http://phylotastic.org/

Making the tree of life

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!