treebase-devel — TreeBASE developer mailing list

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Arlin S. <ar...@um...>]

After our telecon, which suggested that splitting out the  MIAPA part was a better strategy, I started a separate doc for this here: 

  https://docs.google.com/document/d/16bno1sB3gBHHnew5TnoCLawScuoydG-i5LCPcB30OZY/edit?hl=en_US

The focus of this, as currently conceived, is to combine problem-solving with development of a draft standard.  The problem-solving attempts to address relevant user needs (e.g., helping users to create a properly formatted and annotated archive submission).  This way, we will be developing technology support at the same time as the draft standard (which, ideally, will encourage the broader community to try it out and work with us). 

If you are interested, please take a look at the proposal, help us to identify problems to address and possible strategies to address them by leveraging available technologies and resources.  Those who are interested will need to solidify partnerships as soon as possible, as there is only a month left to formulate the plan and write the proposal. 

Arlin
________________________________________
From: mia...@go... [mia...@go...] On Behalf Of Karen Cranston [kar...@ne...]
Sent: Thursday, June 09, 2011 12:58 PM
To: ph...@go...; MIAPA; TreeBASE devel
Subject: Re: ABI proposal for phyloinformatics

Hilmar and I talked to Anne Maglia from NSF this morning. The notes
are on the "Pitches for TreeBASE_ABI" document (which is now editable
by anyone with the link, BTW). She did not see any major issues and
had plenty of advise on how to avoid common pitfalls when writing for
the ABI panel.

Summary:
1. Making the MIAPA component into a separate Innovation proposal is
probably a good idea.
2. The TreeBASE / ToLWeb piece is well-suited for a Development
proposal, and we can discuss MIAPA in this proposal as long as we have
a concrete contingency plan for the possibility that this gets funded
and the MIAPA proposal does not.
3. There is no general rule about incremental improvement vs major
re-engineering, but the goals of the proposal must be novel in some
way and have intellectual merit. A re-engineering proposal could be
computationally novel, while a proposal with only incremental
improvements must instead have novel interface components or strong
biological motivations.
4. There seems to be an empty niche for proposals that include novel
front-end as well as back-end development, but we need to make sure we
have the appropriate expertise for the former.
5. She suggests sharing the draft with someone from BIO (perhaps
Maureen Kearney) to get the user community perspective

Please fill out the doodle poll so that we can plan the next course of action!

Cheers,
Karen

On Wed, Jun 8, 2011 at 4:24 PM, Hilmar Lapp <hl...@ne...> wrote:
> It looks like a response from NSF is still pending. There is not a lot of
> time left until the submission deadline, and I'll be out of commission for
> at least 7 days during that time starting Wed next week. So I suggest we
> start planning and get together independently of the NSF response to hash
> out over a conference call possible contributions and commitments. Here's a
> Doodle poll for scheduling.
>
> http://www.doodle.com/8zvwbidtxm9gzxcp
>
> To make sure that we can have a relatively targeted discussion, my
> suggestion would be that everyone who is willing to play a role in this
> proposal enter their availability, and come prepared for the following
> questions:
>
> 1. What aims would a proposal need to have to for you to commit to be part
> of it, and conversely, what aims should it not have. (Ideally, the aims
> would be from either pitch A or pitch B that Karen sent to NSF for
> feedback.)
>
> 2. What aims, expertise, and partners are we missing from the group. Do you
> have suggestions for how to pull those in.
>
> 3. What role are you interested in playing, for which aim(s). What kind and
> how many resources do you anticipate requiring support for to accomplish
> those aims.
>
> At the end of this, ideally we have a concrete sense for whether there are
> 0, 1, or 2 proposals that are viably going to come together, what size of
> proposal(s) we are talking about, who would take responsibility for what,
> and who else we need to reach out to.
>
> Comments / suggestions / additional items for the enumeration above welcome.
>
>        -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>



--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Karen Cranston, PhD
Training Coordinator and Informatics Project Manager
nescent.org
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

--
You received this message because you are subscribed to the Google
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Re: [Treebase-devel] ABI proposal for phyloinformatics

[Hilmar L. <hl...@ne...>]

Yes, I was going to suggest the same. -hilmar

On Jun 9, 2011, at 2:01 PM, Karen Cranston wrote:

> Tomorrow morning at 11 am EST is a winner so far. It would be good to
> talk before the weekend, so I am going to tentatively schedule that
> block unless I hear otherwise. Connection information will be in the
> Google Doc - please ask if you need access.
>
> Talk to you tomorrow,
> Karen
>
> On Thu, Jun 9, 2011 at 12:58 PM, Karen Cranston
> <kar...@ne...> wrote:
>> Hilmar and I talked to Anne Maglia from NSF this morning. The notes
>> are on the "Pitches for TreeBASE_ABI" document (which is now editable
>> by anyone with the link, BTW). She did not see any major issues and
>> had plenty of advise on how to avoid common pitfalls when writing for
>> the ABI panel.
>>
>> Summary:
>> 1. Making the MIAPA component into a separate Innovation proposal is
>> probably a good idea.
>> 2. The TreeBASE / ToLWeb piece is well-suited for a Development
>> proposal, and we can discuss MIAPA in this proposal as long as we  
>> have
>> a concrete contingency plan for the possibility that this gets funded
>> and the MIAPA proposal does not.
>> 3. There is no general rule about incremental improvement vs major
>> re-engineering, but the goals of the proposal must be novel in some
>> way and have intellectual merit. A re-engineering proposal could be
>> computationally novel, while a proposal with only incremental
>> improvements must instead have novel interface components or strong
>> biological motivations.
>> 4. There seems to be an empty niche for proposals that include novel
>> front-end as well as back-end development, but we need to make sure  
>> we
>> have the appropriate expertise for the former.
>> 5. She suggests sharing the draft with someone from BIO (perhaps
>> Maureen Kearney) to get the user community perspective
>>
>> Please fill out the doodle poll so that we can plan the next course  
>> of action!
>>
>> Cheers,
>> Karen
>>
>> On Wed, Jun 8, 2011 at 4:24 PM, Hilmar Lapp <hl...@ne...>  
>> wrote:
>>> It looks like a response from NSF is still pending. There is not a  
>>> lot of
>>> time left until the submission deadline, and I'll be out of  
>>> commission for
>>> at least 7 days during that time starting Wed next week. So I  
>>> suggest we
>>> start planning and get together independently of the NSF response  
>>> to hash
>>> out over a conference call possible contributions and commitments.  
>>> Here's a
>>> Doodle poll for scheduling.
>>>
>>> http://www.doodle.com/8zvwbidtxm9gzxcp
>>>
>>> To make sure that we can have a relatively targeted discussion, my
>>> suggestion would be that everyone who is willing to play a role in  
>>> this
>>> proposal enter their availability, and come prepared for the  
>>> following
>>> questions:
>>>
>>> 1. What aims would a proposal need to have to for you to commit to  
>>> be part
>>> of it, and conversely, what aims should it not have. (Ideally, the  
>>> aims
>>> would be from either pitch A or pitch B that Karen sent to NSF for
>>> feedback.)
>>>
>>> 2. What aims, expertise, and partners are we missing from the  
>>> group. Do you
>>> have suggestions for how to pull those in.
>>>
>>> 3. What role are you interested in playing, for which aim(s). What  
>>> kind and
>>> how many resources do you anticipate requiring support for to  
>>> accomplish
>>> those aims.
>>>
>>> At the end of this, ideally we have a concrete sense for whether  
>>> there are
>>> 0, 1, or 2 proposals that are viably going to come together, what  
>>> size of
>>> proposal(s) we are talking about, who would take responsibility  
>>> for what,
>>> and who else we need to reach out to.
>>>
>>> Comments / suggestions / additional items for the enumeration  
>>> above welcome.
>>>
>>>        -hilmar
>>> --
>>> ===========================================================
>>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>
>>
>>
>> --
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Karen Cranston, PhD
>> Training Coordinator and Informatics Project Manager
>> nescent.org
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>
>
>
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Karen Cranston, PhD
> 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

