All this cool stuff goes INTO the TreeBASE schema, but only some of it comes OUT in the form of NeXML.  For instance, NeXML uses a prism-based encoding of citation information, but it doesn't encode accession numbers.    

So, to do what you are proposing, which is a great idea, would involve working with the community to implement existing standards and figure out any missing ones.  There is a TDWG standard with supporting language for #4 (geo coordinates).  There are other standards, e.g., dc and prism, for #1 (citations).  One could use a UBio LSID for #2 if its a species identifier, though I've seen various ways of doing this.   Likewise, there are ways to do #3 (accessions) but not a recognized standard.  The phylogenetic community needs #5 (methods annotation) but has made no tangible progress on this.  

Arlin

On Fri, Oct 22, 2010 at 12:06 PM, <tdwg-phylo-request@lists.tdwg.org> wrote:

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Today's Topics:

  1. Re: Publishing a trees in RDF (Arlin Stoltzfus)
  2. Re: Publishing a trees in RDF (Kidd, David M)
  3. Re: Publishing a trees in RDF (Roderic Page)
  4. Re: Publishing a trees in RDF (Arlin Stoltzfus)
  5. Re: Publishing a trees in RDF (William Piel)
  6. Re: Publishing a trees in RDF (Hilmar Lapp)
  7. Re: Publishing a trees in RDF (Richard Ree)
  8. Re: Publishing a trees in RDF (Nico Cellinese)
  9. Re: Publishing a trees in RDF (Hilmar Lapp)
 10. Re: Publishing a trees in RDF (Arlin Stoltzfus)


----------------------------------------------------------------------

Message: 1
Date: Fri, 22 Oct 2010 10:29:31 -0400
From: Arlin Stoltzfus <arlin@umd.edu>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID: <35E60BB1-E806-4AAC-A916-6F4439F48980@umd.edu>
Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes

QED.  The technology is out there.  IMHO, the continual propagation of
new tree-viewers by developers, and the sense of users that there is
no tree viewer that satisfies their needs, is (in the medium-term and
long-term) a cultural-organizational-educational problem and not at
all a technical problem.

If this is true, then in order to solve the real problem, we need to
think about  things like changes in funding structure, standards
development, and modes of user engagement, not new graphics libraries
that do just the right thing with only a few commands.

Arlin

On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote:

> Hi, Dave and Rutger:
>
> My own tree viewer "Archaeopteryx" provides such an overview when
> zoomed
> in, plus some other features described as "missing" in most current
> tools.
>
> See: http://www.phylosoft.org/archaeopteryx/
>
> Example: http://www.phylosoft.org/archaeopteryx/examples/mollusca.html
>
> Archaeopteryx also provides other useful features (at least for
> comparative genomics use cases). For example, the ability to infer
> internal taxonomies (if all external nodes have _some_ taxonomic
> information associated with them; standalone version only; via uniprot
> taxonomy database).
>
> Please let me know if you'd like to know more or have suggestions for
> improvement (although keep in mind that this Archaeopteryx is just a
> peculiar hobby of mine).
>
> Christian
>
>
>
> On 10/21/2010 3:39 AM, Rutger Vos wrote:
>> Hi Dave,
>>
>>> The ability to browse large trees seems to be a particular
>>> limitation of existing tools (I'd love to be corrected if I am
>>> wrong). Having a tree larger than the widget, as in Phylowidget,
>>> is one approach, however, an overview window would be nice to
>>> orientate your view in relation to the entire tree. I have also
>>> been considering displaying only a subset of nodes and then having
>>> 'expand', 'contract' and 'pan' (by expanding and contracting)
>>> functions for navagation. The ability to display node subsets is
>>> probably more important for networks than trees as reticulation
>>> will often result in visual occlusion.
>>
>> Rod Page has coded a web widget (I believe all javascript) that has a
>> small preview window for the whole tree and a larger "zoomed in"
>> view.
>> "TreeJuxtaposer" is a java app(let?) that allows you to contract and
>> expand selections of nodes/clades. I think these come closest to what
>> you are talking about, though neither operates on networks.
>>
>> Cheers,
>>
>> Rutger
>>
>
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

