TR_02NOV09

Owned by Former user (Deleted)
Last updated: Nov 08, 2009 by Sheldon McKayVersion comment
3 min read

Action items

carried forward
ACTION: Sheldon will provide info about software evaluations
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): Review working group email list, revise membership, post membership on the wiki

new
ACTION: Todd will contact Gordon about joining the Tree Reconciliation group.
ACTION: Sheldon will get in touch with Anne Stapleton

Agenda

  • Refining ideas for the November mockups.
  • Ideas for getting John Bowers started evaluating what software to
    incorporate in the DE. I would like to see an evaluation of performance
    that includes both optimization approaches (e.g. NOTUNG, TreeBEST) and
    probabilistic ones (e.g. Prime-GTR).

It's been pointed out that these algorithms differ in whether the gene tree
is supplied or inferred as part of the reconciliation analysis. Before too
long, we will need to discuss the data integration consequences of these two
different approaches. If we go one route or the other, what external
sources, or internal workflows, should we consider for gene sequences, gene
alignments and/or gene trees, so that iPlant can begin to investigate the
different options?

Notes

Attendees: Sheldon McKay, Cecile Ane, Todd Vision, Michael Gonzales, Adam Kubach, John Bowers, Jeremy Beaulieu, Natalie Henriques.

Software Evaluation

  • Link provided for software evaluation - https://pods.iplantcollaborative.org/wiki/display/iptol/TR_Tools+and+Software
  • Two visualization software evaluated ARCHAEOPTERYX and PRIMETV
  • Sheldon will take any suggestions on third party applications
  • Todd suggested PRIME GTR and Sheldon will review
  • Discussed ideas for getting John Bowers started evaluating what software to incorporate in the DE. Group would like an evaluation of performance that includes both optimization approaches (e.g. NOTUNG, TreeBEST) and probabilistic ones (e.g. Prime-GSR).
  • Sheldon: NOTUNG - don’t know how suitable it would be for integration

Refining Ideas for November Mock-up

  • At the last meeting we discussed making the mock-up not functioning software but a vehicle to drive ideas from the meeting attendees. We would use the information to help us deliver our prototype in early 2010.
  • Looking at TreeBEST it is distributed as C source code which is appealing for integration.
    See opportunity to start with sequences. Not sure alignment support in TreeBest but we can add that support if needed.
  • Cecile – it would be a good idea to integrate alignment. Value added in comparing reconciliation among gene families.
  • Pre-compute alignment stored as HMM. Question whether to use existing database of alignment or do plant wide transcript alignment?
  • Sheldon – What are we going to talk about or show in Phoenix? What will we produce as the principal application next year discussing later this month and people flood sequencing in pipeline is not a short term goal.
  • Sheldon – The 1KP folks what will they have in terms of data? We need to get a better sense of where they are in processing analysis.
  • ACTION: Sheldon and Michael will coordinate with John offline to come with a plan to extrapolate all the players to have a substantive discussing for the 1KPmeeting.
  • ACTION: The week of November 14 – 20 Sheldon will start working on a written document and finding materials for the meeting. He will post an address on the wiki and asks for contributions to the document.
  • ACTION: Michael will follow up with Todd and Cecile to get the Computational Biologist job position resolved.