Phylotastic

Please bear with us while we work to refactor and update the material on this page.

Phylotastic is a project to enable convenient, computable, credible access to the Tree of Life comprising expert knowledge of phylogeny: the species tree you want, in ready-to-use form, when you want it. Phylotastic is a project of the NESCent working group called HIP (Hackathons, Interoperability, Phylogenies). The project was launched in June, 2012 at the first Phylotastic hackathon, and continued at iPlant headquarters in January with a second hackathon.

fixing this page (burn after reading)

Our web home at phylotastic.org points to this page as the "wiki". This should be the place where people come to find out more about the project. In particular we want to make this site useful for:

• personnel from other projects who might want to work with us to integrate resources
• anyone who might be in a position to offer support ($$, programmer hours, meeting resources) or influence decisions
• programmers who might be interested in contributing
• end-users who might want to use the system, or make suggestions

Here is a list of things to be done:

• add an up-to-date lead (short!) summarizing the current state of the project and future challenges
  • see Brian's recent report https://docs.google.com/document/d/1VS0WKbosn92cAx9Y53FOaubYCpqDkzDItZ2d4AnvMDA/edit
• integrate the hackathon-related links into a series of short blurbs about Architecture, Pruning, Scaling, TreeStores, Shiny Stuff, TNRS.
  • see Brian's recent report https://docs.google.com/document/d/1VS0WKbosn92cAx9Y53FOaubYCpqDkzDItZ2d4AnvMDA/edit
• add eye candy such as
  • the 2 figures from the paper (DropBox/Phylostastic/Manuscript/Figure*)
  • photos from the PhylotasticGallery
  • Shannon's nice architecture image
• add a catch-all section with links to technical content, resources, and further information
• optionally, add notes for teams to clean up their pages

miscellaneous links to keep (use or discard after rewriting)

• list of participants
• first hackathon
• second hackathon
• see PhylotasticGallery for pics of the event
• resources from the first hackathon
  • Phylotastic web site
  • Phylotastic source code on GitHub
  • Phylotastic/Architecture: Architecture and API for Phylotastic
  • TNRS: resolving taxonomic names
  • Phylotastic/shiny: demos to showcase phylotastic capabilities
  • DateLife: getting divergence times for lists of species using existing trees
  • [[1]]: use-cases page

Summary

this section should have an up-to-date lead (short!) summarizing the current state of the project and future challenges

Sub-projects

TNRS

• TNRS - Name Cleaner
  • Gaurav, Dan, Andy
  • mr-naims on github
  • species-autocomplete on github
  • demo mr-naims report generator (Andy, Dan)
  • demo autocomplete (Gaurav)

Architecture

• Architastic (page in progress) Ben
  • demo with 2 different treestores-- OToL and RDF-- including TNRS + tree finding + pruning
  • wiki page by Shannon
  • + DateLife is in progress
  • Ben, Karen, Derrick, Shannon, Naim, Mark, Cody, Rutger
  • google folder

Scaling

• DateLife
  • Scott, Brian, Klaus and April
  • google doc

Metadata

• Tree Annotation - Enrico, Hilmar, Ramona, Joachim, Arlin and part of Andrea
  • slide presentation - 10 trees annotated, checklist form, MIAPA ontology,
  • demo (Joachim)
  • wiki documentation (Arlin)

Shiny stuff

• PhyloGeoTastic
  • Greg, Ignacio, Mercedes, Jule, Brian S., Meg
  • Google Folder
  • Scope of Work
  • demo

• PhyloStyloTastic
  • Dasie, Mike and Meg
  • google doc example .tss spec
  • Mesquite demo

Resources

this is a stub for a catch-all section with links to technical content, resources, and further information