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TEPR110223

TEPR110223

Trait Evolution Progress Report

February 23rd, 2011

Summary

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Status

(see also iPToL Progress Report)

The group decided to use the implementation of Phylogenetically Independent Contrasts from Joe Felsenstein's software package PHYLIP. This first tool was included in the 2.0 release of the Discovery Environment in April 2010. After a hiatus of approximately 9 months, the working group resumed its activities. The group opted for the integration  of functions from the R packages ape and geiger that implement the methods identified as a priority by the working group. The execution framework to support R scripts has been developed and discrete and continuous ancestral character reconstruction methods have been integrated into the Discovery Environment through the ape function ace and will be part of the 3rd release of the DE. The model fitting functions of the package geiger are currently being integrated. Through the integration work, the members of the group identified and provided a patch for a bug in the function ace that might have caused unreliable results. The group is also actively working in collaboration with the original author to adapt the package geiger to a HPC environment. As part of this process, Jeremy Beaulieu improved the performance of a key function resulting in a >180X faster execution.

Latest developments

(see also TE Meeting minutes)

The Working Group has started an EOT effort in collaboration of the Dolan DNA Learning Center with the goal to produce an educational version of the TE tools. This will be the first educational adaptation of the Discovery Environment and Phylogenetically Independent Contrasts should be the first priority for education, as it is a more difficult concept and can incorporate teaching about hypothesis testing. Ancestral state reconstruction would be next. The Group has started collecting data sets as examples to fit in the biology curriculum in several places and to be 'flashy' (e.g. selfing, carnivory, poisonous plants, medicinal value, use as supplements, seed size, fruit fleshiness...). Sample data sets should be organized by topic (e.g. ecology, plant physiology), especially if topics can overlap.

As the Working Group will be able to work more independently it would be valuable to provide the postdocs with greater access to the CI and development resources so that they can more effectively contribute their expertise and at the same time use or develop these resources for their own research.