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



------------------------------

Message: 2
Date: Fri, 22 Oct 2010 15:55:35 +0100
From: "Kidd, David M" <d.kidd@imperial.ac.uk>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: "tdwg-phylo@lists.tdwg.org" <tdwg-phylo@lists.tdwg.org>
Message-ID:
       <F5AF129F0DF96748BF87616878EA92934EAE05B214@ICEXM5.ic.ac.uk>
Content-Type: text/plain; charset="us-ascii"


Thank you Rutger, Christian, Cindy, Hilmar and Arlin,

Whatever the technological maturity of tools, there remains the hurdle of finding the viewers, assessing their functionality and assessing whether a task can be completed with the available tools given a time-scale and skill set. I have just started to put together a comparison site describing functionality and where the same trees can be viewed in the different viewers.

Sorry for interrupting the RDF flow - it has been very interesting to follow.

 - Dave


David M. Kidd

Research Associate
Center for Population Biology
Silwood Park Campus
Imperial College London
0207 594 2470


-----Original Message-----
From: tdwg-phylo-bounces@lists.tdwg.org [mailto:tdwg-phylo-bounces@lists.tdwg.org] On Behalf Of Arlin Stoltzfus
Sent: 22 October 2010 15:30
To: tdwg-phylo@lists.tdwg.org Interest Group
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF

QED.  The technology is out there.  IMHO, the continual propagation of new tree-viewers by developers, and the sense of users that there is no tree viewer that satisfies their needs, is (in the medium-term and
long-term) a cultural-organizational-educational problem and not at all a technical problem.

If this is true, then in order to solve the real problem, we need to think about  things like changes in funding structure, standards development, and modes of user engagement, not new graphics libraries that do just the right thing with only a few commands.

Arlin

On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote:

> Hi, Dave and Rutger:
>
> My own tree viewer "Archaeopteryx" provides such an overview when
> zoomed
> in, plus some other features described as "missing" in most current
> tools.
>
> See: http://www.phylosoft.org/archaeopteryx/
>
> Example: http://www.phylosoft.org/archaeopteryx/examples/mollusca.html
>
> Archaeopteryx also provides other useful features (at least for
> comparative genomics use cases). For example, the ability to infer
> internal taxonomies (if all external nodes have _some_ taxonomic
> information associated with them; standalone version only; via uniprot
> taxonomy database).
>
> Please let me know if you'd like to know more or have suggestions for
> improvement (although keep in mind that this Archaeopteryx is just a
> peculiar hobby of mine).
>
> Christian
>
>
>
> On 10/21/2010 3:39 AM, Rutger Vos wrote:
>> Hi Dave,
>>
>>> The ability to browse large trees seems to be a particular
>>> limitation of existing tools (I'd love to be corrected if I am
>>> wrong). Having a tree larger than the widget, as in Phylowidget,
>>> is one approach, however, an overview window would be nice to
>>> orientate your view in relation to the entire tree. I have also
>>> been considering displaying only a subset of nodes and then having
>>> 'expand', 'contract' and 'pan' (by expanding and contracting)
>>> functions for navagation. The ability to display node subsets is
>>> probably more important for networks than trees as reticulation
>>> will often result in visual occlusion.
>>
>> Rod Page has coded a web widget (I believe all javascript) that has a
>> small preview window for the whole tree and a larger "zoomed in"
>> view.
>> "TreeJuxtaposer" is a java app(let?) that allows you to contract and
>> expand selections of nodes/clades. I think these come closest to what
>> you are talking about, though neither operates on networks.
>>
>> Cheers,
>>
>> Rutger
>>
>
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

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

_______________________________________________
tdwg-phylo mailing list
tdwg-phylo@lists.tdwg.org
http://lists.tdwg.org/mailman/listinfo/tdwg-phylo


------------------------------

Message: 3
Date: Fri, 22 Oct 2010 16:00:14 +0100
From: Roderic Page <r.page@bio.gla.ac.uk>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID: <C924C5F0-1B8A-4754-A8CC-80C344675835@bio.gla.ac.uk>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

There are other issues here as well. Technology advances rapidly, and
what once seemed a good choice may rapidly become dated. Without
wishing to start a flame war, I think Java applets are dead (sorry
Phylowidget), Flash is fading away (thank you Steve), and increasingly
we will see lightweight SVG and Canvas-based browsers, non-web based
browsers that exploit specific hardware (iPad anyone), and Google-
Earth based browsers.

