Re: [Treebase-devel] ABI proposal for phyloinformatics

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Hi everyone, sorry for joining this thread a bit late but I am catching up
and have been discussing some things about ToLWeb and user interface ideas
with the phylorf committee.  Regarding ToLWeb, we agreed that we need a
point person and so I have volunteered to be that person, with David and
Karen joining to form a three-person group to help steer ToLWeb issues in
this ABI grant.  We are totally open to all ideas about where ToLWeb should
head- we mainly thought having a group with a point person would help get
decisions made.  In order to be effective, I am trying to aggregate
information on ToLWeb features and site maps, existing strengths and
weaknesses, steps needed to go open source, features we need/want, user
interface ideas, past discussions like ToLWebII, etc.  Regarding user
interface issues, I think we can probably all agree that UI design and
implementation is a key issue for both TB and TW.  In talking with Rob G, we
are both really interested in UI, and we both have programmers in our groups
who are working on various UI features for Tree Viz, so that would be an
area where I think we would be interested to help the project as the interop
details are hammered out.  More soon-  Thanks, Mark

On Tue, Jun 14, 2011 at 2:42 PM, David Maddison <
dav...@sc...> wrote:

> Sorry, folks for being silent.  Travelling, daughter's graduation, mom's
> visit, yada yada yada...
>
> Here are some comments, and I must say I haven't read the proposal yet,
> just the pitches, and the emails.
>
>  I like the general plan.
>
> I agree that Jim that fundamentally ToLWeb should be viewed as a test case
> for interoperability, even if there is specific effort in the project on it.
>  I would go so far to say that even TreeBASE should be viewed here as a test
> case.  The most important thing that would be built in the process of doing
> this the vision, understanding of needs, standards, design of the tools, and
> community building and inspiration, rather than the particular
> implementations that will come out in TreeBASE and ToLWeb.    The products
> should be done with enough abstraction that they will serve for other cases.
>  I always find that it is good to have two test cases, just to force one to
> think about alternatives at various decision points.  There is a cost to
> that, of course, and that is the added funds that would be needed to support
> other test cases.  But if we could have a light-weight alternative to
> TreeBASE as an alternative test case at that end, and a light-weight
> alternative to ToLWeb to serve as a test case there, then it might be worth
> thinking about including a bit of effort there that to force greater
> abstraction.
>
> ToLWeb is "emotionally" open source.  That is, it's fully available as far
> as I am concerned, but we haven't gone through the effort of actually making
> it open source.  Anyone who wants the source can have it.  So, I am
> enthusiastically in support of having a small portion of the budget devoted
> to the effort to push it onto Source Forge or somewhere.  Ideally that would
> involve a bit of contract money to Andy Lenards, and possibly Danny Mandel
> (programmer that proceeded Andy; Danny understands more of the source, I
> suspect).
>
> OK, more comments after I look at the proposal.
> David
>
>
> On 7 Jun  2011, at 10:53 AM, Karen Cranston wrote:
>
> >> Karen,
> >>
> >> Will you be sending the pitch to Reed and asking for feedback?  I
> suspect he will want to talk about some of the technical points being
> discussed in the googledoc in order to be certain that this is an ABI
> development proposal.   My sense from our last discussion is that
> development project proposals should include pretty watertight plans for
> software/database engineering and testing.
> >
> > I am putting together two pitches of ~1 page each to send to NSF. One
> > is the grand ToLWeb + TreeBASE version, and the second is the TreeBASE
> > and MIAPA-focused ideas that you, Bill and Rutger submitted (I am
> > merging these into a single doc). This way, we can get a sense of
> > which version is more likely to be viewed favourably by the panel and
> > program officers. Working madly, hoping to send this ASAP.
> >
> > Karen
> >
> >>
> >> Bests,
> >> Jim
> >>
> >> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >> Jim Leebens-Mack
> >> Department of Plant Biology
