGGAT
marmoset GGAGCAGATGTCACACACCCACCAGCAGGGGAT
zebrafinch GGAGCAGATGTCACTCACCCTCCCGCCGGGGAT
green_anole GGGGCAGACGTCACTCACCCGCCAGCCGGGGAC
xenopus GGAGCAGATGTTACACACCCACCTGCTGGTGAT
pufferfish GGTGCGGATGTTACTCATCCTCCTGCTGGTGAT
fugu GGGGCTGATGTTACTCACCCTCCAGCTGGTGAT
stickleback GGTGCAGACGTCACACATCCTCCAGCGGGTGAT
medaka GGTGCCGATGTCACTCATCCTCCTGCCGGGGAC
zebrafish GGGGCAGATGTTACACACCCGCCGGCTGGTGAT
lamprey 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

6. Phylo: re-align human promoters associated with disease
http://phylo.cs.mcgill.ca
Nucleotides are coloured blocks
Create same coloured columns, minimize gaps & mismatches
Kawrykow et al. (2012) Phylo: A Citizen Science Approach for
Improving Multiple Sequence Alignment. PLoS ONE
Paul Gardner Citizen Scientists: Biolive 2013

7. Play!
http://phylo.cs.mcgill.ca
Paul Gardner Citizen Scientists: Biolive 2013

8. Phylo: teaching resource
http://phylo.cs.mcgill.ca/teaching/
Paul Gardner Citizen Scientists: Biolive 2013

9. EteRNA: synthetic biology
http://eterna.cmu.edu
Energy model: stacked basepairs are favoured, loops are
disfavoured
Paul Gardner Citizen Scientists: Biolive 2013

10. Thanks!
J´erˆome Waldisp¨uhl
PPG is supported by a Rutherford Discovery Fellowship from Government funding, administered by the Royal
Society of New Zealand.
Paul Gardner Citizen Scientists: Biolive 2013