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
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Today's Topics:
- Re: Publishing a trees in RDF (Arlin Stoltzfus)
- Re: Publishing a trees in RDF (Kidd, David M)
- Re: Publishing a trees in RDF (Roderic Page)
- Re: Publishing a trees in RDF (Arlin Stoltzfus)
- Re: Publishing a trees in RDF (William Piel)
- Re: Publishing a trees in RDF (Hilmar Lapp)
- Re: Publishing a trees in RDF (Richard Ree)
- Re: Publishing a trees in RDF (Nico Cellinese)
- Re: Publishing a trees in RDF (Hilmar Lapp)
- 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
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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 :
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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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------- 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