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Call-in/WebEx Information

• TR_WebEx - this meeting will include visuals, so WebEx Video will be utilized

Action items

• AI: Verify that taxa with the same 5-characters can be used as inputs to TreeBeST (Sheldon) [DONE]
• AI: Queries to support use cases by May 17 meeting (Sheldon) [NOT DONE]
• AI: Determine status of funding for Jens' group (Andy) [DONE]
• AI: Former user (Deleted) to mockup an expert tree prune/selection w/ auto-complete to find taxa. Common taxa box should be incorporated. APWEB has an example of how to show users where their species/group of interested is placed on the tree. [incomplete]

Agenda

1. Group Discussion: formalize role/interaction for Jamie w/ the working group and engagement team
2. Queries to support the retrieval of the following: (Sheldon)
   • Show all gene duplications in a gene family tree. (Use Case 2)
   • Find all gene trees showing a duplication event at a specific point on a species tree. (Use Case 3)
   • Show sampled gene copy number for all taxa gene family identifier (Use Case 12)
   • 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. (Use Case 4)

Notes

Attendees: Jim Leebens-Mack, Jamie Estill, Cecile Ane, Sheldon McKay, Natalie Henriques, Adam Kubach, Andy Lenards, Nicole Hopkins

Discussion of Jamie's Role on Working Group

Jamie best fit = data model, Sheldon concurs. Communication will be by whatever means that is helpful (email, phone, confluence/wiki, skype).

AI: (For Andy) Jamie needs info for chat server

Re: Jamie interaction
Jim - imagines Jamie and Sheldon = SKYPE x email for day to day over confluence -> frequent interactions
Sheldon: confluence for documentation of offline conclusions - diligence on recording back to group

Upcoming Meetings

Talk about the in-person meeting for Memorial Day at NESCent (May 31, June 1) - Need to utilize email to compensate for the lack of a working group meeting (next meeting scheduled for June 14, 2010).

Review Action Items

• 5 character limit -> confirm - did test and inclusion of long taxon labels does not confound tree - documented under developer notes
• Over us to use cases -> not done - got in touch with EBI - Albert (Someone) to help with this. Sheldon sent him use cases to review - 1st 3 were trivial, one with GO terms requires extra handling. none difficult - all doable per Albert. Sheldon to ping again today.
• Andy will try and have rough UI version for next meeting -> (mockup an expert tree prune/selection with auto complete to find taxa, outstanding AI from many meetings ago). Next steps - to flesh out Balsamiq mockups for more details regarding "steps" of the supported investigation types.
• Funding for Jens - NSF approval - needs to be contract - extra reviews since its international.

Sheldon on direct line for funding, approval is moving a bit slow, this isn't our holdup. Jim - no hold up with getting them here (Jens postdoc, Bengt). -> They can get here fro June meeting? Sheldon says we'll set it up. May 31-June 3 US meeting, starts Memorial Day.

Todd sent email saying he'd have more info, need to check on NESCent availability stuff. Sheldon to follow up. Get Bengt here and assume will be moving forward.

Jim: They have database that can be converted to gene tree database, based on John Bower's work - be great to settle on database- put trees into it and have someone start working on visualizing for prototype. Todd wants to work with Phenoscape data - Sheldon -> not problem with parallel traits. Jim -> most important thing is to start trying top get gene/trees into gene tree database. OR gene family sequences and let TreeBase make trees.

Sheldon: Let's go ahead and start now, will have something by May 31st. -> face-to-face meeting, Andy will not be able to attend.

June 14th -> next available teleconference

Jim to get Jamie the data from John Bower's work. The data will likely be in Access and Excel.