Action items from previous meeting

ACTION (From Oct 7): Ann will work on more detailed needs analysis and provide back to the group
ACTION: Sheldon will provide info about software evaluations
ACTION (Sheldon/Todd): In the current schedule is the seedling group considering these issues? What information is necessary when people upload trees? Gene names with species name? We need to consider it and articulate the needs to the developer.
ACTION (Sheldon) Infro on high level software evaluation – integrating vis tools
ACTION (Sheldon/Michael): Links to the wiki are obscure, hard to find and split between the iPToL page and the Core Software page. Set up another tree or a separate site of interest page
ACTION (Michael): Evaluate current access levels on wiki, work with iPlant group to consider setting accounts and having password protected pages.
ACTION (Michael): Ensure that the personal information for team members is not present on the public website.
ACTION (Michael): There is a meeting time conflict for two team members, an email will be sent checking availability for a meeting time change to Monday mornings.
ACTION (Michael): Review working group email list, revise membership, post membership on the wiki

Agenda

Urgent to to articulate requirements for the mockup/prototype for November meeting
More discussion on tree resolution service

Attendees: Sheldon McKay, Cecile Ane, Jim Leebens-Mack, Bill Piel, Jennifer Young, Todd Vision, Michael Gonzales, Natalie Henriques.

Jim – Gordon Burleigh from the 1KP analysis group would like to join this group. He is in data compilation but this is the central theme for his research program and he would like to be in this group.
ACTION: Todd will contact Gordon about joining the Tree Reconciliation group.
ACTION: Sheldon will get in touch with Anne Stapleton

Urgent to articulate requirements for the mockup/prototype for November meeting

Sheldon - Core software group spending time dealing with the first iteration, but we are trying not to get bogged down trying to do too much at one. I am concerned with this working group and think I should delegate other working groups to other engagement team members.
Prototype – integration take two to three months to get a web based working prototype Tree Reconciliation services that tackle data integration issues. Final implementation of Discovering Environ in 2010.
First implementation – start with database trees with some standard
Sheldon suggested starting by have a short list of inputs with a pull down menu then move on to taking actual user input.
For the meeting next month in Phoenix we need to do a demo, a mockup or something but we need clear pointers as to what form it should take so that proper research can be done.
Todd suggested starting from the user’s perspective. Will there be visualization? A place to start would be with user questions.
Sheldon – 1st bullet would be Tree Based Entry Point, support for uploading trees. Grabbing a subset of trees in an external repository
We need to discuss to what extent do we want to be hand holding users? To what degree? Do we want to provide a foolproof way for data to be entered? How far do we want to take that?

What strengths do we want to promote in the first release of Discovery Environs?

Sheldon – We want to make things possible that wouldn’t be possible. Want to have value added convenience. Help with file formatting to meet specifications within reason.
Todd – The biggest effect will be what we can enable people to do not what we do.
Sheldon – The marquee thing is to facilitate creation of the Tree of Life for all green plants, portal to browse and analyze data. Mapping traits and reconciling trees.
Something to consider – where gene duplication occurred on the species tree? How to reduce the frustration.
Sheldon – Valid species tree sparse taxon names, select species in subset. This is a reasonably good starting point. Working on that leads into what Discovering Environ will be like.
Bill – instead of having users choose a skeletal tree, as the user submits gene tree the species tree is generation from there. Mapping gene tree to species tree.
Todd – introduce basic function in the 1st release then improve on it. We can’t expect to have full service on the first iteration. Work on a model that cover the basics then build up.
Michael – we need to deliver something with the greatest value. Aggregation of activities brings together value of iPlant.
Jim – iPlant should come up with a standard of how species are recognized

Managing Expectations for the Workshop

What we present at the workshop may not be working software. We can discuss with them what is needed which would give us a good launching point to have a good product to release in January.
Implement solutions to provide one stop shopping.
What are we going to have for the meeting? 1. Making sub trees from species tree 2. Implement Tree ? to do reconciliation make gene tree minimize duplication. Start with sequencing of Gene Tree?
Make a more detailed plan without losing sight of the deliverable.
Can we have a prototype ready for the workshop? Sheldon – It is possible to have something working but my top priority is to have enough information to share.

Outputs