TR120206

Owned by tjv
Last updated: Feb 06, 2012Version comment
2 min read

Attending

Jamie Estill, Jim Leebens-Mack, Todd Vision

Notes

  1. 1KP: Jim notes that the analysis has encountered a hiccup in that the previous dataset contained artificially concatenated sequences in ~1/2 gene families, will cause some delay.  But still aiming to submit paper on first ~90 spp roundabouts May 1st.
  2. Multiple reconciliations: Jamie has been documenting changes needed to support multiple reconciliations here.  We discussed the proposal to add reconciliation_sets to the schema.  All are in agreement.  We discussed the desirability of allowing one reconciliation_set attribute to be that all the reconcililations use a common species tree.  We agreed that allowing the user to switch between sets by opening multiple viewers (possibly with tabs) is a higher priority than figuring out how to allow users to compare results for different sets in one view.  Jamie will discuss how to implement these changes with iPlant, and can contribute time to updating the schema and data loading pieces.
  3. Test data: Jim pointed out that the Bowers gold standard data has a potential problem in that it depend on Populus being in the wrong position.  Also mentioned the availability of the dataset recently or soon-to-be published looking at the timing of gamma relative to Ranunculids and Asterids. Jamie emphasized having a many-species dataset would be be valuable to test the performance of the queries, etc.  Jim will look into getting quick-and-dirty trees from the existing 1KP dataset (they don't need to be right, just numerous). And Jamie will look into the test dataset from Ensembl Compara that comes with Phylodog.
  4. Ontology paper: Brief discussion of status.  Jamie will share status/draft shortly.  Will include Dan Barker in thread.
  5. GSoC: Brief discussion of whether to propose another GSoC project this year.  Jamie will consider.
  6. It was agreed that Mondays at 1:30 eastern will work as a regular time.

Action items

  1. Jamie  to document outcome of discussion of multiple reconciliations and talk to Naim about implementation.  Aim would be to have a functional interface by May 1st.
  2. Jim to contact Natalie about setting up a time for a meeting next Monday at same time to follow up.  Also set this as regular time for future every-other-week meetings
  3. Jim to inquire with John Kerry about assembling some quick-and-dirty 1KP test data for scalability tests. Jamie to look at other many-species reconciliation datasets.
  4. Jamie to share ontology paper status with group.