[Tdwg-phylo] Publishing trees in RDF
Arlin Stoltzfus
arlin at umd.edu
Fri Oct 22 23:20:04 CEST 2010
On Oct 22, 2010, at 1:20 PM, Chris Baron wrote:
> Are there any ideas for getting phylogentic data into CDAO format ?
Currently, the best way to get data into CDAO is via XSLT-mediated XML
translation from NeXML files to CDAO RDF-XML files. This is
developmental software that is very incomplete. However, its possible
to take translated files and display them using Nexplorer3 (http://exon.niaid.nih.gov/nexplorer/
), a viewer based on CDAO.
There are many ways to get data into NeXML, including applications
such as Mesquite, toolboxes such as Bio::Phylo and DendroPy, and a
phylogeny archive called TreeBASE that accepts published submissions.
TreeBASE produces NeXML and also can generate CDAO RDF-XML files from
them.
> Its probably a bad idea to choose one existing viewer, add the
> functionality, and ask everyone to use it. Apologies for the
> proposition.
>
> I'll suggest a web based tool that takes phylogenetic data in a
> common format ( Newick, Nexus, etc ), asks a few questions ( i.e. -
> what do the labels, lengths correspond to? ), and fills in some of
> the basic CDAO elements using this data. If the user wants to
> describe their tree in more detail, the tool will provide methods
> for filling in any/all of the CDAO fields.
From where I'm standing, that's a really promising development
target. The most obvious kinds of metadata that we would want to add
to the core tree structure are
1. citation information, especially authorship
2. species identifiers or other taxonomic concept identifiers (LSIDs,
NCBI taxon ids, etc)
3. accession numbers for data sources (GenBank or other accessions)
4. geographic coordinates
5. methods information
The TreeBASE submission process provides a web-based interface to do
all of this. One uploads a NEXUS file and then supplies publication
info, matches species names, supplies methods info, etc. I strongly
suggest that you check it out. You can load data just for testing
purposes without actually publishing it.
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 at 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 at umd.edu>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID: <35E60BB1-E806-4AAC-A916-6F4439F48980 at 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 at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>
> -------
> Arlin Stoltzfus (arlin at 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 at imperial.ac.uk>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: "tdwg-phylo at lists.tdwg.org" <tdwg-phylo at lists.tdwg.org>
> Message-ID:
> <F5AF129F0DF96748BF87616878EA92934EAE05B214 at 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 at lists.tdwg.org [mailto:tdwg-phylo-bounces at lists.tdwg.org
> ] On Behalf Of Arlin Stoltzfus
> Sent: 22 October 2010 15:30
> To: tdwg-phylo at 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 at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>
> -------
> Arlin Stoltzfus (arlin at 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 at 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 at bio.gla.ac.uk>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID: <C924C5F0-1B8A-4754-A8CC-80C344675835 at 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 at lists.tdwg.org
> >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
> >
> > -------
> > Arlin Stoltzfus (arlin at 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 at 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 at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at 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 at umd.edu>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID: <B7CBB320-0453-47A9-AC16-6CFD952BA21D at 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 at lists.tdwg.org
> >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
> >
> > -------
> > Arlin Stoltzfus (arlin at 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 at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>
> -------
> Arlin Stoltzfus (arlin at 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 at yale.edu>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID: <ED033676-380C-4CBF-B5BE-C0E465DAF1B0 at 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 at nescent.org>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: William Piel <william.piel at yale.edu>
> Cc: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID: <F56AA1E2-8162-486C-9D74-C04563957BC4 at 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 at fieldmuseum.org>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID:
> <AANLkTimHXsPgiL4J=f5C1b=eXoTA3dusJYO0vXOcbdmF at 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 at 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 at 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 at flmnh.ufl.edu>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: Richard Ree <rree at fieldmuseum.org>
> Cc: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID: <48C2E497-DAB3-47E0-8F77-0F4921F51CC5 at 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 at 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 at lists.tdwg.org
> >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
> >>
> > _______________________________________________
> > tdwg-phylo mailing list
> > tdwg-phylo at 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 at nescent.org>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: Richard Ree <rree at fieldmuseum.org>
> Cc: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID: <D5F11390-E3DB-4712-8444-2A136876E58F at 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 at umd.edu>
> Subject: Re: [Tdwg-phylo] Publishing a trees in RDF
> To: "tdwg-phylo at lists.tdwg.org Interest Group"
> <tdwg-phylo at lists.tdwg.org>
> Message-ID: <7C7A6642-2219-429C-BC2D-4F88BBC3CAA0 at 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 at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>
> -------
> Arlin Stoltzfus (arlin at 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 at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
>
>
> End of tdwg-phylo Digest, Vol 2, Issue 8
> ****************************************
>
>
>
> --
> Chris Baron
> <ATT00001.txt>
-------
Arlin Stoltzfus (arlin at 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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