I doubt one-size-fits all will work. Standards themselves won't
address this issue, and I personally doubt RDF is where we want to be
focussing efforts anyway. A decent JSON format for trees and
associated metadata would be much more palatable for developers. It's
worth remembering that the great success of Newick (and Nexus) was
largely due to the ease of parsing.

Regards

Rod

On 22 Oct 2010, at 15:29, Arlin Stoltzfus wrote:

> QED.  The technology is out there.  IMHO, the continual propagation of
> new tree-viewers by developers, and the sense of users that there is
> no tree viewer that satisfies their needs, is (in the medium-term and
> long-term) a cultural-organizational-educational problem and not at
> all a technical problem.
>
> If this is true, then in order to solve the real problem, we need to
> think about  things like changes in funding structure, standards
> development, and modes of user engagement, not new graphics libraries
> that do just the right thing with only a few commands.
>
> Arlin
>
> On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote:
>
>> Hi, Dave and Rutger:
>>
>> My own tree viewer "Archaeopteryx" provides such an overview when
>> zoomed
>> in, plus some other features described as "missing" in most current
>> tools.
>>
>> See: http://www.phylosoft.org/archaeopteryx/
>>
>> Example: http://www.phylosoft.org/archaeopteryx/examples/
>> mollusca.html
>>
>> Archaeopteryx also provides other useful features (at least for
>> comparative genomics use cases). For example, the ability to infer
>> internal taxonomies (if all external nodes have _some_ taxonomic
>> information associated with them; standalone version only; via
>> uniprot
>> taxonomy database).
>>
>> Please let me know if you'd like to know more or have suggestions for
>> improvement (although keep in mind that this Archaeopteryx is just a
>> peculiar hobby of mine).
>>
>> Christian
>>
>>
>>
>> On 10/21/2010 3:39 AM, Rutger Vos wrote:
>>> Hi Dave,
>>>
>>>> The ability to browse large trees seems to be a particular
>>>> limitation of existing tools (I'd love to be corrected if I am
>>>> wrong). Having a tree larger than the widget, as in Phylowidget,
>>>> is one approach, however, an overview window would be nice to
>>>> orientate your view in relation to the entire tree. I have also
>>>> been considering displaying only a subset of nodes and then having
>>>> 'expand', 'contract' and 'pan' (by expanding and contracting)
>>>> functions for navagation. The ability to display node subsets is
>>>> probably more important for networks than trees as reticulation
>>>> will often result in visual occlusion.
>>>
>>> Rod Page has coded a web widget (I believe all javascript) that
>>> has a
>>> small preview window for the whole tree and a larger "zoomed in"
>>> view.
>>> "TreeJuxtaposer" is a java app(let?) that allows you to contract and
>>> expand selections of nodes/clades. I think these come closest to
>>> what
>>> you are talking about, though neither operates on networks.
>>>
>>> Cheers,
>>>
>>> Rutger
>>>
>>
>> _______________________________________________
>> tdwg-phylo mailing list
>> tdwg-phylo@lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>
> -------
> Arlin Stoltzfus (arlin@umd.edu)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
>
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>

---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email: r.page@bio.gla.ac.uk
Tel: +44 141 330 4778
Fax: +44 141 330 2792
AIM: rodpage1962@aim.com
Facebook: http://www.facebook.com/profile.php?id=1112517192
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html









------------------------------

Message: 4
Date: Fri, 22 Oct 2010 11:25:44 -0400
From: Arlin Stoltzfus <arlin@umd.edu>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID: <B7CBB320-0453-47A9-AC16-6CFD952BA21D@umd.edu>
Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes

On Oct 22, 2010, at 10:29 AM, Arlin Stoltzfus wrote:

> QED.  The technology is out there.  IMHO, the continual propagation of
> new tree-viewers by developers, and the sense of users that there is
> no tree viewer that satisfies their needs, is (in the medium-term and
> long-term) a cultural-organizational-educational problem and not at
> all a technical problem.

