Lrug, lightning talk, 11th feb 2013
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Transcript of Lrug, lightning talk, 11th feb 2013
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Anurag Priyamyeban
Wurm lab - http://yannick.poulet.org
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how does life work?
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genomes
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SequenceServer.com
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SequenceServer.com
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obtaining gene model
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Genes
on a DNA strand gene model
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Gene
on a DNA strand gene model
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gene prediction
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refining predicte models● experts go through the predicted gene● compare it to the evidences● manually refine the gene model
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It's tedious
● One gene: one hours to days.
● But a "normal" project: 100s to 1000s of genes.
● Thus many projects are impossible...
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Afracollectively annotating genomes
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gamification
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social network
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Scheduler
>> user = session.user>> difficulty_level = linear_map user.score>> tasks.first(:difficulty => difficulty_level)
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gene_model.difficulty
● easier to find mistakes in prediction with○ multiple supporting evidences○ "good" evidences
● we look for these and assign a gene model a difficulty score
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automatic validation>> candidates = gene_model.candidates
[gene_model1, gene_model2]
>> if candidates.first == candidates.last
users = candidates.map(&:user)
users.each{|u| u.score.bump}
gene_model.transition_to :verified
else
gene_model.difficulty.bump
end
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instant feedback
● some edits are easier to validate○ exon-intron boundaries○ EST alignment
● validate these on the client side○ provide immediate feedback○ compute putative score
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Thank you :)-- yeban
Wurm lab (http://yannick.poulet.org) @