Agenda

• Tree reconciliation pipeline update (Sheldon)

• Questions about future clusters (Sheldon)

• Database update (Jamie)

• Feedback from PIs (Jim, Cecile)?

• Meeting time change

Notes

Attendees: Nicole Hopkins, Eric Lyons, Jamie Estill, Lim Leebens-Mack, Cecile Ane, Vicki Bryan

Database Update

• Jamie - writing code to populate the database, figuring out a good way to reconcile tree in time format, will finish in the next day.

• Jim – Looked at the incubator project notes and in reviewing the details of the pipeline - is what was done, what we agreed upon? ( precomputed reconciliation).

• Discussed having a comparison of the two types of reconciliations TreeBest and PrIMETV

• Nicole – We need to start thinking about user interface, to interact with what is stored in the database, how to search, and what is returned on the search.

• Discussed the four questions in scope https://pods.iplantcollaborative.org/wiki/display/coresw/Tree+Reconciliation:

  1. Show all gene duplications in a gene family tree

  2. Find all gene trees showing a duplication event at a specific point on a species tree

  3. Show sampled gene copy number for all taxa

  4. Find points on a species tree where a set of genes (e.g. all genes within a pathway or GO category) originated and/or diversified.

• Need to evaluation which reconciliation algorithm is working the fastest. Suggestion to let users select the algorithms they would like to use?

• @elyons is getting up to speed and working with developers on how best to do a three screen vis on the available space. How do we want it visualized? The use of tabs was suggested as a simple solution.

Meeting Time Change

• To accomodate everyones schedule we are looking into changing the time of this meeting. A poll was sent to select a new time http://www.doodle.com/cqb2rvpfc79pqhsg