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Karen C. <kar...@ne...>]

Tomorrow morning at 11 am EST is a winner so far. It would be good to
talk before the weekend, so I am going to tentatively schedule that
block unless I hear otherwise. Connection information will be in the
Google Doc - please ask if you need access.

Talk to you tomorrow,
Karen

On Thu, Jun 9, 2011 at 12:58 PM, Karen Cranston
<kar...@ne...> wrote:
> Hilmar and I talked to Anne Maglia from NSF this morning. The notes
> are on the "Pitches for TreeBASE_ABI" document (which is now editable
> by anyone with the link, BTW). She did not see any major issues and
> had plenty of advise on how to avoid common pitfalls when writing for
> the ABI panel.
>
> Summary:
> 1. Making the MIAPA component into a separate Innovation proposal is
> probably a good idea.
> 2. The TreeBASE / ToLWeb piece is well-suited for a Development
> proposal, and we can discuss MIAPA in this proposal as long as we have
> a concrete contingency plan for the possibility that this gets funded
> and the MIAPA proposal does not.
> 3. There is no general rule about incremental improvement vs major
> re-engineering, but the goals of the proposal must be novel in some
> way and have intellectual merit. A re-engineering proposal could be
> computationally novel, while a proposal with only incremental
> improvements must instead have novel interface components or strong
> biological motivations.
> 4. There seems to be an empty niche for proposals that include novel
> front-end as well as back-end development, but we need to make sure we
> have the appropriate expertise for the former.
> 5. She suggests sharing the draft with someone from BIO (perhaps
> Maureen Kearney) to get the user community perspective
>
> Please fill out the doodle poll so that we can plan the next course of action!
>
> Cheers,
> Karen
>
> On Wed, Jun 8, 2011 at 4:24 PM, Hilmar Lapp <hl...@ne...> wrote:
>> It looks like a response from NSF is still pending. There is not a lot of
>> time left until the submission deadline, and I'll be out of commission for
>> at least 7 days during that time starting Wed next week. So I suggest we
>> start planning and get together independently of the NSF response to hash
>> out over a conference call possible contributions and commitments. Here's a
>> Doodle poll for scheduling.
>>
>> http://www.doodle.com/8zvwbidtxm9gzxcp
>>
>> To make sure that we can have a relatively targeted discussion, my
>> suggestion would be that everyone who is willing to play a role in this
>> proposal enter their availability, and come prepared for the following
>> questions:
>>
>> 1. What aims would a proposal need to have to for you to commit to be part
>> of it, and conversely, what aims should it not have. (Ideally, the aims
>> would be from either pitch A or pitch B that Karen sent to NSF for
>> feedback.)
>>
>> 2. What aims, expertise, and partners are we missing from the group. Do you
>> have suggestions for how to pull those in.
>>
>> 3. What role are you interested in playing, for which aim(s). What kind and
>> how many resources do you anticipate requiring support for to accomplish
>> those aims.
>>
>> At the end of this, ideally we have a concrete sense for whether there are
>> 0, 1, or 2 proposals that are viably going to come together, what size of
>> proposal(s) we are talking about, who would take responsibility for what,
>> and who else we need to reach out to.
>>
>> Comments / suggestions / additional items for the enumeration above welcome.
>>
>>        -hilmar
>> --
>> ===========================================================
>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>> ===========================================================
>>
>>
>>
>>
>
>
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Karen Cranston, PhD
> Training Coordinator and Informatics Project Manager
> nescent.org
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Karen Cranston, PhD
Training Coordinator and Informatics Project Manager
nescent.org
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Karen C. <kar...@ne...>]

Hilmar and I talked to Anne Maglia from NSF this morning. The notes
are on the "Pitches for TreeBASE_ABI" document (which is now editable
by anyone with the link, BTW). She did not see any major issues and
had plenty of advise on how to avoid common pitfalls when writing for
the ABI panel.

Summary:
1. Making the MIAPA component into a separate Innovation proposal is
probably a good idea.
2. The TreeBASE / ToLWeb piece is well-suited for a Development
proposal, and we can discuss MIAPA in this proposal as long as we have
a concrete contingency plan for the possibility that this gets funded
and the MIAPA proposal does not.
3. There is no general rule about incremental improvement vs major
re-engineering, but the goals of the proposal must be novel in some
way and have intellectual merit. A re-engineering proposal could be
computationally novel, while a proposal with only incremental
improvements must instead have novel interface components or strong
biological motivations.
4. There seems to be an empty niche for proposals that include novel
front-end as well as back-end development, but we need to make sure we
have the appropriate expertise for the former.
5. She suggests sharing the draft with someone from BIO (perhaps
Maureen Kearney) to get the user community perspective

Please fill out the doodle poll so that we can plan the next course of action!

