Call-in/WebEx Information

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

Action items

AI: A draft of the data model to support dependent use cases will be prepared by Sheldon & Sharon for the next meeting.
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

Brief review
Prototype Development Update
Prototype Data Model Discussion
- How will the following be supported?
  - Use Case 2 - Show all gene duplications in a gene family tree.
  - Use Case 3 - Find all gene trees showing a duplication event at a specific point on a species tree.
  - Use Case 12 - Show sampled gene copy number for all taxa gene family identifier
  - Use Case 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.

Notes

Attendees: Jim Leebens-Mack, Todd Vision, Sharon Wei, Adam Kubach, Sheldon McKay, Cecile Ane, Jamie Estill, Nicole Hopkins, Andrew Lenards

Data Model Discussion

TreeBeST to generate gene trees to feed info prime TV take outputs and query on UI

Sheldon does not have a draft data model for discussion complete. Sheldon working on setting dedicated server.

Issues:

Prime TV still giving error -
TreeBeST - NCBI file not formatted correctly.

Tried with smaller file and tested it with Gramene and it did work.
Need to use Swiss Prot naming convention (5-char length limit). This means we would need to transform NCBI tree

Sharon - has not figured out strategy.

Quick hex generation to represent groups contained in Viridiplantae and map from the hex-values to the full species/group names. So lookup table or modify code on TreeBeST?

Discussion of Lookup Table solution vs. Modifying code

Cecile - how will it affect user?
Sheldon - under the hood, see species binomials.
Cecile - will it scale up in the future?
Sheldon - mock up with look up table.

Sheldon is to look into source code for TreeBeST to get around 5 character limit.

Jim - can you use NCBI taxonomy IDs?

Sharon mentioned that she considered using NCBI taxon IDs and perhaps do a hexadecimal transformation of the taxon ID.

Todd - general desire to improve tools is part of iPToL effort. If we can convince authors to do this as well (include iPlant’s patch for the improvements/changes)

Moving toward getting development done in standardized environment -> box/virtual-machine up and running shortly

(Action Item): Get virtual machine for development

(Action Item): Sheldon to investigate source modification 1st then look at lookup table solution.

Jamie - works with Jim - background in google summer of code, did work on BioSQL, familiar with issues with query architecture.

Interim Solution - add to the TreeFam schema as needed to support functionality.
Sheldon hasn't thought about it fully yet.
Sharon - use TreeFam to store tree?
Todd - not sure if TreeFam does support
—
Ensembl compara does support it. (Todd suggested looking at Ensembl compara)

What's the plan for having a schema?

Sharon/Andy/Sheldon will come up with a plan and get back in 1 week. Need to include Jamie.

(Action Item): Status reports on development of prototype need to be made weekly.

Sheldon – will include whole mailing list in discussion. All members said they're okay with it.

Sheldon also to help Sharon with getting software to run code base solution to issue.

Need to consider the pipeline from gene catalog to alignments to TreeBeST. Todd can help with Sheldon.