Arlin Stoltzfus edited this page Mar 31, 2016 · 11 revisions

Welcome to the phylotastic wiki!

Overview

When experts build a "phylogeny" or "tree" showing the relationships of species, they may spend months on gathering data, doing quality-control, and carrying out statistical inference using software so compute-intensive it often requires special servers running for weeks at a time. For non-experts, the cost of getting a custom phylogeny is usually prohibitive; for an educator, student, or lay-person, it is almost unthinkable.

This situation is about to change.

The Phylotastic project is creating tools to deliver custom species phylogenies in seconds rather than months. The system does not compute trees from scratch. Instead, it takes advantage of years of phylogeny research along with efforts in data archiving and tree-synthesis that together make available information on relationships of millions of species— ultimately derived from the work of experts— from sources such as OpenTree, TreeBASE, and ToLWeb.

Our products in development currently include a web tool targeted for general use, including classroom use, and a mobile app that acquires a tree for species names harvested by OCR (e.g., from signage).

Beneath these new tools is a new ecosystem of web services that interact via standard interfaces. This system will be open and public, so that (1) anyone will be able to build new Phylotastic tools, and (2) anyone with data to offer will be able to add a web service that others can use.

The Phylotastic system aims at rapid and broad dissemination of knowledge ultimately derived from scientific experts. The system does not replace original research on phylogeny— just as the existence of wikipedia and other encyclopedias results in the broad dissemination of knowledge on many topics, but does not replace the need for ongoing expert research on those topics. Nevertheless, just as real researchers often make use of wikipedia, we expect that real phylogeneticists will find ways to make use of Phylotastic.

Resources

Open development model

The Phylotastic project has an open-source open-development model. We have a public channel for project communication, a public issue tracker, and public github repos for all of our source-code. The way to join the project is just to start participating by making a comment or request.

Throughput Graph

About us

The system owners of the Phylotastic project are funded by the National Science Foundation (NSF). We are

  • the IBBR team of Arlin Stoltzfus (design, testing, outreach)
  • the NMSU team of Enrico Pontelli (knowledge representation and reasoning)
  • the DateLife team of Brian O'Meara at UTK (phylogeny calibration)
  • the Global Names team of Dmitry Mozzherin at UIUC (taxonomic intelligence)
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