1. Making the Tree of Life Accessible for Research This is a 20-minute overview with links to screencasts and demos, providing an introduction to the project and to the upcoming 2 nd hackathon (Jan 28 to Feb 1, 2013, Tucson, AZ). http://phylotastic.orhttp://phylotastic.org/ A project of the NESCent HIP (hackathons, interoperability, phyogenies) working group.

2. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci RE-USE OF TREES Producers Consumers (re-users) Repositories “Most attempts at re-use seem to end in disappointment” [1] [1] Stoltzfus, et al., 2012, “Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis”, http://www.ncbi.nlm.nih.gov/sites/entrez/23088596

3. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci USE CASE: LEAF VEIN EVOLUTION R.L. Walls with Linnaeus aextoxicaceae/aextoxicon/aextoxicon_puntatum anacardiaceae/anacardium/anacardium_excelum anacardiaceae/rhus/rhus_glabra annonaceae/dugetia/dugetia_furfuraceae... Phylomatic Input list from Walls, 2011 APG framework with 1566 taxa 98-species tree of Walls, 2011 ?

4. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci THE “TREE OF LIFE” =  Some big trees *  4,500 mammal species  55,473 angiosperm species  1,827 angiosperm taxa  800 fish families  16,000 taxa in ToLWeb  73,060 eukaryotic species  400,000 prokaryotic 16S rDNAs  250,000 species NCBI taxonomy  And other trees not listed * Proper phylogenies as well as phylogeny-based taxonomic hierarchies

5. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci ARCHITECTURE OVERVIEW DataOperations User Controller Rectify Names (TNRS) NameBanks Find matching treesSource treesGraft missing taxaPrune extra taxaTranslate formatsGet branch lengthsCalibrations Species1 Species2 Species3 condition1 condition2 Species1 Species2 Species3 condition1 condition2 Phylotastic

6. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci PHYLOTASTIC  Phy· lo· tas· tic/fī lō ˈ t ă s tĭk/ 1. Adjective: providing computable, convenient and credible access to expert knowledge of the phylogeny of species 2. Noun: an open-source project of HIP* to prototype and disseminate a distributed, web-services- based phylotastic system  Synonyms:ToL-o-matic  Web home: http://www.phylotastic.org * Hackathons, Interoperability, Phylogenies, a NESCent working group

7. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci HACKATHON #1, JUNE 4 TO 8 @ NESCENT  Teams:  TNRS - taxonomic name resolution  TreeStore - triple store with REST API  Architecture - controllers, interfaces, pruners  Branch lengths - scaling trees using chronograms  Shiny - other demos and cool front-end stuff  30 participants  high diversity  2 remote sites

8. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci PHYLOTASTIC.ORG It’s all open source Screencasts & live demonstrations

9. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci SCREENCAST: SCRIPTABLE PRUNER, WEB FORM   YouTube video at http://bit.ly/U1VGA1 (3 min)http://bit.ly/U1VGA1  Web form invokes URL API, like this:  http://phylotastic- wg.nescent.org/script/phylotastic.cgi?species=Felis+silvestris%2C+Canis+lupus%2C+Cavi a+porcellus&tree=mammals&format=newick http://phylotastic- wg.nescent.org/script/phylotastic.cgi?species=Felis+silvestris%2C+Canis+lupus%2C+Cavi a+porcellus&tree=mammals&format=newick  So, you can run it with curl  Or with a simple Perl script: #!/usr/bin/perl –w my $base = "http://phylotastic-wg.nescent.org/script/phylotastic.cgi"; my ( $tree, $taxa ) = @ARGV; $taxa =~ s/[ _]/+/g; $taxa =~ s/,/%2C/g; system( "curl \"$base?species=$taxa&tree=$tree&format=newick\" > out.tre; open out.tre" ); exit; Rutger Vos

10. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci SCREENCAST: MESQUITE-O-TASTIC   YouTube screencast at http://bit.ly/QjymbK (3 min)http://bit.ly/QjymbK  Installable Mesquite module is here: I  https://github.com/phylotastic/mesquite-o-tastic https://github.com/phylotastic/mesquite-o-tastic Peter Midford NESCent Arlin Stoltzfus NIST

11. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci RECONCILIOTASTIC  Reconcile-tree problem  Very common use-case  Inputs are gene tree, species tree  Gene tree: easy to get  Species tree: hard to get  Approach (see Reconciliotastic demo at http://www.phylotastic.org/demos)  Load gene tree ( with NCBI identifiers embedded in labels)  Compute species list  Extract identifiers from labels  Map IDs to species sources via NCBI web service  Get species tree phylotastically  Reconcile gene tree and species tree using Zmasek’s SDI library

12. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci ROLE OF TNRS IN PHYLOTASTIC (BRIEF) 40 species auto-extract species names from text Riek, 2011 (Mammalian Biology 76(1):3- 11) Manually key in species list from tree image 36 species + 2 extras* 36 species Phylotastic * named in text but not used in phylogenetic analysis 40 species Phylotastic Copy & paste species named in Table 1 33 species Phylotastic 5 minutes <1 minute 12 minutes Hours or days

13. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci ROLE OF TNRS — MORE DETAIL  screencast: http://bit.ly/T5ikoG (7 min)http://bit.ly/T5ikoG  Riek, 2011 (case study)  Cool demo:  PDF  auto-extracted names  tree  What Taxonomic Name Resolvers do  What the phylotastic TNRS team did  Using the Taxosaurus URL API  http://api.phylotastic.org/tnrs/submit?query=Ce phalophus+monticola http://api.phylotastic.org/tnrs/submit?query= TNRS team Naim Matasci iPlant Gaurav Vaidya U. Colorado Siavash Mirarab UT Austin

14. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci THE OTHER KIND OF DATING WITH FOSSILS r8s, pathd8, Multidivtime Calibrating a tree using fossil timepoints

15. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci PHP 11 studies >4,000 trees 6,973 taxa 620,868 leaves DateLife engine (R, FastRWeb, Rserve) DateLife engine (R, FastRWeb, Rserve) http://www.datelife.org DATELIFE

16. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci CURRENT STATUS - WYSIWYG There are some holes We haven’t put the pieces together yet The interfaces are unstable Branches could shift without warning You might crash

17. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci WHAT’S NEXT?  Phylotastic hackathon #2 (Jan 2013, AZ)  Themes  Integration – get components to work together  Use-cases – give users what they want  More Shiny Stuff — make it look good  Your idea here  To apply  http://tinyurl.com/PhyloTastic2  More partners & sponsors

18. Latest version of this file: http://bit.ly/RWRgIc (ppt) or http://bi.ly/Poaoci (PDF)http://bit.ly/RWRgIc http://bi.ly/Poaoci ACKNOWLEDGEMENTS  www.phylotastic.org www.phylotastic.org  Send feedback to Arlin Stoltzfus (arlin@umd.ed) HIP Leadership Team Participants Sponsors