Action Items

1. ACTION: Todd provide agenda items for the call and Michael send out the reminder on Fridays.
2. ACTION: Michael look into a dedicated conference call number for the TR working group to use.
3. ACTION: Rewrite the information given at the meeting in a form that can be reviewed by the group, prioritized and turned into use cases (Jim)

Agenda

• Review action items from previous meeting
• Introduce Andy Lenards as the ETA for the working group
• Open discussion

From Todd's email:

Status:
1: Critical for initial proof of principle
2: Critical for a functional large-tree reconciliation or data integration service
3: Noncritical but desirable
4: Out of scope

Phase
1: prototype by Feb 2010
2: prototype by Aug 2010
3: prototype by Feb 2011
4: out of scope

The four items that I think deserve immediate attention (for the Feb 2010 prototype) are these:
1. Reconcile a gene tree and species tree chosen from tree databases or submitted in some standard form.
2. Show all gene (but not all genome) duplications in a gene family tree.
3. Find all gene trees showing a duplication event at a specific point on a species tree.
12. Show sampled gene copy number for all taxa

Notes

Attendees: Todd Vision, Cecile Ane, Sheldon McKay, Andrew Lenards, Jim Leebens-Mack
John Bowers, Jerry, Michael Gonzales, Natalie Henriques.

• Reviewed action items. Michael is still working on a dedicated conference call number for the TR working group to use. Other items complete.
• Andrew Lenards was introduced as the new engagement team analyst to the TR working group. He will work with Sheldon primarily on two things – help accelerate requirement gathering and in the long term getting TR services integrated into DE.
• Todd reworked the list from the meeting in Phoenix in order of priorities. The four items that deserve immediate attention (for the Feb 2010 prototype) are these:
  • 1. Reconcile a gene tree and species tree chosen from tree databases or submitted in some standard form.
  • 2. Show all gene (but not all genome) duplications in a gene family tree.
  • 3. Find all gene trees showing a duplication event at a specific point on a species tree.
  • 4. Show sampled gene copy number for all taxa
• We need to come to a consensus on what the top priorities are.
• TR method used should be designed in a modular way so that it can be changed if necessary.
• Defer discussion on Jens collab/postdoc until next week
• Defer action on 1KP/TACC resource sharing until tomorrow or Wed
• ACTION: Assess PlantTribes, Phytozome, Plaza, and Ensembl Plants as sources of gene family data, especially aligned sequences
• ACTION: Get started on TreeBeST as the reconciliation tool
• ACTION: Think about database/model to support queries as specified in use cases 1-4.