Cheers,
Karen

On Wed, Jun 8, 2011 at 4:24 PM, Hilmar Lapp <hl...@ne...> wrote:
> It looks like a response from NSF is still pending. There is not a lot of
> time left until the submission deadline, and I'll be out of commission for
> at least 7 days during that time starting Wed next week. So I suggest we
> start planning and get together independently of the NSF response to hash
> out over a conference call possible contributions and commitments. Here's a
> Doodle poll for scheduling.
>
> http://www.doodle.com/8zvwbidtxm9gzxcp
>
> To make sure that we can have a relatively targeted discussion, my
> suggestion would be that everyone who is willing to play a role in this
> proposal enter their availability, and come prepared for the following
> questions:
>
> 1. What aims would a proposal need to have to for you to commit to be part
> of it, and conversely, what aims should it not have. (Ideally, the aims
> would be from either pitch A or pitch B that Karen sent to NSF for
> feedback.)
>
> 2. What aims, expertise, and partners are we missing from the group. Do you
> have suggestions for how to pull those in.
>
> 3. What role are you interested in playing, for which aim(s). What kind and
> how many resources do you anticipate requiring support for to accomplish
> those aims.
>
> At the end of this, ideally we have a concrete sense for whether there are
> 0, 1, or 2 proposals that are viably going to come together, what size of
> proposal(s) we are talking about, who would take responsibility for what,
> and who else we need to reach out to.
>
> Comments / suggestions / additional items for the enumeration above welcome.
>
>        -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Karen Cranston, PhD
Training Coordinator and Informatics Project Manager
nescent.org
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Hilmar L. <hl...@ne...>]

It looks like a response from NSF is still pending. There is not a lot  
of time left until the submission deadline, and I'll be out of  
commission for at least 7 days during that time starting Wed next  
week. So I suggest we start planning and get together independently of  
the NSF response to hash out over a conference call possible  
contributions and commitments. Here's a Doodle poll for scheduling.

http://www.doodle.com/8zvwbidtxm9gzxcp

To make sure that we can have a relatively targeted discussion, my  
suggestion would be that everyone who is willing to play a role in  
this proposal enter their availability, and come prepared for the  
following questions:

1. What aims would a proposal need to have to for you to commit to be  
part of it, and conversely, what aims should it not have. (Ideally,  
the aims would be from either pitch A or pitch B that Karen sent to  
NSF for feedback.)

2. What aims, expertise, and partners are we missing from the group.  
Do you have suggestions for how to pull those in.

3. What role are you interested in playing, for which aim(s). What  
kind and how many resources do you anticipate requiring support for to  
accomplish those aims.

At the end of this, ideally we have a concrete sense for whether there  
are 0, 1, or 2 proposals that are viably going to come together, what  
size of proposal(s) we are talking about, who would take  
responsibility for what, and who else we need to reach out to.

Comments / suggestions / additional items for the enumeration above  
welcome.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Arlin S. <ar...@um...>]

Regarding ToLWeb, two comments.  I think this proposal is not going to  
do as well if it focuses on updating specific resources and bringing  
them closer to meeting user needs, as opposed to starting with the  
user needs and bringing to bear whatever tools or resources solve the  
problem most easily.   But we can wait to see what the program  
officers tell us.

Having said that, I'm pretty sure from the analysis of literature  
(that Brian and I are doing) that re-use of large species trees is an  
important use-case.  In a sample of 40 recent papers that hit  
"phylogen*" in the title or topic (obviously not a random sample, but  
we wanted to find the folks who focus on trees), we found 5 that use  
phylomatic or APG trees, and 1 that uses the animal supertree from  
Bininda-Emonds.

APG and phylomatic appear to be leaving ToLWeb and TreeBASE in the  
dust, in terms of scientific re-use.  Whatever they are doing to bring  
trees to users, we should be doing.

Arlin

On Jun 7, 2011, at 3:20 PM, William Piel wrote:

>
> Yeah, since ToLWeb provides an XML dump of the whole tree, from the  
> TreeBASE side a cross-walk with ToLWeb (or mechanisms to benefit  
> from the ToLWeb skeleton for enhancing the searching of TreeBASE)  
> could be done without *any* modifications of ToLWeb (or at least we  
> could provide ToLWeb with clade-level query links that they can add  
> to each clade page if they choose to).  Likewise, we will no-doubt  
> want to provide higher-name-sensitive queries using NCBI and ITS  
> (etc) without requiring permission to change their code (to say the  
> least!).
>
> But clearly we want something tighter than just consuming ToLWeb's  
> XML -- and we want ToLWeb to benefit as much as TreeBASE. But in  
> that case, I think some sort of tap on David Maddison and Andrew  
> Lenards's shoulder is needed (David is on the phylorf mailing list,  
> but is he following this?).  I gather that ToLWeb code is not yet  
> Open Source...
>
> bp
>
>
> On Jun 7, 2011, at 1:48 PM, Hilmar Lapp wrote:
>
>> Jim:
>>
>> On Jun 7, 2011, at 1:30 PM, Jim Leebens-Mack wrote:
>>
>>> I am a bit concerned about the tight connection between TB and  
>>> ToLWeb that is outlined in the pitch.  Are folks intending to re- 
>>> engineer BOTH TB and ToLWeb?  In my mind, ToLWeb would be just one  
>>> of many platforms from which folks may want to delve into the  
>>> phylogenetic knowledge that could be accessed in TreeBASE.
>>
>>
>> Good points, and indeed what I had in mind technically(*). The way  
>> I am envisioning this to be implemented is indeed using  
>> technologies (HTTP/REST APIs, canonical resolvable identifiers,  
>> RDF) that allow very loose coupling. I left that out as I thought  
>> the tech soup shouldn't be in there, but I agree what's missing now  
>> is the notion that this will be achieved through loose coupling.
>>
>> So as for reengineering, the idea is to engineer (or reengineer  
>> where that's necessary) components for *both* systems that allow  
>> that loose coupling in a way that achieves the stated goals.  
>> Components that need not change to achieve this would not be touched.
>>
>> 	-hilmar
>>
>> (*)  Socially (as opposed to technically), I think ToLWeb can, and  
>> should, play a much more important role in enhancing TreeBASE  
>> content in the sense of turning data into knowledge than other  
>> platforms that we would enable here. Perhaps a useful analogy to  
>> think about is Genbank as the the raw sequence data repository and  
>> NCBI Gene (and its predecessor LocusLink) as well as RefSeq as  
>> resources that attempt to turn this into curated knowledge.
>
>
>
>
> -- 
> 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

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Jim Leebens-M. <jle...@pl...>]

I would only change the second paragraph of specific objective 1:

- change "a future-proof" to "an extensible"
- change "TreeBASE III will to ingest the large and complex..." to  
"TreeBASE III will be designed to ingest the large and complex..."


