TE26OCT08

Participants

Bill Piel, Brian O'Meara, Liya Wang, Michael Gonzales, Natalie Henriques, Sheldon McKay, Jeremy Beaulieu, Joe Felsenstein

Agenda

• Progress on wrapping Contrast 
• Dealing with intraspecific data 1) with Contrast 2) generally (i.e., whether to calculate species means in the discovery environment).

(do first two items first since Joe Felsenstein has to leave after 30 min)

• Ordered list of next methods to implement. Current proposal:

1. Contrasts
2. Discrete ancestral state reconstruction
3. Pagel 1994 character correlation
4. Fitting models (OU, BM, etc.: various stretching models like those in Blomberg et al. 2003).
5. Continuous ancestral state reconstruction [wasn't on the list]
6. [Many more to add eventually]

• Progress on Seedling
• Progress on Sapling
• What is the discovery environment?
• What is the discovery environment's interface like?

Notes

Minutes taken by Natalie Henriques and Jeremy Beaulieu

·      Liya discussed output of contrast program. Plan for using contrast within species variation.

·       Important to get Contrast to work and not worry as much about in species variation, it should not be the first priority.

·      Allow the data environment to allow the import of multiple observations per species but subvert contrast.

·      No machinery for missing data. Is there a no missing data policy? Retrieve only complete data sets. Currently no straight forward solution to missing data sets.

·      We have to strike a balance, solving all the problems in the first iteration will delay the release. We can write instructions to the effect “If you have missing data click here…” which would link to a help page.

·      A priority is to get something on the web for people to start working on it interactively.

·      A release date of January/February 2010 is being targeted, Iterations between releases will be one to two months apart

·      More focus on how to load data, how to load trees, and less on the technical trees.

Ordered List of Next Methods to Implement

1.     Contrasts

2.     Discrete ancestral state reconstruction

3.     Pagel 1994 character correlation

4.     Fitting models (OU, BM, etc.: various stretching models like those in Blomberg et al. 2003).

5.     Continuous ancestral state reconstruction [wasn't on the list]

6.    [Many more to add eventually]

·      Item 2 and 3 would be the most used and the most important.

·      ACTION: Get a list of programs related to items 2 & 3. – will be done by Jeremy Beaulieu

·      May explore other discrete methods before continuing with continuous ones.

·      Some discussions about incorporating molecular techniques, such as understanding substitution rate variation.  It was noted that it may not be within the scope of the project, but should look into this further.

Seedling/Sapling

·      Liya attended all the groups bi-weekly meetings. Seedling has done some things, not much on Sapling but they might be waiting on the Seedling group

·      Currently seedling can upload and store a tree as well as a large data table.

·      Did not see any progress on Vis.

·      Annotation Info – If there are annotations not discussed itemize those. In general we would rather have more exhaustive information and err on the side of excess. Don’t hesitate to email the requirements to Sheldon and Liya.

Discovery Environment

·      Not a lot to report at this time.

·      User friendly for user environment. Still looking at internal and low level stuff, but user friendliness will be there. It would be a web application