Sequencing cost• Sequencing genomes is now inexpensive.• Many many genomes are now being sequenced.
Gene predictionab initioSearch genome for signsSequence similarity basedSearch genome for known sequences
Gene prediction ischallengingSome examples:• missing exon• truncated or overextended exon• gene split into several gene predictions (e.g. if introns are very large)• merged genes (two adjacent gene models are predicted to be a single “megagene”)
Manual curation• yields the best gene models• is time consuming• plausible for large communities (e.g. Human, C. elegans)• but what if a small lab sequenced their favorite bug’s genome?
Foldit players contribute to real science!• Christopher B Eiben et al (2012) Increase Diels-Alderase activity through backbone remodelling guided by Foldit players. Nature Biotechnology.• Firas Khatib et al (2011) Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural and Molecular Biology.• Firas Khatib et al (2011) Algorithm discovery by protein folding game players. Proceeding of the National Academy of Sciences.
Crowdsourcing works• GalaxyZoo volunteers have discovered real galaxies.• Foldit players have guided real scientific questions.
Lower the entry barrier tocontribution• contributors refine one gene model at a time• present gene model based on user’s experience – beginners see easy to curate models• tutorial or learning tasks• assisting UI
Social network• Passive recruitment: post curation activities of contributors to social network. • Cathy contributed to cancer research by refining three gene models. Can you help too? • Mike helped researchers understand how ant societies are organised by refining two gene models. • Amos earned the “expert gene curator badge” by curating 1000 gene models.• Active recruitment of friends on social network.
Retaining contributorsLearning experienceHelping sciencePrestige & pride:• points and badges.• being featured on our leaderboard.• acknowledgement or coauthorship in publication• responsibility: “senior” contributors are • asked to arbitrate between conflicting submissions of junior contributors. • asked to curate a specific set of genes (developing expertise)
Begin Create initia t asks Needs curatio n l Curate Curate CurateBeing curated Being curated Being curated Submit Submit Submit te t: crea isten task ons iew” Inc rev “ Auto-check Consistent: create next required task Done
Ensure quality genemodels• make tasks small & simple• beginners are trained• redundant curation• review of conflicts by experienced users.
Work in progress• gene prediction: MAKER2• gene visualization & editing: Jbrowse (WebApollo)• http://afra.sbcs.qmul.ac.uk• Our code: Ruby, Sinatra, DataMapper, jQuery
Summary• many emerging model organsims are being studied• gene prediction hasn’t caught up yet• manual curation requires huge amount of time• crowdsourcing exists• crowdsourcing works – even in science• there are many challenges• work in progress
http://afra.sbcs.qmul.ac.uk Thanks Dr. Yannick Wurm Dr. Mitchell E. Skinner Dr. Mark Yandell
Recruiting alternatives• Force upon students –curriculum (learn / practical)• Pay people
Summing up• 180+ eukaryotic genomes and more coming• gene prediction hasn’t caught up• best gene models are manually curated• manual curation can take hours to days • curating a full genome can take years