Thanks!
Jim



To remedy this situation, we envision an extensible TreeBASE III that  
is designed, architected, and implemented using modern information  
science-informed paradigms for engineering robust, highly efficient,  
cloud-ready online digital information repositories. This re- 
engineering also extends to the existing interfaces for data  
deposition, query and retrieval. TreeBASE III will to ingest the large  
and complex phylogenetic data packages produced by current research,  
add new search tools through integration with external services such  
as for taxon name resolution, georeferencing or BLAST and support  
large-scale data query and retrieval.

On Jun 7, 2011, at 2:26 PM, Karen Cranston wrote:

> There is now a link to the two pitches in the Google Doc. Please
> review, particularly pitch A, where I have merged ideas from several
> authors (and hopefully have not misrepresented anyone too poorly).
>
> On Tue, Jun 7, 2011 at 1:53 PM, Karen Cranston
> <kar...@ne...> 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
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>
>
>
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Karen Cranston, PhD
> Training Coordinator and Informatics Project Manager
> nescent.org
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Jim Leebens-Mack
4505 Miller Plant Scinces
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
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Karen C. <kar...@ne...>]

I was thinking that ToLWeb would provide a framework for the community
engagement / annotation aspects outlined in the original list of
TreeBASE "problems". This may include metadata annotations (from
ToLWeb -> TreeBASE), as well as possibilities for synthesizing
published phylogenies into the tree of life (TreeBASE -> ToLWeb).
Hopefully, closer integration would also prevent parallel development
of similar search, browse or visualization interfaces in each
resource.

I will ping David Maddison about this discussion.

Karen

On Tue, Jun 7, 2011 at 3:20 PM, William Piel <wil...@ya...> wrote:
>
> Yeah, since ToLWeb provides an XML dump of the whole tree, from the TreeBASE side a cross-walk with ToLWeb (or mechanisms to benefit from the ToLWeb skeleton for enhancing the searching of TreeBASE) could be done without *any* modifications of ToLWeb (or at least we could provide ToLWeb with clade-level query links that they can add to each clade page if they choose to).  Likewise, we will no-doubt want to provide higher-name-sensitive queries using NCBI and ITS (etc) without requiring permission to change their code (to say the least!).
>
> But clearly we want something tighter than just consuming ToLWeb's XML -- and we want ToLWeb to benefit as much as TreeBASE. But in that case, I think some sort of tap on David Maddison and Andrew Lenards's shoulder is needed (David is on the phylorf mailing list, but is he following this?).  I gather that ToLWeb code is not yet Open Source...
>
> bp
>
>
> On Jun 7, 2011, at 1:48 PM, Hilmar Lapp wrote:
>
>> Jim:
>>
>> On Jun 7, 2011, at 1:30 PM, Jim Leebens-Mack wrote:
>>
>>> I am a bit concerned about the tight connection between TB and ToLWeb that is outlined in the pitch.  Are folks intending to re-engineer BOTH TB and ToLWeb?  In my mind, ToLWeb would be just one of many platforms from which folks may want to delve into the phylogenetic knowledge that could be accessed in TreeBASE.
>>
>>
>> Good points, and indeed what I had in mind technically(*). The way I am envisioning this to be implemented is indeed using technologies (HTTP/REST APIs, canonical resolvable identifiers, RDF) that allow very loose coupling. I left that out as I thought the tech soup shouldn't be in there, but I agree what's missing now is the notion that this will be achieved through loose coupling.
>>
>> So as for reengineering, the idea is to engineer (or reengineer where that's necessary) components for *both* systems that allow that loose coupling in a way that achieves the stated goals. Components that need not change to achieve this would not be touched.
>>
>>       -hilmar
>>
>> (*)  Socially (as opposed to technically), I think ToLWeb can, and should, play a much more important role in enhancing TreeBASE content in the sense of turning data into knowledge than other platforms that we would enable here. Perhaps a useful analogy to think about is Genbank as the the raw sequence data repository and NCBI Gene (and its predecessor LocusLink) as well as RefSeq as resources that attempt to turn this into curated knowledge.
>
>
>
>
>



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Karen Cranston, PhD
Training Coordinator and Informatics Project Manager
nescent.org
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Treebase-devel] ABI proposal for phyloinformatics

[William P. <wil...@ya...>]

Yeah, since ToLWeb provides an XML dump of the whole tree, from the TreeBASE side a cross-walk with ToLWeb (or mechanisms to benefit from the ToLWeb skeleton for enhancing the searching of TreeBASE) could be done without *any* modifications of ToLWeb (or at least we could provide ToLWeb with clade-level query links that they can add to each clade page if they choose to).  Likewise, we will no-doubt want to provide higher-name-sensitive queries using NCBI and ITS (etc) without requiring permission to change their code (to say the least!). 

But clearly we want something tighter than just consuming ToLWeb's XML -- and we want ToLWeb to benefit as much as TreeBASE. But in that case, I think some sort of tap on David Maddison and Andrew Lenards's shoulder is needed (David is on the phylorf mailing list, but is he following this?).  I gather that ToLWeb code is not yet Open Source... 

bp


On Jun 7, 2011, at 1:48 PM, Hilmar Lapp wrote:

> Jim:
> 
> On Jun 7, 2011, at 1:30 PM, Jim Leebens-Mack wrote:
> 
>> I am a bit concerned about the tight connection between TB and ToLWeb that is outlined in the pitch.  Are folks intending to re-engineer BOTH TB and ToLWeb?  In my mind, ToLWeb would be just one of many platforms from which folks may want to delve into the phylogenetic knowledge that could be accessed in TreeBASE.
> 
> 
> Good points, and indeed what I had in mind technically(*). The way I am envisioning this to be implemented is indeed using technologies (HTTP/REST APIs, canonical resolvable identifiers, RDF) that allow very loose coupling. I left that out as I thought the tech soup shouldn't be in there, but I agree what's missing now is the notion that this will be achieved through loose coupling.
> 
> So as for reengineering, the idea is to engineer (or reengineer where that's necessary) components for *both* systems that allow that loose coupling in a way that achieves the stated goals. Components that need not change to achieve this would not be touched.
> 
> 	-hilmar
> 
> (*)  Socially (as opposed to technically), I think ToLWeb can, and should, play a much more important role in enhancing TreeBASE content in the sense of turning data into knowledge than other platforms that we would enable here. Perhaps a useful analogy to think about is Genbank as the the raw sequence data repository and NCBI Gene (and its predecessor LocusLink) as well as RefSeq as resources that attempt to turn this into curated knowledge.

