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arbor:
             Enabling tree-thinking at broad spatial and temporal scales




Monday, June 4, 12
arbor


                             Application and
                               GUI logic


                              Visualization




Monday, June 4, 12
arbor

       •      Visual, extensible software

       •      Load your data or use web services   Application and
                                                     GUI logic
       •      Use visual workflow interface to
              Interactively build models

       •      Scale analyses to very large trees
                                                    Visualization
       •      Interact with cross-linked data

       •      Format and export results


Monday, June 4, 12
this software will allow you to:




Monday, June 4, 12
this software will allow you to:


                        test key evolutionary hypotheses


                     with methods that are new and flexible


                         using massive amounts of data




Monday, June 4, 12
visual interface




Monday, June 4, 12
Figure	
  	
  2.	
  Web	
  services	
  in	
  phyloFlow.	
  phyloFlow	
  will	
  combine	
  local	
  computation	
  with	
  remote	
  access	
  to	
  data,	
  computation,	
  and	
  archiving.




Monday, June 4, 12
A Sample of arbor models


                                                     Varies on a
                     birth-death     Constraints
                                                       branch



                                        Species     Varies across
                 Brownian motion
                                     interactions      clades



                                                    Varies through
                     Mk model       Sudden jumps
                                                         time



Monday, June 4, 12
A Sample of arbor models


                                                     Varies on a
                     birth-death     Constraints
                                                       branch



                                        Species     Varies across
                 Brownian motion
                                     interactions      clades



                                                    Varies through
                     Mk model       Sudden jumps
                                                         time



Monday, June 4, 12
A Sample of arbor models


                                                     Varies on a
                     birth-death     Constraints
                                                       branch



                                        Species     Varies across
                 Brownian motion
                                     interactions      clades



                                                    Varies through
                     Mk model       Sudden jumps
                                                         time



Monday, June 4, 12
A Sample of arbor models


                                                     Varies on a
                     birth-death     Constraints
                                                       branch



                                        Species     Varies across
                 Brownian motion
                                     interactions      clades



                                                    Varies through
                     Mk model       Sudden jumps
                                                         time



Monday, June 4, 12
A Sample of arbor models


                                                     Varies on a
                     birth-death     Constraints
                                                       branch



                                        Species     Varies across
                 Brownian motion
                                     interactions      clades



                                                    Varies through
                     Mk model       Sudden jumps
                                                         time



Monday, June 4, 12
A Sample of arbor models


                                                     Varies on a
                     birth-death     Constraints
                                                       branch



                                        Species     Varies across
                 Brownian motion
                                     interactions      clades



                                                    Varies through
                     Mk model       Sudden jumps
                                                         time



Monday, June 4, 12
A Sample of arbor models


                                                     Varies on a
                     birth-death     Constraints
                                                       branch



                                        Species     Varies across
                 Brownian motion
                                     interactions      clades



                                                    Varies through
                     Mk model       Sudden jumps
                                                         time



Monday, June 4, 12
test case: grasslands




Monday, June 4, 12
Figure	
  	
  4.	
  Proposed	
  phyloFlow	
  work<low	
  for	
  Test	
  Case	
  1.	
  Information	
  processing	
  <lows	
  from	
  remote	
  sources	
  to	
  <ive	
  phyloFlow	
  modules.	
  First,	
  the	
  dataIntegrator	
  (A)	
  combines	
  phylogenetic,	
  distributional,	
  and	
  climactic	
  data	
  sources.	
  openModeller	
  
        (B)	
  then	
  creates	
  species	
  distribution	
  models,	
  and	
  Lagrange	
  (C)	
  tests	
  historical	
  biogeographic	
  hypotheses	
  incorporating	
  those	
  models.	
  Next,	
  	
  phyloView	
  allows	
  geographic	
  (D)	
  and	
  phylogenetic	
  (E)	
  visualization	
  of	
  	
  results.	
  Outputs	
  are	
  directed	
  to	
  
        the	
  dataOutput	
  module	
  (F),	
  which	
  can	
  save	
  results	
  both	
  locally	
  and	
  remotely.




Monday, June 4, 12
Monday, June 4, 12
Monday, June 4, 12
Monday, June 4, 12
Monday, June 4, 12
Monday, June 4, 12
How do species interactions
                     shape long-term patterns of
                              evolution?




