Agenda

Tree Reconciliation Service update (Sheldon)
Other Business

Notes

Database Update

• Working on a developer release by the 15th for testing and feedback

• The first release will not be hightly interactive, but each release stage will have more functionality. We do not want to delay the release by waiting on interactions.

• 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?

• Eric Lyons 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.