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Karen C. <kar...@ne...>]

There is now a link to the two pitches in the Google Doc. Please
review, particularly pitch A, where I have merged ideas from several
authors (and hopefully have not misrepresented anyone too poorly).

On Tue, Jun 7, 2011 at 1:53 PM, Karen Cranston
<kar...@ne...> 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
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Karen Cranston, PhD
Training Coordinator and Informatics Project Manager
nescent.org
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Jim Leebens-M. <jle...@pl...>]

Hi Folks,

The "pitch" - ABI Development: Towards a comprehensive, community-owned and sustainable repository of reusable phylogenetic knowledge - now in the googledocs document looks good.  I think this would be a very ambitious project, but there is clearly need for resources to improve access to phylogenetic knowledge.   

I am a bit concerned about the tight connection between TB and ToLWeb that is outlined in the pitch.  Are folks intending to re-engineer BOTH TB and ToLWeb?  In my mind, ToLWeb would be just one of many platforms from which folks may want to delve into the phylogenetic knowledge that could be accessed in TreeBASE.     I understand the desire to use ToLWeb as resource for integrating data in TreeBASE relating to species relationships, but wonder if this connection could be better presented as an example or test-case for interoperability with TB rather than a primary feature of the proposal.  

Along these lines, I would think the AVAToL panel/ideas lab participants would be very enthusiastic about development of ToLWeb as an integrator of phylogenetic trees/knowledge obtained from TreeBASE or any other source.  Let's hope some of us have a chance to discuss this in August!

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.

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
> 

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Karen C. <kar...@ne...>]

> 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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Hilmar L. <hl...@ne...>]

Jim:

On Jun 7, 2011, at 1:30 PM, Jim Leebens-Mack wrote:

> I am a bit concerned about the tight connection between TB and  
> ToLWeb that is outlined in the pitch.  Are folks intending to re- 
> engineer BOTH TB and ToLWeb?  In my mind, ToLWeb would be just one  
> of many platforms from which folks may want to delve into the  
> phylogenetic knowledge that could be accessed in TreeBASE.


Good points, and indeed what I had in mind technically(*). The way I  
am envisioning this to be implemented is indeed using technologies  
(HTTP/REST APIs, canonical resolvable identifiers, RDF) that allow  
very loose coupling. I left that out as I thought the tech soup  
shouldn't be in there, but I agree what's missing now is the notion  
that this will be achieved through loose coupling.

So as for reengineering, the idea is to engineer (or reengineer where  
that's necessary) components for *both* systems that allow that loose  
coupling in a way that achieves the stated goals. Components that need  
not change to achieve this would not be touched.

	-hilmar

(*)  Socially (as opposed to technically), I think ToLWeb can, and  
should, play a much more important role in enhancing TreeBASE content  
in the sense of turning data into knowledge than other platforms that  
we would enable here. Perhaps a useful analogy to think about is  
Genbank as the the raw sequence data repository and NCBI Gene (and its  
predecessor LocusLink) as well as RefSeq as resources that attempt to  
turn this into curated knowledge.
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] ABI proposal for phyloinformatics

[William P. <wil...@ya...>]

On Jun 6, 2011, at 1:08 PM, Arlin Stoltzfus wrote:

> OK, I agree that it is weakened, but while we are waiting for all the other problems in the world to be solved so that we can achieve metadata perfection, does this approach at least solve 80 % of problem #3 for molecular users?  Or do you think it is a much smaller fraction than that?

Don't get me wrong -- I'm totally in favor of doing anything that improves metadata -- especially features that make it easier for the submitter to assemble and submit the data.  

Another thing we could do, for example, is try to validate bio-collection codes with services at GBIF. e.g., if the researcher has deposited his specimens in the AMNH, we could search GBIF for each species (plus the AMNH museum code) and return a ranked list with most-recently-deposited specimens at the top. If the user sees his/her specimen, clicks on it, all other darwin core metadata get sucked in. (course, we still have the chicken-egg problem of those who submit to TreeBASE before depositing specimens in a museum). 

bp

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Arlin S. <ar...@um...>]

On Jun 6, 2011, at 12:44 PM, William Piel wrote:

> Just some minor commentary:
>
> - I've written scripts that take Genbank accessions numbers, extract  
> metadata out of Genbank, and format it ready for ingest by TreeBASE  
> -- but I'm surprised at the number of times that people submit  
> alignments containing sequences that are still embargoed by Genbank.  
> (arg...). A lot of people just pick the default one-year embargo  
> period, not knowing how long it will take for their article to get  
> through the publishing system. So at the time of submitting to  
> TreeBASE, we can't take advantage of any automatic cross-walking  
> with Genbank.

"any" only applies to the case of those newly determined sequences  
still subject to embargo, right?  In other cases, sequences used in  
alignments are not embargoed, because they were published already, or  
because the author's embargo has expired.  Do you know what fraction  
of cases are embargoed?  Can TreeBASE periodically search post- 
submission to discover GenBank matches for any of its undocumented  
sequences (there would have to be some way to query the author to  
approve, I suppose)?

> - Unfortunately, BLAST frequently doesn't work in that it often  
> produces false positives. At best, we should use BLAST to *assist*  
> the submitter in preparing metadata, but human eyes have to  
> supervise this process. This also assumes that Genbank is richly  
> annotated, and unfortunately that's not true. For example, in a  
> sample of 21,736 records in Genbank that are found in TreeBASE, only  
> 373 of them were tagged with lat/long metadata. :-(

I agree. Automated methods to fill in the metadata blanks should be  
treated as suggestions, subject to the user's final approval.

> taken together, this weakens the statement that this "solves #3 for  
> molecular users"


OK, I agree that it is weakened, but while we are waiting for all the  
other problems in the world to be solved so that we can achieve  
metadata perfection, does this approach at least solve 80 % of problem  
#3 for molecular users?  Or do you think it is a much smaller fraction  
than that?