Monday, June 4, 12
How do species interactions
                                                   Can we predict the genome
                     shape long-term patterns of
                                                    structure of extinct taxa?
                              evolution?




Monday, June 4, 12
How do species interactions
                                                   Can we predict the genome
                     shape long-term patterns of
                                                    structure of extinct taxa?
                              evolution?




                                                   Why are some parts of the
                                                   tree of life so much more
                                                      diverse than others?




Monday, June 4, 12
How do species interactions
                                                   Can we predict the genome
                     shape long-term patterns of
                                                    structure of extinct taxa?
                              evolution?




                                                   Why are some parts of the
                        (your question here)       tree of life so much more
                                                      diverse than others?




Monday, June 4, 12

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Phylotastic presentation - Harmon

  • 1. arbor: Enabling tree-thinking at broad spatial and temporal scales Monday, June 4, 12
  • 2. arbor Application and GUI logic Visualization Monday, June 4, 12
  • 3. arbor • Visual, extensible software • Load your data or use web services Application and GUI logic • Use visual workflow interface to Interactively build models • Scale analyses to very large trees Visualization • Interact with cross-linked data • Format and export results Monday, June 4, 12
  • 4. this software will allow you to: Monday, June 4, 12
  • 5. this software will allow you to: test key evolutionary hypotheses with methods that are new and flexible using massive amounts of data Monday, June 4, 12
  • 7. Figure    2.  Web  services  in  phyloFlow.  phyloFlow  will  combine  local  computation  with  remote  access  to  data,  computation,  and  archiving. Monday, June 4, 12
  • 8. A Sample of arbor models Varies on a birth-death Constraints branch Species Varies across Brownian motion interactions clades Varies through Mk model Sudden jumps time Monday, June 4, 12
  • 9. A Sample of arbor models Varies on a birth-death Constraints branch Species Varies across Brownian motion interactions clades Varies through Mk model Sudden jumps time Monday, June 4, 12
  • 10. A Sample of arbor models Varies on a birth-death Constraints branch Species Varies across Brownian motion interactions clades Varies through Mk model Sudden jumps time Monday, June 4, 12
  • 11. A Sample of arbor models Varies on a birth-death Constraints branch Species Varies across Brownian motion interactions clades Varies through Mk model Sudden jumps time Monday, June 4, 12
  • 12. A Sample of arbor models Varies on a birth-death Constraints branch Species Varies across Brownian motion interactions clades Varies through Mk model Sudden jumps time Monday, June 4, 12
  • 13. A Sample of arbor models Varies on a birth-death Constraints branch Species Varies across Brownian motion interactions clades Varies through Mk model Sudden jumps time Monday, June 4, 12
  • 14. A Sample of arbor models Varies on a birth-death Constraints branch Species Varies across Brownian motion interactions clades Varies through Mk model Sudden jumps time Monday, June 4, 12
  • 16. Figure    4.  Proposed  phyloFlow  work<low  for  Test  Case  1.  Information  processing  <lows  from  remote  sources  to  <ive  phyloFlow  modules.  First,  the  dataIntegrator  (A)  combines  phylogenetic,  distributional,  and  climactic  data  sources.  openModeller   (B)  then  creates  species  distribution  models,  and  Lagrange  (C)  tests  historical  biogeographic  hypotheses  incorporating  those  models.  Next,    phyloView  allows  geographic  (D)  and  phylogenetic  (E)  visualization  of    results.  Outputs  are  directed  to   the  dataOutput  module  (F),  which  can  save  results  both  locally  and  remotely. Monday, June 4, 12
  • 22. How do species interactions shape long-term patterns of evolution? Monday, June 4, 12
  • 23. How do species interactions Can we predict the genome shape long-term patterns of structure of extinct taxa? evolution? Monday, June 4, 12
  • 24. How do species interactions Can we predict the genome shape long-term patterns of structure of extinct taxa? evolution? Why are some parts of the tree of life so much more diverse than others? Monday, June 4, 12
  • 25. How do species interactions Can we predict the genome shape long-term patterns of structure of extinct taxa? evolution? Why are some parts of the (your question here) tree of life so much more diverse than others? Monday, June 4, 12