Re: [Treebase-devel] ABI proposal for phyloinformatics

[Vision, T. J <tj...@bi...>]

It is great to see these threads coming together!  

Sadly, I can't be directly involved because I will be submitting a proposal to ABI in the same round (for Dryad).  But that does not disqualify other NESCentians from participating.

One word of caution.  The document as it stands now harps a bit too much on the problems with the current system.  As it gets transformed into a proposal, I would hope that the solutions take center stage, and that it emphasizes the potential for what lies ahead, rather than the limitations of what lied behind.

OK, a second word of caution.  I would not take entirely at face value NSF's protestations that scientific goals are not important to the success of ABI Development proposals.  It may not be as important, but it stll matter.   In particular, I think there's an opportunity here to really see what can be achieved by looking synthetically at a large body of phylogenetic trees.  How much incongruence is there?  Does incongruence descrease over time?  How is it affected by the type of study (morphological vs molecular, amount of data, extent of taxonmic sampling, parsimony vs probabilistic, etc)?  Where are the holes in phylogenetic knowledge?  In which groups is there enough overlap to build supertrees or grafted trees?  These kinds of questions can only be answered with a resource like TB, and emphasizing such synthetic outcomes would help motivate the whole endeavour.

cheers,
Todd

On May 27, 2011, at 8:46 AM, Rutger Vos wrote:

> I'd like to second this initiative, I think the blurb at the end of
> the google doc nicely puts the finger on the sore spots, e.g.:
> 
> "TreeBASE arguably falls into the latter category, with ingest and
> retrieval of data constituting the predominant uses, yet the design of
> its current version chiefly aims at a fully transactional database for
> frequent and concurrent updates.  This legacy design choice places
> serious limitations on extensibility and robustness of the software,
> and has resulted in a degree of complexity of the code and deployment
> procedure that threatens its long-term sustainability."
> 
> The first half, i.e. "Ideas for New Development" has a lot of good
> ideas in it, hopefully we can make it so that some of those ideas are
> the meat on the bones of the sentiment expressed in the second half.
> 
> Let's fill out the doodle poll, its window is for next week.
> 
> Rutger
> 
> On Thu, May 26, 2011 at 8:00 PM, Karen Cranston
> <kar...@ne...> wrote:
>> There has been some interest among various groups in an ABI proposal
>> for development of phyloinformatics resources. This email is an
>> attempt to connect those threads and move the process forward. The
>> conversations that have been happening up to this point are:
>> 
>> 1. The Phyloinformatics Research Foundation (phylofoundation.org,
>> stewards of TreeBASE and ToLWeb) started a Google doc aimed at
>> TreeBASE
>> 2. MIAPA developers started a wiki page
>> (https://www.nescent.org/sites/evoio/NSF_ABI_2011), recognizing the
>> need for coordination with TreeBASE and other resources
>> 3. NESCent (Todd, Hilmar and myself), as the current TreeBASE host and
>> as a third party interested in coordinated development across
>> resources started a third document (now added to the already mentioned
>> Google doc)
>> 
>> If you are interested in this discussion and do not already have
>> access to the Google doc entitled TreeBASE_ABI.doc, let me know and I
>> can grant you access. Hilmar and I made some substantial edits earlier
>> this morning. I point you specifically to the section at the end
>> entitled "An attempt to re-think all of this". Briefly, we wanted to
>> encourage some radical thinking and explore the idea of developing a
>> PhyloCommons that incorporates both TreeBASE and ToLWeb into the
>> proposal (as the data repository and the data sharing / dissemination
>> / synthesis platform, respectively).
>> 
>> The ABI deadline is July 7, so we have a short period of time to pull
>> this together. Here is a link to a Doodle poll for an initial
>> teleconference.
>> 
>> http://doodle.com/zf2tz7sftyk3naxy
>> 
>> During this meeting, we hope to come to agreement on the broad
>> direction of the grant, identify possible leaders of the various
>> components and create a plan for getting this pulled together in time
>> for the deadline. Please feel free to continue the conversation on the
>> Google doc between now and the teleconference. If there are others who
>> you think should be invited, feel free to do so. Not everyone who
>> participates in this first phase will end up being named on the grant,
>> but these resources require input from a much larger group.
>> 
>> Cheers,
>> Karen
>> 
>> 
>> --
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Karen Cranston
>> Training Coordinator and Informatics Project Manager
>> nescent.org
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> 
>> --
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>> 
> 
> 
> 
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading, RG6 6BX, United Kingdom
> Tel: +44 (0) 118 378 7535
> http://rutgervos.blogspot.com
> 
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