[Taxacom] Visualizing Biodiversity

Tony.Rees at csiro.au Tony.Rees at csiro.au
Wed Aug 31 22:41:07 CDT 2011

I was wondering whether any of the example data plots here might be amenable for plotting biodiversity data e.g. nos. of taxa per higher taxon:


Just trying to think outside the square here a bit...

Regards - Tony

From: Timothy Jones [mailto:tjone54 at tigers.lsu.edu]
Sent: Thursday, 1 September 2011 9:18 AM
To: Rees, Tony (CMAR, Hobart)
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Visualizing Biodiversity

Hi Tony,
Here is an example that provides substantial visualization capabilities as well as the ability to analyze what we are looking at.  It uses PivotViewer, a technology previously called Deepzoom and prior to that, Seadragon.  Developed by Microsoft Live Labs which is now defunct unfortunately .   MS has now bundled it into Silverlight, an app runtime freely available online for both Macs and PCs.
Here is an example of it being used for biodiversity identification studies - http://www.herbarium2.lsu.edu/grass2/
Requires Microsoft Silverlight runtime and will prompt you to install it if required.  IMHO best experienced with a mouse with a scroll wheel to zoom in an out on images.  All images are fully zoomable upon first loading.  The limitations top out at ten thousand images or so (with Silverlight 5) on one screen but is probably best limited to three thousand or so at a time.  Ten thousand image tends to scare/intimidate people...and is almost too much to digest in a sitting.  We tested it during a recent workshop and found it to be  successful with all skill levels.


On Tue, Aug 30, 2011 at 11:08 PM, <Tony.Rees at csiro.au> wrote:
Dear Taxacomers,

In my efforts to produce a listing of all genera I end up with, among other things, summary data on higher levels of my taxonomic hierarchy plus the number of child taxa each contains (current example by phylum: http://www.marine.csiro.au/mirrorsearch/ir_search.list_phylum). I realise that this tabular approach is pretty much as unexciting as it gets so was wondering about an improved visual manner to present this type of information, preferably in the form  of a navigable hierarchy as per the present hyperlinks.

One example I have come across which seems really neat is Kris Urie's EOL Tree Viewer (aka "VOLE" - Viewer of life on EOL), for example starting point see http://kurie.github.com/EOL-tree-viewer/#COL, however I was wondering whether taxacomers have more suggestions or personal favourites worth looking at. Of course I would also have to work out how to load in my data, but that's a detail maybe.

All suggestions / examples welcome (and may even be used on my site if I can figure out how to implement one or more of them). (Also I have a feeling that Rod Page may have some experience in this area). Of course it would also be nice if someone could take this on as a pet project for free, however I would never dream of asking such a thing (for comparison / light relief see http://www.27bslash6.com/p2p.html).

Regards - Tony

Tony Rees
Manager, Divisional Data Centre,
CSIRO Marine and Atmospheric Research,
GPO Box 1538,
Hobart, Tasmania 7001, Australia
Ph: 0362 325318 (Int: +61 362 325318<tel:%2B61%20362%20325318>)
Fax: 0362 325000 (Int: +61 362 325000<tel:%2B61%20362%20325000>)
e-mail: Tony.Rees at csiro.au
Manager, OBIS Australia regional node, http://www.obis.org.au/
Biodiversity informatics research activities: http://www.cmar.csiro.au/datacentre/biodiversity.htm
Personal info: http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566


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Timothy M. Jones
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Louisiana State University
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Website - http://www.herbarium.lsu.edu/keys/

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