> >> University of Georgia
> >> Athens, GA 30602-7271
> >>
> >> Phone: 706-583-5573
> >> Fax: 706-542-1805
> >> email: jle...@pl...
> >> url: http://www.plantbio.uga.edu/~jleebensmack/JLMmain.html
> >> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >>
> >>
> >> ----- Original Message -----
> >> From: Karen Cranston
> >> [mailto:kar...@ne...]
> >> To: Arlin Stoltzfus
> >> [mailto:ar...@um...]
> >> Cc: MIAPA [mailto:mia...@go...],
> >> ph...@go..., TreeBASE devel
> >> [mailto:Tre...@li...]
> >> Sent: Mon, 06 Jun 2011
> >> 10:04:48 -0400
> >> Subject: Re: ABI proposal for phyloinformatics
> >>
> >>
> >>> There are several pitches now in the Google doc, with a fair bit of
> >>> overlap between them. I am willing to consolidate into a single page
> >>> and send to NSF (Reed?) and see what he has to say about the various
> >>> components. It seems like these components are:
> >>> 1. some level of re-engineering of TreeBASE
> >>> 2. further development of MIAPA, with annotation tools and TreeBASE
> >>> integration
> >>> 3. use of ToLWeb as a crowd sourcing and data synthesis platform
> >>> 4. NeXML refinement and development
> >>>
> >>> I don't think this one-pager needs to capture all of the ideas and
> >>> details we currently have, but instead give a general sense of what we
> >>> are proposing and if all / some of these ideas is potentially
> >>> fundable.
> >>>
> >>> Everyone in agreement? I will post the single page in the doc later
> today.
> >>>
> >>> Karen
> >>>
> >>> On Fri, Jun 3, 2011 at 3:38 PM, Arlin Stoltzfus <ar...@um...> wrote:
> >>>> Today is the deadline for our 1-page synopsis to pitch to an NSF
> program
> >>>> officer (before going further).   Currently we seem to have 3 pitches.
> >>>  It
> >>>> is time now for some energetic person to consolidate this, so that we
> can
> >>>> move ahead.
> >>>>
> >>>> Arlin
> >>>>
> >>>> On May 31, 2011, at 12:19 PM, Karen Cranston wrote:
> >>>>
> >>>>> Tomorrow morning (Wed, June 1) looks to be good for everyone, and
> >>>>> sooner seems better than later. I propose we talk at 9:00 am EST. I
> >>>>> will send connection information later today.
> >>>>>
> >>>>> Cheers,
> >>>>> Karen
> >>>>>
> >>>>> On Thu, May 26, 2011 at 3:00 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
> >>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>>>> Karen Cranston
> >>>>> Training Coordinator and Informatics Project Manager
> >>>>> nescent.org
> >>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>>>>
> >>>>> --
> >>>>> You received this message because you are subscribed to the Google
> >>>>> Groups "MIAPA" group.
> >>>>> For more options, visit this group at
> >>>>> http://groups.google.com/group/miapa-discuss?hl=en
> >>>>
> >>>> -------
> >>>> Arlin Stoltzfus (ar...@um...)
> >>>> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> >>>> IBBR, 9600 Gudelsky Drive, Rockville, MD
> >>>> tel: 240 314 6208; web: www.molevol.org
> >>>>
> >>>> --
> >>>> You received this message because you are subscribed to the Google
> >>>> Groups "MIAPA" group.
> >>>> For more options, visit this group at
> >>>> http://groups.google.com/group/miapa-discuss?hl=en
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>> Karen Cranston
> >>> Training Coordinator and Informatics Project Manager
> >>> nescent.org
> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>>
> >>> --
> >>> You received this message because you are subscribed to the Google
> >>> Groups "MIAPA" group.
> >>> For more options, visit this group at
> >>> http://groups.google.com/group/miapa-discuss?hl=en
> >>>
> >>
> >
> >
> >
> > --
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Karen Cranston, PhD
> > Training Coordinator and Informatics Project Manager
> > nescent.org
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> ---------------------------------
> David R. Maddison
> Department of Zoology
> 3029 Cordley Hall
> Oregon State University
> Corvallis, OR  97331   USA
>
> dav...@sc...
>
> http://david.bembidion.org
> http://mesquiteproject.org
> http://macclade.org
> http://tolweb.org
>
> (541) 737 2834
>
>
>
>
>

-- 
Mark W. Westneat
Curator of Zoology
Robert A. Pritzker Director, Biodiversity Synthesis Center of the
Encyclopedia of Life
Field Museum of Natural History
1400 S Lake Shore Dr.,  Chicago, IL  60605-2496
(312) 665-7734

My website: http://synthesis.eol.org/users/mwestneat<http://biosync.fieldmuseum.org/users/mwestneat>
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