[Tdwg-phylo] Publishing a trees in RDF

Arlin Stoltzfus arlin at umd.edu
Thu Oct 21 15:30:24 CEST 2010


This raises two issues that I don't quite understand.

The problem of visualizing large trees, e.g., hundreds of thousands or  
millions of nodes, has been solved again and again by computer  
scientists.  We've all seen some visualizations of the internet done  
with such tools.  There is no fundamental technology barrier.  The  
technology exists to visualize large trees and zoom around and  
navigate and so on.

The problem has to do with how to develop stable and adaptable  
software for a community that is poor, dispersed, fractious (unable to  
agree on standards), and constantly changing in its needs.

Likewise, computer scientists and hackers have repeatedly solved the  
problem of designing a framework for automating bioinformatics  
workflows.  So why don't more bioinformaticians use automated workflows?

Probably the group that is getting closest to what you want is the  
TreeViz group of EoL at the Field Museum.   Karen Cranston (cc) has  
some cool slides on this.

The second issue that I don't understand is: what is the proper  
netiquette when a list message is cc'ed to half a dozen people?  If we  
all keep repeating the cc pattern, recipients may be getting lots of  
messages that they don't want.  If we stick to the list only, they  
could miss out.


On Oct 21, 2010, at 5:20 AM, Kidd, David M wrote:

> I am yet to consider the visualizing RDF trees, however, I have am  
> interest in visualizing and interacting with trees and networks in a  
> web context.
> I've been looking at the various web tree visualizers, as well as  
> more generic visualization libraries, for the last week or so.  
> Understanding the functionality, maturity, user community and inter- 
> browser compatability is time consuming, and not always simple to  
> determine.
> Specifically, I am looking for a tool that supports, or can extended  
> to support;
> 1. Both both trees and networks,
> 2. The selection of multiple nodes, e.g. subtrees
> 3. The browsing of large trees/networks - I get some weird effects  
> with large trees in jsPhyloSVG.
> 4. (Readable) Labels at all nodes.
> 5. Alternate layouts (circular, hyperbolic, etc.)
> 6. Works in as many browsers as possible.
> 7. A variety of I/O formats - I store my trees in PhyloDB, which I  
> am thinking of generalizing for networks.
> 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.
> I would be very interested in any comments regarding existing tools  
> and the above issues (an others I have not thought about). I would  
> be happy to compile all comments and perhaps some comparative demos  
> somewhere.
> - 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 Richard Ree
> Sent: 20 October 2010 21:47
> To: Hilmar Lapp
> Cc: tdwg-phylo at lists.tdwg.org Interest Group; Chris Baron
> Subject: Re: [Tdwg-phylo] Publishing a tree in RDF
> The purposes of tree visualization are many and varied, so it seems  
> natural to me that tool development reflects that diversity.  One  
> distinction of tred is that it exposes server-side and client-side  
> functionality.
> -Rick
> On Wed, Oct 20, 2010 at 3:17 PM, Hilmar Lapp <hlapp at nescent.org>  
> wrote:
>> On Oct 20, 2010, at 2:43 PM, Chris Baron wrote:
>> Also, I've been working on a phylogentic tree editor called tred.
>> http://code.google.com/p/tred/
>> Interesting. How does your editor compare to the dozens of tree
>> editors and visualizers already available. For example PhyloWidget,  
>> or jsPhyloSVG?
>> I may sound like a broken record here, and I don't want to discourage
>> you at all from developing tools for phylogenetics. We certainly need
>> more developers. I also do think though that as a community we make
>> the most progress if we aren't sprouting new tools for the same  
>> purpose all the time.
>> -hilmar
>> --
>> ===========================================================
>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>> ===========================================================
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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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