Arlin
-------
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

Re: [Treebase-devel] ABI proposal for phyloinformatics

[William P. <wil...@ya...>]

On Jun 6, 2011, at 10:48 AM, Arlin Stoltzfus wrote:

> The TreeBASE submission process doesn't help with #1, although Mesquite actually can help users load up their data from other formats into NEXUS.  The TB submission process exposes problem #2 but doesn't help the user to fix it.  However, matching N things with N other things is a classic problem in comp sci called "the marriage problem".   There are many solutions.  We just need to implement one and allow the user to accept or edit the suggested matching in a nice graphical way.    If users have sequences, we can BLAST them and get both a suggested accession and a suggested species identifier.  That solves #3 for molecular users.
> Support for #4 is already part of what the MIAPA people are proposing.

Just some minor commentary:

- I've written scripts that take Genbank accessions numbers, extract metadata out of Genbank, and format it ready for ingest by TreeBASE -- but I'm surprised at the number of times that people submit alignments containing sequences that are still embargoed by Genbank. (arg...). A lot of people just pick the default one-year embargo period, not knowing how long it will take for their article to get through the publishing system. So at the time of submitting to TreeBASE, we can't take advantage of any automatic cross-walking with Genbank. 

- Unfortunately, BLAST frequently doesn't work in that it often produces false positives. At best, we should use BLAST to *assist* the submitter in preparing metadata, but human eyes have to supervise this process. This also assumes that Genbank is richly annotated, and unfortunately that's not true. For example, in a sample of 21,736 records in Genbank that are found in TreeBASE, only 373 of them were tagged with lat/long metadata. :-(

taken together, this weakens the statement that this "solves #3 for molecular users" 

bp

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Arlin S. <ar...@um...>]

On Jun 6, 2011, at 10:24 AM, Rutger Vos wrote:

> (3) We must always be well-grounded in the ways in which biologists
> actually work, not just how we would like them to work -- the software
> they use, the work flows that they use, etc. We know that in their
> analysis phase, they use codes and abbreviations for their taxon
> labels.
. . .
> (4) The MIIDI minimum metadata editor
> (http://www.miidi.org:8080/orbeon/miidi-review/report?id=14) is
> totally cool  . . . The problem is
> there is no way in hell that biologists will invest the time in this:
> can you imagine taking a 1,000-taxon tree, and for each 1,000 OTUs you
> have to click a set of nested boxes to enter the Genbank taxID number,


I agree with the thinking here-- IMHO our proposal will fare better if  
we focus on solving user problems (in sexy ways, of course).  The main  
problem is that users need to archive (to comply with policies) but  
the crap that they are poised to archive is not re-usable.    
(TreeGrabber exists because most authors publish and archive pictures  
of trees rather than logically encoded trees).   Archiving is going to  
happen, because it's being pushed by policies, but this won't have a  
huge impact on re-use until we make it easy for users to submit re- 
useable data.

To break this down into manageable chunks, the biggest problems that I  
see are 1) most users need to translate their data into formats better  
suited to archiving; 2) the OTU names don't match within the user's  
own files; 3) the data objects referenced in the files do not have  
GUIDs or accessions that can be machine-processed; 4) the record does  
not have sufficient metadata annotations for potential re-users to  
judge accurately the prospects for re-use.

The TreeBASE submission process doesn't help with #1, although  
Mesquite actually can help users load up their data from other formats  
into NEXUS.  The TB submission process exposes problem #2 but doesn't  
help the user to fix it.  However, matching N things with N other  
things is a classic problem in comp sci called "the marriage  
problem".   There are many solutions.  We just need to implement one  
and allow the user to accept or edit the suggested matching in a nice  
graphical way.    If users have sequences, we can BLAST them and get  
both a suggested accession and a suggested species identifier.  That  
solves #3 for molecular users.
Support for #4 is already part of what the MIAPA people are proposing.

Arlin
-------
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

Re: [Treebase-devel] ABI proposal for phyloinformatics

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

Hi Karen,

In a separate discussion on this topic with Bill he had the following
comments, reproduced below. This to emphasize (as I also did in the
google doc) that my ideas for TreeBASE redevelopment are only my own
blue sky thinking. Bill favours a more gradual approach, and if that
is something that could go into an ABI proposal it is probably the
wiser option. Anyway, here are the remarks:

===============
I've been struggling a bit -- vacillating between Hilmar's phases
(phases 1 - 3 in the doc).  Some thoughts:

(1) Yes, this is mainly a document storage/retrieval system, but
nonetheless there are still some very sexy queries that can be more
easily implemented if at least some portion of the data are relational
(such as the trees) -- such as functionalities that blend TreeBASE and
ToLWeb (as desired by Karen).  And no matter what ABI says re. just
nuts/bolts/hammer stuff, sexy functionalities are still important
because at the end of the day the grant reviewers will be biologists
from outside of NSF -- so Vladimir's comments are still relevant.

(2) Phylogenetic data objects have complex components that must
interdigitate to work properly. For example, TreeBASE's ability to
verify that the sets of taxon labels in matrices and their daughter
trees match up perfectly catches errors in the great majority of all
submissions. Which is just to say that the sad truth is that people
try to deposit broken crap whenever they can get away with it --
that's just a fact of life, and it highlights the fact that Dryad is a
very poor solution for data sharing. That TreeBASE guarantees that all
of our analysis downloads can be opened in Mesquite without error is
fabulously important. (In theory, of course, well-written document
preparation software and validators can do the same thing as what
TreeBASE currently does -- but that essentially shifts the problem to
an earlier stage, such as writing a Mesquite plugin for data
submission preparation, which itself contains all validation/error
checking features, and then dumps rich NeXML for NoSQL-style storage.
But if we do invest in developing a Mesquite plug-in, we won't be
addressing how to ingest matrices and trees that exceed Mesquite's
capabilities -- e.g. genomic-scale data -- so in a way we are just
back to square one)

(3) We must always be well-grounded in the ways in which biologists
actually work, not just how we would like them to work -- the software
they use, the work flows that they use, etc. We know that in their
analysis phase, they use codes and abbreviations for their taxon
labels. When it comes time to submitting to TreeBASE, suddenly they
have to upgrade their data (e.g. writing taxa in full, for example),
and that's when NEXUS files start to break. They often use software
that produced poorly formed NEXUS. They often produce Newick trees
that are incorrectly rooted/oriented (rooting in their figures being
produced by special PAUP commands rather than the implicit order of
parentheses).  The idea that biologists will use a work-flow such that
all metadata are nicely captured from the get-go, and therefore
submission of metadata is trivially easy, is our fantasy of how we
would like them to work, not how they actually work.

