Phylotastic hackathon report from 2012 iEvoBio meting

1. Making the tree of life
http://phylotastic.org/

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. 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. 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. 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. Making it happen
• NESCent working group
o HIP: Hackathons, Interoperability, Phylogenetics
• Targeted hackathon
o intensive collaborative coding event

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. Invitation + open call for participation

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

11. Some tangible outcomes (evoio.org)
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 http://datelife.org 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

12. demos
phylotastic.org/demos.html

13. galaxy implementation
http://galaxy.phylotastic.net
http://youtu.be/kMME658xOu4

14. 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!

16. future hackathons?
• HIP group planning two additional events;
topics TBA
• NESCent hackathon proposals (“informatics
whitepaper”)
• Ask us about running your own!