To clarify this-- I didn't mean to imply that there are no gaps.  In
the *short-term*, there may be real gaps between what users want (or
think they want) and what developers are providing and maintaining.
I'm just saying that, by virtue of repeated failures, we should have
learned by now that the way to close these gaps is NOT for the Nth
independent developer to go out and developer the Mth independent tree
viewer using the latest GUI fashions.

Arlin

> If this is true, then in order to solve the real problem, we need to
> think about  things like changes in funding structure, standards
> development, and modes of user engagement, not new graphics libraries
> that do just the right thing with only a few commands.
>
> Arlin
>
> On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote:
>
>> Hi, Dave and Rutger:
>>
>> My own tree viewer "Archaeopteryx" provides such an overview when
>> zoomed
>> in, plus some other features described as "missing" in most current
>> tools.
>>
>> See: http://www.phylosoft.org/archaeopteryx/
>>
>> Example: http://www.phylosoft.org/archaeopteryx/examples/
>> mollusca.html
>>
>> Archaeopteryx also provides other useful features (at least for
>> comparative genomics use cases). For example, the ability to infer
>> internal taxonomies (if all external nodes have _some_ taxonomic
>> information associated with them; standalone version only; via
>> uniprot
>> taxonomy database).
>>
>> Please let me know if you'd like to know more or have suggestions for
>> improvement (although keep in mind that this Archaeopteryx is just a
>> peculiar hobby of mine).
>>
>> Christian
>>
>>
>>
>> On 10/21/2010 3:39 AM, Rutger Vos wrote:
>>> Hi Dave,
>>>
>>>> The ability to browse large trees seems to be a particular
>>>> limitation of existing tools (I'd love to be corrected if I am
>>>> wrong). Having a tree larger than the widget, as in Phylowidget,
>>>> is one approach, however, an overview window would be nice to
>>>> orientate your view in relation to the entire tree. I have also
>>>> been considering displaying only a subset of nodes and then having
>>>> 'expand', 'contract' and 'pan' (by expanding and contracting)
>>>> functions for navagation. The ability to display node subsets is
>>>> probably more important for networks than trees as reticulation
>>>> will often result in visual occlusion.
>>>
>>> Rod Page has coded a web widget (I believe all javascript) that
>>> has a
>>> small preview window for the whole tree and a larger "zoomed in"
>>> view.
>>> "TreeJuxtaposer" is a java app(let?) that allows you to contract and
>>> expand selections of nodes/clades. I think these come closest to
>>> what
>>> you are talking about, though neither operates on networks.
>>>
>>> Cheers,
>>>
>>> Rutger
>>>
>>
>> _______________________________________________
>> tdwg-phylo mailing list
>> tdwg-phylo@lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>
> -------
> Arlin Stoltzfus (arlin@umd.edu)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
>
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

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



------------------------------

Message: 5
Date: Fri, 22 Oct 2010 12:22:29 -0400
From: William Piel <william.piel@yale.edu>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID: <ED033676-380C-4CBF-B5BE-C0E465DAF1B0@yale.edu>
Content-Type: text/plain; charset=us-ascii


On Oct 22, 2010, at 11:00 AM, Roderic Page wrote:

> There are other issues here as well. Technology advances rapidly, and
> what once seemed a good choice may rapidly become dated

True.. but another aspect is just that in order to explore whether a particular graphical concept or tool will work, or will benefit people, you have to knock out prototypes and implementations. e.g., drag-and-drop branch rearrangement in MacClade was great for small trees but not for big ones, hence phylowidget was looking to implement something that worked for large trees (via concentric menus on nodes) and to experiment with auto-pruing, etc. People have to keep knocking out GUI software efforts to test the waters for new features. And the search is not over, for example:

- Do we really have a completely satisfying way of visualizing patterns of gene duplication within a species tree?
- If I handed you a tree with 200k nodes, is there a visual / GUI way that would allow you to easily find interesting patterns in it, such as points of incongruence with a conventional taxonomy?
-  If I gave you 1,000 trees, is there a visual / GUI way that would allow you to see which branches in each tree probably crossed an ancient land bridge together?

