Re: [Treebase-devel] ABI proposal for phyloinformatics

[Rutger V. <R....@re...>]

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