iPToL_ET_10JUN09

Owned by Sheldon McKay
Last updated: Sept 08, 2009Version comment
3 min read

Attendees: Damian Gessler, Sriram Srinivasan, Andy Lenards, Nick Murphy, Karla Gendler, MMS, Adam Kubach, Jerry Lu, Liya Wang, Matt Vaughn, Scott Menor, Nirav Merchant, Sheldon McKay, Edwin Skidmore, Dan Stanzione

Action Items:

  • Create link on Tools page for Felsenstein's Phylogeny Programs Website (Karla or Andy)

Agenda

  • Review 03JUN09 Action Items (Sheldon)
  • General Update (Sheldon)
  • Tool Reports (All)
  • Roundtable

Notes

1. Review 03Jun09 action items

  • Discovery Environments talk put on hold due to recent staff changes. Will possible discuss with Sanderson and Dan on 6/11 at 1:30 pm AZ time.

2. General Updates (Sheldon)

  • Sheldon met with Todd Vision regarding the tree recon working group. A. sharing in compensation of outside experts, B. publishing in results. We want to change that the only way people work with us is if we compensate them.
  • Met with Val Tannen and Bill Piel, concerning the ToL Visualization proposal. Laid the very basic groundwork for data integration. Got copy of Encyclopedia of Life proposal. Must snail-mail a copy to you due to security constraints of writers. Goals of their visualization group similar to ours. Should free up some of our resources if it gets funded (don’t know when it will get funded, possibly October). We perhaps shouldn’t get too gung-ho with our visualization group until we know the status of this proposal.
  • Got ball rolling on getting working groups initiated. We are trying to encourage them to self-start earlier.
  • Sheldon will attend Evolution meeting in Idaho next week, more than 1000 attendees. Will present on pre-project and some iPToL/iPlant collaboration.
  • First steering committee meeting today at 2pm.
  • Andy – AP Web – Not sure of APWeb’s goal/vision. They can continue to use the tools they are comfortable with and we can make it look nice to the outside world. It would be in the best interest to get them to use XML or Phylo XML. If they want to go with facading over what looks like services and then adoption a more support XML dialect, they should be able to achieve that with a grad student (? mo) and 1/3 developer. They are expected to be provided with these two staff members in addition to the XML back-end. We are not sure what they want (web services?), no user cases. They were very please with what they had at the iPToL kickoff. It looks like they need a new user interface. This is a proposal that came in from Soltis to be an EOT activity in connection with iPToL.

3. Tool Reports (All)

ATV: (Adam) PhyloWidgit easer to read than ATV.

PrIMETV: (Adam) has a side tool that PrIMETV can read.

SimMap1.0: (Jerry) host a tree anaylsis to make inference about molecular and character evolution. Uses Bayesian approach for calculations. Mac OS X executable.

SimMap2.0: (Jerry) Re-write of SimMap 1.0 but with more features. It can be run on Mac, Linux, and Windows. Not finished.

~Might want to consider a rating scale (1-10) for maturity.

Parafit: (Liya) Mature product. Output is clear.

AxParafit: (Liya) Mature product. Both deal with co-evolution parasite problems.

NOTUNG: (Phil) Reconcile gene trees, root trees that are unrooted. Novel: ability to resolve a non-binary tree and make binary. Notung format is an extension of NHX with a little more information. Well annotated. Option to use their visualizer. Scalability limitations? It cannot deal with genome tree data.

TreeTapper: (Karla) more a collection of all the tools that have been created for phylogenetics. It will help you find the program you can run given a set of parameters. You have to know what you are looking for and it does require some knowledge. It is a conglomerate. It also says this is N area where more work and tools needs to be developed.

Organizational Note: Meeting Name change: iPToL Engagement Team Meeting