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Phylotastic hackathon report from 2012 iEvoBio meting
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Acer macrophyllumBetula luteaAesculus glabraTilia americanaUlmus rubra
comparative analysis of leaf vein patterns
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.
• most cited example of reuse in phylogenetics
• extracts subtrees from APG plant phylogeny
• how can we expand to multiple (and larger) trees?
Cam Webb
?
Phylotastic!
A. macrophyllum
B. alleghaniensisA. glabra
U. rubra
T. americana
Species listAcer macrophyllumBetula luteaAesculus glabraTilia americana Ulmus rubra
available mega-trees
TNRS
Components
• 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
{ cat, dog, squirrel, human }
Making it happen
• NESCent working group
o HIP: Hackathons, Interoperability, Phylogenetics
• Targeted hackathon
o intensive collaborative coding event
OpenSpace Targeted
vague topic, e.g. “database interoperability”
specific goal, e.g. “generalize Phylomatic”
participants pitch projects at event projects largely defined a priori
free to select participants via any criteria particular skills needed
less pre-event planning more pre-event planning
disconnected subgroups subgroups must work together
Invitation + open call for participation
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
Some tangible outcomes (evoio.org)Description Item (link) Docs (link)
demo galaxy server live demo and code on github
base class and screencast
demo topology server live demo and code on github
README.pod
prototype controller architecture in nodeJS
github project [1]
demo service to annotate tree with dates
http://datelife.org NA
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 store
live demo NA
demos
phylotastic.org/demos.html
galaxy implementation
http://galaxy.phylotastic.nethttp://youtu.be/kMME658xOu4
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!
future hackathons?
• HIP group planning two additional events; topics TBA
• NESCent hackathon proposals (“informatics whitepaper”)
• Ask us about running your own!