So I think we still have lots more GUI / visual / ergonomic challenges that still need to be solved (even if lots of challenges have already been solved). And we should not expect each new idea to be implemented in a pristine killer app that does everything that everyone wants out of a tree visualizer -- that takes too long to build, and the right person for dreaming up a new idea is not necessarily the best person for creating clean, robust, off-the-shelf software.

We need to be okay with seeing a rich plethora of quick-and-dirty efforts, each focusing on articulating/investigating sets of novel ideas -- despite some obvious redundancy in some of the more general functions.  And then periodically, someone's got to assemble the best of these ideas into a robust, jack-of-all-trades, off-the-shelf software package.

bp




------------------------------

Message: 6
Date: Fri, 22 Oct 2010 12:38:37 -0400
From: Hilmar Lapp <hlapp@nescent.org>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: William Piel <william.piel@yale.edu>
Cc: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID: <F56AA1E2-8162-486C-9D74-C04563957BC4@nescent.org>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes


On Oct 22, 2010, at 12:22 PM, William Piel wrote:

> We need to be okay with seeing a rich plethora of quick-and-dirty
> efforts, each focusing on articulating/investigating sets of novel
> ideas -- despite some obvious redundancy in some of the more general
> functions.  And then periodically, someone's got to assemble the
> best of these ideas into a robust, jack-of-all-trades, off-the-shelf
> software package.


That sounds nice indeed, but frankly I've never seen it happen. The
quick-and-dirty efforts that I have seen become standard parts of
reusable and sustainable software have almost all started from their
early beginnings as parts of reusable software. For a while rather
experimental and unstable parts, obviously, but the future course was
charted not as an afterthought.

Truth of the matter is that we're all scientists. No scientist is
interested in, or gets promotion, scientific recognition, or
publications from assembling entirely incompatible, mostly redundant
except for a few features, quick-and-dirty pieces of software into
some grand jack-of-all-trades software package.

My $0.02, from about 13 years of software engineering.

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





------------------------------

Message: 7
Date: Fri, 22 Oct 2010 11:39:44 -0500
From: Richard Ree <rree@fieldmuseum.org>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID:
       <AANLkTimHXsPgiL4J=f5C1b=eXoTA3dusJYO0vXOcbdmF@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Both technology and users' needs evolve rapidly - so the "gaps" will
never be closed, at least in the time frame required by grants, etc.
Also, in phylogenetics a lot of developers are themselves users, so
quick and dirty solutions to scratch individual itches is inevitable.
It's a good thing, IMO.

-Rick


On Fri, Oct 22, 2010 at 11:22 AM, William Piel <william.piel@yale.edu> wrote:
>
> On Oct 22, 2010, at 11:00 AM, Roderic Page wrote:
>
>> There are other issues here as well. Technology advances rapidly, and
>> what once seemed a good choice may rapidly become dated
>
> True.. but another aspect is just that in order to explore whether a particular graphical concept or tool will work, or will benefit people, you have to knock out prototypes and implementations. e.g., drag-and-drop branch rearrangement in MacClade was great for small trees but not for big ones, hence phylowidget was looking to implement something that worked for large trees (via concentric menus on nodes) and to experiment with auto-pruing, etc. People have to keep knocking out GUI software efforts to test the waters for new features. And the search is not over, for example:
>
> - Do we really have a completely satisfying way of visualizing patterns of gene duplication within a species tree?
> - If I handed you a tree with 200k nodes, is there a visual / GUI way that would allow you to easily find interesting patterns in it, such as points of incongruence with a conventional taxonomy?
> - ?If I gave you 1,000 trees, is there a visual / GUI way that would allow you to see which branches in each tree probably crossed an ancient land bridge together?
>
> So I think we still have lots more GUI / visual / ergonomic challenges that still need to be solved (even if lots of challenges have already been solved). And we should not expect each new idea to be implemented in a pristine killer app that does everything that everyone wants out of a tree visualizer -- that takes too long to build, and the right person for dreaming up a new idea is not necessarily the best person for creating clean, robust, off-the-shelf software.
>
> We need to be okay with seeing a rich plethora of quick-and-dirty efforts, each focusing on articulating/investigating sets of novel ideas -- despite some obvious redundancy in some of the more general functions. ?And then periodically, someone's got to assemble the best of these ideas into a robust, jack-of-all-trades, off-the-shelf software package.
>
> bp
>
>
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>