(4) The MIIDI minimum metadata editor
(http://www.miidi.org:8080/orbeon/miidi-review/report?id=14) is
totally cool in that it provides the ability to mark up almost any
data package for submission/storage using tons of metadata with
controlled vocabularies, and where the extent of metadata provided can
be verified as to whether it meets minimum standards. The problem is
there is no way in hell that biologists will invest the time in this:
can you imagine taking a 1,000-taxon tree, and for each 1,000 OTUs you
have to click a set of nested boxes to enter the Genbank taxID number,
the museum collection code, the lat-long, etc etc. ? Ha! No f*cking
way (pardon my language).  Realistically, we have to think in terms of
both our fantasy system (like this MIIDI editor) and in terms of what
is likely to be the case for most biologists -- i.e. spreadsheets --
things where people can copy/paste from Excel, etc.

So... for a beefed up Hilmar phase 1 approach:  (a) continue solving
bugs, but going deeper -- i.e. solve those the deeper bug problems
like the hanging queries, excess memory problems, etc, that require
frequent reboots, with the goal that the application will be stable
for much longer stretches of time (b) fix some of our really dumb
data-model problems -- e.g. fuse the submission table with the study
table. (c) soft-type all of our metadata for all objects: matrices,
trees, nodes, etc. (d) provide alternative parsers for larger data
imports, (e) provide automated taxon intel tools for alternative data
sources (e.g. GNI) to just uBio, (f) pre-cache serializations for all
major data objects so that mass downloads don't tax us of memory and
CPU, (g) bring in the NCBI classification and/or connections with
ToLWeb and provide sexy queries for questions of generic topology, (h)
integrate sequence data with a BLAST engine for yet another sexy query
option, (i) integrate the lat/long metadata with Google Earth or Map
for yet another sexy query option, (j) totally redo the search
interface to make it sexy and fun to use, (k) expand out the API, (l)
modify the submission system so for MIAPA compliance, (m) provide a
way to ingest MIAPA-compliant NeXML or submissions. (n) export all
TreeBASE data into CouchDB as an alternative way to access/distribute
the data.

Now, granted, a huge problem is the service-layer bloat and the
general headache of a fat and complex codebase. Can we solve this by
putting programmers hard at work making major changes to the existing
code, or must be start from scratch? And if we start from scratch, how
do we know that we won't find ourself back in the same situation in
five years hence??  It is easier to justify starting from scratch if
we are saying that we need a whole new platform/architecture (e.g.
NoSQL) -- otherwise we don't sound so good if we have to admit that
the code that we wrote is dying under its own weight. On the other
hand, as long as we budget enough fte programmer time into redoing it
all from scratch, we might be able to avoid admitting that we are
forced to redo from scratch. (or blame all our problems on Hibernate
and argue for some other MVC framework).

So one thing I'm saying is that sticking with SQL (but caching all
data objects, and/or dumping to a JSON NoSQL server) would, I think,
solve all the major performance/functionality issues while retaining
the data integrity advantages and ability to do certain fancy queries
which are more easily done by a RDMS.  I don't think that an RDMS is
necessarily

An alternative is to build a Mesquite plugin that has a very rich
interface, with all the data integrity checks, and with easy
copy/paste spreadsheets for metadata, or metadata marked up directly
on tree nodes and edges, etc, etc, and then have this push rich NeXML
on to a NoSQL document storage system. Certain sexy queries
(phylogeographic queries, BLAST searching, topology searching) might
be sacrificed. And we'd be dealing with Mesquite -- which has its own
limitations, idiosyncrasies, and code-bloat, etc.


On Mon, Jun 6, 2011 at 3:04 PM, Karen Cranston
<kar...@ne...> wrote:
> 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
>



-- 
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

Re: [Treebase-devel] couple questions regarding JUnit test

[Rutger V. <rut...@gm...>]

On Thu, Jun 2, 2011 at 9:17 PM, Laurel Yohe <lol...@gm...> wrote:
> SoI have been working a little more on the unit test and am getting a little
> closer I believe. I might just be a little confused as to what is what.
> Maybe if you can answer some questions it would help me out a little bit:
> 1) Can you clarify the purpose of the NexmlDocumentConverter() Class?

A NeXML document is a document in NeXML syntax. The document contains
taxa, character state matrices and trees.

TreeBASE submissions also contain taxa, character state matrices and
trees, in its own object representation.

NexmlDocumentConverter converts TreeBASE submissions into NeXML
documents and back.

> 2) What is the purpose of the setNexmlProject(Document) function?

In order to guarantee that a NeXML document is coherent in the way
taxa, matrices and trees refer to each other these objects all need to
be instantiated from the document object. For example, to create a
NeXML character state matrix you have to do:

CategoricalMatrix xmlMatrix = document.createCategoricalMatrix(xmlOTUs);

This way it is clear which set of taxa the matrix refers to, and which
document it belongs to. Hence, any of the subclasses of the document
converter (such as NexmlMatrixConverter) need to have access to the
same document when they are converting the respective TreeBASE objects
they operate on. They do this by calling getDocument(), which will
return the document that was provided to setNexmlProject(Document) at
the start of the conversion process.

> 3) In the NexmlMatrixConverter(), there is the same method for different
> types of Matrices--i.e. CategoricalMatrix, StandardMatrix, CharacterMatrix,
> etc. It seems that I want to focus on testing public
> org.nexml.model.Matrix<?> fromTreeBaseToXml(CharacterMatrix tbMatrix)
> because it calls the populateXmlMatrix() function. Within this function
> though it checks if the CharacterMatrix is an instance of other types of
> matrices and I am just getting a little confused. What makes one matrix
> different from the other/why are there so many different types of matrices?

There are different types of TreeBASE character matrices because they
contain different data types which have different mappings onto the
database and have different optimizations. For example, a matrix with
continuous-valued character states is stored differently in the
database than a matrix with DNA sequences, because DNA sequences are
typically long (many characters) and therefore costly to reconstitute
if each cell in the matrix is stored as an individual database record.
On the other hand, continuous matrices are usually smaller, and
relational databases have optimizations to store numbers of different
types (longs, doubles, etc.).

