[ToLWeb2.0] should we resume our efforts

[Hilmar Lapp]

Hi all,

I'm wondering where everyone's intentions and energy stands here in
regard to picking back up this effort where we left it about 3 months
ago.

In particular, are we still committed enough to make the stakeholders
meeting happen, and if so, what time frame might be realistic.

The concrete reason I'm asking this now is that originally we were
thinking to have that stakeholders meeting take place back-to-back
with the TreeBASE foundation meeting. That foundation meeting should
take place in the not-so-distant future as otherwise the pursuit of
funding opportunities for TreeBASE continues to be stalled, which is a
rather undesirable situation.

-hilmar
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[Karen Cranston]

We lost most of our momentum, and I am not sure how much of that was
due to the change of focus from ToLWeb to a more abstract question -
i.e. we were motivated to rally around ToLWeb as a specific resource,
and how much was the 'distraction' of developing the AToL proposal. If
it was the former, then do we want to re-create that focus on ToLWeb?
What's been proposed for ToLWeb in the AToL grant won't come anywhere
near the grand vision that this group had for the project. On the
other hand, if there are rumblings about other upcoming grant
opportunities where ToLWeb might feature predominantly, then perhaps
this is not needed.

I've been at an iPlant conference for the last two days, and have
heard lots of examples of people wanting phylogenies for their
research project but not wanting to build trees themselves. Makes me
excited about the idea of synthesizing and re-using phylogenetic data.

I'll be out of email contact for the next few days (starting in about
5 minutes) but I'll check back in next week.

Karen

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karen.c...@gmail.com
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[bemb...@gmail.com]

I don't know of any near-future grant opportunities where ToLWeb would feature predominantly, nor can I imagine writing a grant myself should such an opportunity appear. Because I am stepping down at the end of December leading ToLWeb, I view my grant writing for it as done (except as a helper for other folks' grants, if necessary).

Hilmar, I presume you mean the "Phyloinformatics Research Foundation" rather than the "TreeBASE Foundation". The PRF includes both TreeBASE and ToLWeb within its mission.

I think a back-to-back meeting of a ToLWeb 2 group with PRF would be ideal (ideally after news about the ATOL grant is available), and I also think the ToLWeb 2 group (or whatever it will be called) should definitely consider forging ahead. You have a great group of phyloinformaticians and can make a lot of progress. But exactly how the ToLWeb 2 group should proceed - centered around ToLWeb or thinking about it de-novo - I'm not sure.

David

[Nico Cellinese]

I am still very interested in this mission. Although it would be very
helpful to know about the outcome of the ATOL proposal, this is a
completely different, more comprehensive effort and we should consider
to move ahead at this stage. And I think it would be ideal to have a
meeting in conjunction with the Foundation. I am still in the field
and therefore on and off the digital sphere.

Nico

[Rutger Vos]

> In particular, are we still committed enough to make the stakeholders
> meeting happen, and if so, what time frame might be realistic.

It sounds like there is an interest by a number of people and that the
ideal time frame would be after the AToL decision (which is when?) and
in the Fall at the latest.

What would the next action items be if we wanted to move forward?

The most recent artefact is the new tolweb2 whitepaper
(http://docs.google.com/Doc?docid=0AQ-1ley90MKnZGhmZzZ4M2NfMzlmcHN4a3NmOA&hl=en),
last touched by Karen on March 31st. It suggests that at that time we
had a fairly clear idea of the format and substance of a stakeholder
meeting. Would that be a basis to start planning that meeting?

--
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://www.nexml.org
http://rutgervos.blogspot.com

[Hilmar Lapp]

Hi David:

On May 25, 2010, at 9:13 PM, bemb...@gmail.com wrote:

Hilmar, I presume you mean the "Phyloinformatics Research Foundation" rather than the "TreeBASE Foundation". The PRF includes both TreeBASE and ToLWeb within its mission. 

Yes, that's indeed what I mean, sorry for the misquoting of the name.