------------------------------

Message: 8
Date: Fri, 22 Oct 2010 12:42:10 -0400
From: Nico Cellinese <ncellinese@flmnh.ufl.edu>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: Richard Ree <rree@fieldmuseum.org>
Cc: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID: <48C2E497-DAB3-47E0-8F77-0F4921F51CC5@flmnh.ufl.edu>
Content-Type: text/plain; charset=us-ascii

Inevitable. Good thing inded. But not enough to make significant progress and fill the gaps. I agree with Hilmar.

Nico


On Oct 22, 2010, at 12:39 PM, Richard Ree wrote:

> Both technology and users' needs evolve rapidly - so the "gaps" will
> never be closed, at least in the time frame required by grants, etc.
> Also, in phylogenetics a lot of developers are themselves users, so
> quick and dirty solutions to scratch individual itches is inevitable.
> It's a good thing, IMO.
>
> -Rick
>
>
> On Fri, Oct 22, 2010 at 11:22 AM, William Piel <william.piel@yale.edu> wrote:
>>
>> On Oct 22, 2010, at 11:00 AM, Roderic Page wrote:
>>
>>> There are other issues here as well. Technology advances rapidly, and
>>> what once seemed a good choice may rapidly become dated
>>
>> True.. but another aspect is just that in order to explore whether a particular graphical concept or tool will work, or will benefit people, you have to knock out prototypes and implementations. e.g., drag-and-drop branch rearrangement in MacClade was great for small trees but not for big ones, hence phylowidget was looking to implement something that worked for large trees (via concentric menus on nodes) and to experiment with auto-pruing, etc. People have to keep knocking out GUI software efforts to test the waters for new features. And the search is not over, for example:
>>
>> - Do we really have a completely satisfying way of visualizing patterns of gene duplication within a species tree?
>> - If I handed you a tree with 200k nodes, is there a visual / GUI way that would allow you to easily find interesting patterns in it, such as points of incongruence with a conventional taxonomy?
>> -  If I gave you 1,000 trees, is there a visual / GUI way that would allow you to see which branches in each tree probably crossed an ancient land bridge together?
>>
>> So I think we still have lots more GUI / visual / ergonomic challenges that still need to be solved (even if lots of challenges have already been solved). And we should not expect each new idea to be implemented in a pristine killer app that does everything that everyone wants out of a tree visualizer -- that takes too long to build, and the right person for dreaming up a new idea is not necessarily the best person for creating clean, robust, off-the-shelf software.
>>
>> We need to be okay with seeing a rich plethora of quick-and-dirty efforts, each focusing on articulating/investigating sets of novel ideas -- despite some obvious redundancy in some of the more general functions.  And then periodically, someone's got to assemble the best of these ideas into a robust, jack-of-all-trades, off-the-shelf software package.
>>
>> bp
>>
>>
>> _______________________________________________
>> tdwg-phylo mailing list
>> tdwg-phylo@lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>>
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo



------------------------------

Message: 9
Date: Fri, 22 Oct 2010 12:56:21 -0400
From: Hilmar Lapp <hlapp@nescent.org>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: Richard Ree <rree@fieldmuseum.org>
Cc: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID: <D5F11390-E3DB-4712-8444-2A136876E58F@nescent.org>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes


On Oct 22, 2010, at 12:39 PM, Richard Ree wrote:

> Both technology and users' needs evolve rapidly - so the "gaps" will
> never be closed, at least in the time frame required by grants, etc.
> Also, in phylogenetics a lot of developers are themselves users, so
> quick and dirty solutions to scratch individual itches is inevitable.
> It's a good thing, IMO.