For NeXML there are similar reasons for needing to distinguish between
different types of matrices. For example, NeXML is designed to be
explicit in enumerating all possible character states that occur in a
matrix ahead of the actual matrix itself (in the <format/> element) -
but for continuous matrices you can't enumerate all possible states,
because that would be an infinite number.

The converter needs to deal with these separate cases.

> 4)In my test, I am creating a NexmlMatrixConverter object by using a test
> studyId "1787". (It was a studyId that a different unit test used). When I
> try to "getMatrices()" it comes up as null. I don't know if this is because
> there are no matrices associated with it, if it is not of type
> CharacterMatrix so it won't work, or something else.

It is something else. What we are trying to do is convert TreeBASE
objects to XML. For this we use the method fromTreeBaseToXml.

You used fromXmlToTreeBase, which is intended to convert NeXML objects
into TreeBASE objects. I've corrected your NexmlMatrixConverter class
to demonstrate how this is supposed to work.

> If it the first case,
> is there a different test study that I could try that you know works? Is
> there an issue with getting matrices from a Study? I saw that getStudy()
> method and setStudy() method were commented out for RowSegment() class so I
> didn't know if that might be affecting things.
> I think those are my four major classes. I committed the code none the less.
> I also added a few lines of code in the NexmlMatrixConverter class to add
> more annotations. However, I am not sure if I have the adding of the
> annotation in the right format. For example:
>
> String accessionNumber = tbSegment.getSpecimenLabel().getGenBankAccession();
>
> if ( null != accessionNumber) {
>
> xmlOTU.addAnnotationValue("DwC:StringGenbankAcessionNumber",
> Constants.DwCURI, accessionNumber);
>
> }
>
> I was making my best educated guess. Alright that is all for now. In the
> meantime, I will break from this and work a little on the charsets issue.

That was a pretty good guess. Looking forward to your charsets results.

> Hope you are having a good week!

Thank you, you too!

Rutger



-- 
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

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Arlin S. <ar...@um...>]

Thanks, Karen. I'll take a look at it, too.

Arlin

On Jun 6, 2011, at 10:04 AM, Karen Cranston wrote:

> 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
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-------
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

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Karen C. <kar...@ne...>]

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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Treebase-devel] ABI proposal for phyloinformatics

[Arlin S. <ar...@um...>]

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

Re: [Treebase-devel] TreeBASE Production Build

[David P. <dav...@ne...>]

The TreeBASE production build # 897 was completed with no errors.

Thanks, David

From: David Palmer <dav...@ne...<mailto:dav...@ne...>>
Date: Fri, 3 Jun 2011 08:27:44 -0400
To: "tre...@li...<mailto:tre...@li...>" <tre...@li...<mailto:tre...@li...>>
Subject: TreeBASE Production Build

NESCent would like to schedule a build on the production TreeBASE site to the latest version.  We are tentatively scheduling this change for 2:00 pm EST.  Please let me know if you have questions or concerns.

David Palmer
NESCent
IT Analyst
"dav...@ne...<mailto:dav...@ne...>"
919 668 6520

Re: [Treebase-devel] Metadata forms for minimal information reporting standards

[Arlin S. <ar...@um...>]

On May 29, 2011, at 12:52 PM, Hilmar Lapp wrote:

> I thought this may be relevant to some of the on-going efforts at
> building a MIAPA-compliant metadata collection form or tool for
> annotating phylogenetic trees or data, such as for deposition into
> TreeBASE. This is an input form built apparently using Orbeon [1], for
> creating a MIIDI-compliant [2] metadata record:
>
> Screenshots: http://www.miidi.org/wiki/index.php/Metadata_Editor
> Live metadata editor: http://www.miidi.org:8080/orbeon/miidi-review/dataset
>
> This is work by Tanya Gray and David Shotton, both of whom are
> involved in the DryadUK project.   One of the ideas here that the
> resulting xml file could then be submitted to Dryad along with the
> data object(s) itself. But that concept may well apply to TreeBASE
> too. (Is Laurel subscribed to this ist?)


That is the general idea that we were thinking, too.  Jim Leebens-Mack  
and Maryam Panehiazar are working on this.  The ultimate goal is a  
tool for users to annotate a phylogenetic analysis and create a record  
for submission, in the form of a single NeXML file.  As a separate  
issue, a protocol (e.g,. web services interface) could be developed to  
handle the submission of such a record to an archive such as TreeBASE  
or Dryad.  The plan is for the annotations to use CDAO and other  
ontologies.

Arlin
-------
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

Re: [Treebase-devel] TreeBASE Production Build

[Jon A. <ja...@ba...>]

It should not take but about a minute.

The new war is built in hudson then deployed through tomcat manager.  It's generally not even enough time for a browser to timeout.

-Jon

On Jun 3, 2011, at 8:59 AM, Hilmar Lapp wrote:

> How long do you expect the downtime to be? Since this  is production, is there a chance that this can be scheduled during or closer to what would be off-hours at least in the Americas? E.g., 8am Eastern or earlier?
> 
> -hilmar
> 
> Sent with a tap.
> 
> On Jun 3, 2011, at 6:27 AM, David Palmer <dav...@ne...> wrote:
> 
>> NESCent would like to schedule a build on the production TreeBASE site to the latest version.  We are tentatively scheduling this change for 2:00 pm EST.  Please let me know if you have questions or concerns.
>> 
>> David Palmer
>> NESCent
>> IT Analyst
>> "dav...@ne..."
>> 919 668 6520
>> ------------------------------------------------------------------------------
>> Simplify data backup and recovery for your virtual environment with vRanger.
>> Installation's a snap, and flexible recovery options mean your data is safe,
>> secure and there when you need it. Discover what all the cheering's about.
>> Get your free trial download today. 
>> http://p.sf.net/sfu/quest-dev2dev2
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
> 
> ------------------------------------------------------------------------------
> Simplify data backup and recovery for your virtual environment with vRanger.
> Installation's a snap, and flexible recovery options mean your data is safe,
> secure and there when you need it. Discover what all the cheering's about.
> Get your free trial download today. 
> http://p.sf.net/sfu/quest-dev2dev2 
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

Jon Auman
Systems Administrator
Bandwidth.com
4001 Weston Parkway
Cary, NC 27513
919-434-2919
ja...@ba...