[Karen Cranston]

I am hoping to re-start this conversation (yet) again. The AToL grant
was not funded. The Phyloinformatics Research Foundation board meeting
will be happening sometime between September and December. If we want
to organize a stakeholders meeting to coincide with the PRF board
meeting, we should try and get a whitepaper submitted within the next
couple of weeks.

One of the big questions at this point is whether we want to focus on
ToLWeb or take a broader view. In the latest version of the whitepaper
(links below), we have taken a broad focus, looking at a variety of
resources and technologies important for sharing evolutionary data.
The original version of the whitepaper is largely about ToLWeb, and
includes much discussion about leadership that may instead fall to the
PRF board. The participants for each of these visions may be quite
different - with the latest (broadly focused) version, will ToLWeb
contributors feel as engaged about the process?

Moving forward, should we focus on ToLWeb (or ToLWeb / TreeBASE)?

Current version of whitepaper:
http://docs.google.com/Doc?docid=0AQ-1ley90MKnZGhmZzZ4M2NfMzlmcHN4a3NmOA&hl=en
Original version:
http://docs.google.com/Doc?docid=0AQ-1ley90MKnZGhmZzZ4M2NfMzlmcHN4a3NmOA&hl=en

Karen

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[Rutger Vos]

David Maddison wants to step back from ToL by December this year. If
that means that ToL is to be handed over to "us" (in whatever formal
structure, like PRF) in December we will have enough to do just
focusing on that, for now.

On Tuesday, July 20, 2010, Karen Cranston <karen.c...@gmail.com> wrote:
> I am hoping to re-start this conversation (yet) again. The AToL grant
> was not funded. The Phyloinformatics Research Foundation board meeting
> will be happening sometime between September and December. If we want
> to organize a stakeholders meeting to coincide with the PRF board
> meeting, we should try and get a whitepaper submitted within the next
> couple of weeks.
>
> One of the big questions at this point is whether we want to focus on
> ToLWeb or take a broader view. In the latest version of the whitepaper
> (links below), we have taken a broad focus, looking at a variety of
> resources and technologies important for sharing evolutionary data.
> The original version of the whitepaper is largely about ToLWeb, and
> includes much discussion about leadership that may instead fall to the
> PRF board. The participants for each of these visions may be quite
> different - with the latest (broadly focused) version, will ToLWeb
> contributors feel as engaged about the process?
>
> Moving forward, should we focus on ToLWeb (or ToLWeb / TreeBASE)?
>
> Current version of whitepaper:

> new tolweb2 whitepaper <http://docs.google.com/Doc?docid=0AQ-1ley90MKnZGhmZzZ4M2NfMzlmcHN4a3NmOA&hl=en>
> Original version:
> new tolweb2 whitepaper <http://docs.google.com/Doc?docid=0AQ-1ley90MKnZGhmZzZ4M2NfMzlmcHN4a3NmOA&hl=en>

>
> Karen
>
> On Wed, May 26, 2010 at 9:09 AM, Rutger Vos <rutge...@gmail.com> wrote:
>>> In particular, are we still committed enough to make the stakeholders
>>> meeting happen, and if so, what time frame might be realistic.
>>
>> It sounds like there is an interest by a number of people and that the
>> ideal time frame would be after the AToL decision (which is when?) and
>> in the Fall at the latest.
>>
>> What would the next action items be if we wanted to move forward?
>>
>> The most recent artefact is the new tolweb2 whitepaper

>> (new tolweb2 whitepaper <http://docs.google.com/Doc?docid=0AQ-1ley90MKnZGhmZzZ4M2NfMzlmcHN4a3NmOA&hl=en>),

[bemb...@gmail.com]

Yes, I am stepping down from ToLWeb on 31 December, but exactly what happens next is unclear. 31 December if the time at which the administration of ToLWeb becomes unclear. Mark Westneat says he is willing to take the reins for a year, but I don't know if that's 2011 or some later year. But at a broader level, ToLWeb will be within the framework of PRF. It may eventually be within The Group Formerly or Currently Known as ToLWeb 2.0, but I don't think that's going to happen by 31 December. Or, at least, I can't say that until the nature of this group crystallizes, and an appropriately administrative leader for ToLWeb emerges.