I agree entirely with the "solutions to scratch individual itches is
inevitable and a Good Thing(tm)".

What I don't agree with is if this is portrayed as being mutually
exclusive with reusable and more sustainable software. Projects like
Bioconductor, the Bio* libraries, and other similar ones demonstrate
that it clearly does not need to be mutually exclusive if we don't
want it to be. Every piece of code in BioPerl is there because it
first scratched someone's itch. The rate of innovation in Bioconductor
is pretty rapid.

The barrier, if there is perceived to be one, is social, not technical
or scientific. If we as a community of practice don't care about
sustainable software, it won't happen, and we'll continue to lose
software. If we want to think that the software we produce is an
integral part of our science, we lose part of our science every time a
piece of software is no longer maintained. And if we want to think
that writing a new piece of software is part of our scientific
progress, then every time someone writes code for something that code
has already been written for, our rate of scientific progress is
slowed down unnecessarily.

Again, just my own $0.02.

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





------------------------------

Message: 10
Date: Fri, 22 Oct 2010 13:06:06 -0400
From: Arlin Stoltzfus <arlin@umd.edu>
Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
To: "tdwg-phylo@lists.tdwg.org Interest Group"
       <tdwg-phylo@lists.tdwg.org>
Message-ID: <7C7A6642-2219-429C-BC2D-4F88BBC3CAA0@umd.edu>
Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes

This discussion doesn't really belong here, but I'm not sure where
else it belongs, and I sure would hate to stop, because its
interesting and valuable.

Hilmar, are you referring to various quick-and-dirty BioPerl modules,
for instance, as cases in which software that ended up being reusable
started out as part of a reusable software package?  Are there other
kinds of contexts where this would work?  How could we get different
developers working on the same architecture, building a shared
foundation but creating different solutions from it?

One idea used in nexplorer3 (and in some other viewers) is a Model-
View-Controller design pattern that separates the business logic from
the user interface.

It seems to me that ATV has been pretty successful. I've seen half a
dozen sites that use it (that's a success by my standards).

Arlin

On Oct 22, 2010, at 12:38 PM, Hilmar Lapp wrote:

>
> On Oct 22, 2010, at 12:22 PM, William Piel wrote:
>
>> We need to be okay with seeing a rich plethora of quick-and-dirty
>> efforts, each focusing on articulating/investigating sets of novel
>> ideas -- despite some obvious redundancy in some of the more general
>> functions.  And then periodically, someone's got to assemble the
>> best of these ideas into a robust, jack-of-all-trades, off-the-shelf
>> software package.
>
>
> That sounds nice indeed, but frankly I've never seen it happen. The
> quick-and-dirty efforts that I have seen become standard parts of
> reusable and sustainable software have almost all started from their
> early beginnings as parts of reusable software. For a while rather
> experimental and unstable parts, obviously, but the future course was
> charted not as an afterthought.
>
> Truth of the matter is that we're all scientists. No scientist is
> interested in, or gets promotion, scientific recognition, or
> publications from assembling entirely incompatible, mostly redundant
> except for a few features, quick-and-dirty pieces of software into
> some grand jack-of-all-trades software package.
>
> My $0.02, from about 13 years of software engineering.
>
>       -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

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



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End of tdwg-phylo Digest, Vol 2, Issue 8
****************************************

--
Chris Baron
<ATT00001.txt>

-------

Arlin Stoltzfus (arlin@umd.edu)

Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST

IBBR, 9600 Gudelsky Drive, Rockville, MD

tel: 240 314 6208; web: www.molevol.org