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Phylotastic @iEvoBio



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2008 Jun Zhao Eswc
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Phylotastic @iEvoBio

  1. 1. Making the tree of life
  2. 2. comparative analysis of leaf vein patterns Acer macrophyllum Betula lutea Aesculus glabra Tilia americana Ulmus rubra Leaf patterns image from Walls RL: Angiosperm leaf vein patterns are linked to leaf functions in a global-scale data set. American Journal of Botany 2011, 98(2):244-253.
  3. 3. Cam Webb • most cited example of reuse in phylogenetics • extracts subtrees from APG plant phylogeny • how can we expand to multiple (and larger) trees?
  4. 4. Species list ? Acer macrophyllum Betula lutea TNRS Aesculus glabra Tilia americana Ulmus rubra Phylotastic! A. macrophyllum available mega-trees B. alleghaniensis A. glabra T. americana U. rubra
  5. 5. Components { cat, dog, squirrel, human } • name resolution - fix typos, use preferred synonyms, resolve taxonomy • tree storage - store megatrees with metadata • pruning & grafting - remove & add branches • scaling - add branch lengths • controllers - manage workflow
  6. 6. Making it happen • NESCent working group o HIP: Hackathons, Interoperability, Phylogenetics • Targeted hackathon o intensive collaborative coding event
  7. 7. OpenSpace Targeted vague topic, e.g. “database specific goal, e.g. “generalize interoperability” Phylomatic” participants pitch projects at event projects largely defined a priori free to select participants via any particular skills needed criteria less pre-event planning more pre-event planning disconnected subgroups subgroups must work together
  8. 8. Invitation + open call for participation
  9. 9. The event: June 4-8 @NESCent • 25 local + 5 remote participants • 5 Subgroups: • TNRS - taxonomic name resolution • TreeStore - triple store with REST API • Architecture* - flow control, interoperability (*and pruning services) • DateLife - scaling trees using chronograms • Shiny - other demos and cool front-end stuff
  10. 10. Some tangible outcomes ( Description Item (link) Docs (link) demo galaxy server live demo and code on base class and screencast github demo topology server live demo and code on README.pod github prototype controller architecture in github project [1] nodeJS demo service to annotate tree with NA dates Reconcile-o-tastic live demo NA Mesquite-o-tastic demo module Java code on github screencast TNRS API specification API TNRS TNRS Demonstration Demo TNRS PhyloWS REST wrapper around tree live demo NA store
  11. 11. demos
  12. 12. galaxy implementation
  13. 13. what did we learn? • lots of enthusiasm and hard work at the event o but pre-event planning & post-event follow-up more difficult • important to scope carefully for targetted event • remote participation via Google hangouts added value o needs dedicated on and off-site participants • getting diverse participation required active invitation • spent way too much time on taxonomic name reconciliation for a phylogeny event!
  14. 14. future hackathons? • HIP group planning two additional events; topics TBA • NESCent hackathon proposals (“informatics whitepaper”) • Ask us about running your own!