There's several issues here - one is the administration of the project, which I don't think "we" are ready to assume, and so I don't think it will be "handed over" to ToLWeb 2.0 in January; the other is handing over copies of the data and code of the project, which will be available to the group whenever they wish, and possibly handing over full control of the source code.

I think the best approach is to go for the broader vision, but to have ToLWeb, including its data and its code, as one component of a playground to explore the vision. That could range from source code access to the live site to improve it, to just having copies to goof around with. The former requires some plan about who has access and to what extent; the latter is certainly viable any time. I also think it makes sense to have TreeBase as part of this, too.

BTW, I just heard from Andy Lenards that he has cleaned up the code some more, and this week we are finally ready to test the new implementation at Oregon State. If all goes well, the server transfer will happen soon. All of this also means the source is now in better shape, and better documented, meaning it will be easier to have other folks start poking at it.

I'm not too worried about engaging the ToLWeb contributors in the process if it is not ToLWeb-focused. If by "ToLWeb contributors" you mean the biologists who contribute content, as long as they see that the vision that they care about is included within the ToLWeb 2.0 group's vision, and that what they have already done will be maintained and improved, I think all will be well - at least some of the good ones will be engaged. If by "ToLWeb contributors" you mean me and Katja, especially, then I know I at least am on board as long as the vision I care about is still there. As it seems the vision of ToLWeb 2.0 is the same as ToLWeb 1, but with a bigger group more capable of turning that vision into reality, I'm good.

My biggest concern about shooting high now, i.e., going straight for the big, long-term vision, is that it becomes very easy to spend a lot of time talking, developing standards, blah blah blah. I'm a very firm believer in doing things, rather than sitting in meetings and talking. So, I think there needs to be a short-term focus on building things, too. Thus the value of having some focus now on ToLWeb/TreeBase as a playground.

david

[Hilmar Lapp]

I like having a concrete target that focuses our energy, but I am also
leery about 1) tying the greater vision of this to a concrete
implementation that isn't even our own, and 2) preempting (or
appearing to do so) the future direction of ToLWeb prior to its
custodian body having ever met let alone discussed anything.

I see now that David has basically said the same thing (or at least
that's how I understand his email). I concur with him that ToLWeb
would be a great playing ground for some ideas, provided that these
are endorsed by the PRF, which again I would not want to preempt.

-hilmar

--

[Arlin Stoltzfus]

Should we try to find ways to build momentum that would not pre-empt
the foundation's authority or limit its vision? We could focus on
obvious things (that we discussed last winter) like open-sourcing the
code and implementing some integrative services.

I don't see what stops us or any other group from proposing to partner
with the PRF in some way. Why can't we just partner with them in
producing the whitepaper calling for a broader stakeholder process?

Arlin

-------
Arlin Stoltzfus (ar...@umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

[Hilmar Lapp]

On Jul 21, 2010, at 4:27 PM, Arlin Stoltzfus wrote:

> Should we try to find ways to build momentum that would not pre-empt
> the foundation's authority or limit its vision? We could focus on
> obvious things (that we discussed last winter) like open-sourcing
> the code and implementing some integrative services.

In principle yes. I.e., I don't think we need to or should restrain
ourselves in building momentum especially when we identify appropriate
vehicles, and I agree that open-sourcing the code would be a good
first target.

That being said, the first BoD meeting actually isn't so far away, so
I don't feel either that we need to launch some kind of push that we
otherwise wouldn't.

> I don't see what stops us or any other group from proposing to
> partner with the PRF in some way. Why can't we just partner with
> them in producing the whitepaper calling for a broader stakeholder
> process?

