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).A project of the NESCent HIP (hackathons, interoperability, phyogenies) working group. Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcRE-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, Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcUSE 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 ? Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcTHE 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 Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcARCHITECTURE 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 Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcPHYLOTASTIC Phy lo tas tic/f l t s tk/ 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:* Hackathons, Interoperability, Phylogenies, a NESCent working group Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcHACKATHON #1, JUNE 4 TO 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 Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcPHYLOTASTIC.ORG Its all open source Screencasts & live demonstrations Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcSCREENCAST: SCRIPTABLE PRUNER, WEB FORM YouTube video at(3 min)http://bit.ly/U1VGA1 Web form invokes URL API, like this: wg.nescent.org/script/phylotastic.cgi?species=Felis+silvestris%2C+Canis+lupus%2C+Cavi a+porcellus&tree=mammals&format=newickwg.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 ) $taxa =~ s/[ _]/+/g; $taxa =~ s/,/%2C/g; system( "curl \"$base?species=$taxa&tree=$tree&format=newick\" > out.tre; open out.tre" ); exit; Rutger Vos Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcSCREENCAST: MESQUITE-O-TASTIC YouTube screencast at(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 Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcRECONCILIOTASTIC 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 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 Zmaseks SDI library Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcROLE 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 4,000 trees 6,973 taxa 620,868 leaves DateLife engine (R, FastRWeb, Rserve) DateLife engine (R, FastRWeb, Rserve)DATELIFE Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcCURRENT STATUS - WYSIWYG There are some holes We havent put the pieces together yet The interfaces are unstable Branches could shift without warning You might crash Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcWHATS 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 More partners & sponsors Latest version of this file:(ppt) or(PDF)http://bit.ly/RWRgIcACKNOWLEDGEMENTS Send feedback to Arlin Stoltzfus HIP Leadership Team Participants Sponsors