Of course we can. In fact I might say we do already (as at least
several if not the majority of PRF BoD members are on this list, and
some are noted as co-authors already).

That being said, I see this as more "partnering" with the individuals
who are on the Board, rather than the PRF itself. I'm hesitant to
expect a cohesive voice from or on behalf of the PRF before its Board
has ever had a chance to constitute itself and discuss what that voice
ought to be.

-hilmar

[Arlin Stoltzfus]

We seem to have left this conversation hanging (again). It looks like
we left it with the idea that we would let the PRF's board meet, so as
not to short-circuit the decision-making process. That sounds good to
me.

I would like to suggest that we submit some kind of proposal for the
PRF board to consider at its meeting. This could be a proposal to do
precisely what we have been proposing all along, which is to have
stakeholder meetings, form interest groups, and develop a funding plan
with specific proposals.

When is the PRF board meeting?

What do you think?

Arlin

-------

[Rutger Vos]

Thanks for picking this up again. This is just to echo that I think
this would be the right way to move forward. We should probably have a
conference call to agree more explicitly on action items to make this
happen.

[Mark Westneat]

[sorry if you got this twice]

Hi all, thanks for keeping this discussion going- I think its really important to keep everyone active on this.  Lets definitely keep our enthusiasm even though the first few grant proposals didn't get funded, and we are sort of waiting to see what happens with the PRF Foundation meeting this Fall, and there is some uncertainty on how to mix the various projects and visions to generate the best program.  That mix of perspectives and the recent progress on multiple fronts is a strength, even though its a bit confusing right now.  I look forward to talking more about it, and have agreed to be in the PRF group.  Speaking for myself, I think its a *great* idea to have a prospectus of some sort on the goals this group has, as items for discussion.  Thanks, Mark 

[Arlin Stoltzfus]

There seems to be interest here, but not much momentum-- the project just keeps rolling to a stop if no one is pushing.  Maybe we will get momentum if, with a commitment from the foundation, we can start working on the TolWeb 2 project in some way (as per David's suggestion), instead of just talking about it?  

Meanwhile, we seem to agree on the value of submitting some form of our proposal to the PRF board.  Could I have a volunteer to 

1.  find out when is the PRF board meeting

2.  set up a teleconference to decide what needs to be done to our proposal before submitting it to the board for consideration

?  Thanks, 

Arlin

[Rutger Vos]

Prospective board members of the PRF are to be polled about when the
first meeting will be held. So far the time frame is no more precise
than "between September and December of 2010".

[Karen Cranston]

> Meanwhile, we seem to agree on the value of submitting some form of our
> proposal to the PRF board.  Could I have a volunteer to
> 1.  find out when is the PRF board meeting

The date has not been set, but we should know within the next week or so.

> 2.  set up a teleconference to decide what needs to be done to our proposal
> before submitting it to the board for consideration

Poll is here: http://www.doodle.com/p5fsiw5sknfsh6t3

Karen

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[William Piel]

Michael, who probably has the tightest schedule, thinks that his schedule will have openings in October / November. I'm trying to peg down some specific slots in there, and then poll the rest of the group.

bp

[Karen Cranston]

I've changed the times on the doodle poll to reflect hours where most
of us should actually be awake...
Sorry about that.
Karen

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[Arlin Stoltzfus]

No one has stepped forward to volunteer for #2, so we are at risk of dropping the ball, again.  

I'm just making a note of that.  

Arlin

[Karen Cranston]

I set up a doodle poll for the teleconference on Tuesday. So far, only
Hilmar and I have responded.

Poll is here: http://www.doodle.com/p5fsiw5sknfsh6t3

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karen.c...@gmail.com
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[Nico Cellinese]

I got mine in. Sorry !

Nico

[Arlin Stoltzfus]

Thanks! I don't know how I missed that.

Arlin

On Sep 3, 2010, at 10:10 AM, Karen Cranston wrote:

[Rutger Vos]

I have mine in. Sorry about the time difference - hard to find
overlap, it looks like.

Rutger