Thursday, March 3, 2011

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============================================================================================================================ My sense of this thread is that some people are arguing that "species pages " would be time consuming to create, aren't much good for taxonomists (to quote Mike Dallwitz "In brief, to make simplified and attractive information about taxa easily available to casual users?"), and nobody gets credit for making them. In short, "they're not for me, I don't get credit for making them, so why bother?" Others (e.g., Doug Yanega) see species pages -- properly constructed -- to be a research tool. If we extend this to its logical conclusion, we could envisage these pages being the primary source of information on taxa. Indeed, new taxa could be described in this way. In short, "this is the future of taxonomic publication". One obvious way to realise species pages sensu Doug is using a wiki, but then there are those that horrified by the prospect of just "anyone" being able to edit that content. In short, "wikis are not for serious people, the ignorant might mess up my stuff". Others have had a more positive experience. I realise this doesn't do justice to these positions, but this make things a little concrete, I've put together a demo based on a wiki I'm constructing. The aim of this wiki is to link together taxonomic names, specimens, images, classifications, publications, phylogeny, people in one place. It's a bit like a wiki version of my Elsevier Challenge entry http://iphylo.org/~rpage/challenge/www/ . This is some way off being ready for prime time, but I thought it might be useful to show the sort of thing that can be done. As a starting point, /itaxon.org/wikidev/Chromis_circumaurea is a page about Chromis circumaurea, one of the fish Rich Pyle et al recently described in Zootaxa. This page contains a map and some specimen images, and an abbreviated description copied from the Zootaxa article. The images and the map are generated automaticaly by the wiki, based on the links it has to the specimens, e.g. http://itaxon.org/wikidev/BMNH_2007.10.31.3 http://itaxon.org/wikidev/USNM_391138_%28Fishes%29 The USNM specimen is linked to a GenBank sequence http://itaxon.org/wikidev/EU358583 . Specimens themselves are linked to Museum collections (using data from http://biocol.org ). The name itself is linked to a publication http://itaxon.org/wikidev/Jacc:1175-5326:1671%403 which is also linked to the authors. The wiki supports GUIDs, so that you can link to the page about Chromis circumaurea using it's ZooBank LSID, for example: http://itaxon.org/wikidev/Urn:lsid:zoobank.org:act:8ADC4817-8F1C-4C88-8B8A-5372A84CAEC9 What I hope this crude example demonstrates is a framework where we can support all the kinds of objects we care about, and easily create links between them that can generate useful information. For example, the page for Chromis circumaurea doesn't explicitly list the images shown, they are there because of the links between Chromis circumaurea, the specimens, and the images of those specimens. The same applies to the map. What this means is that very little information needs be entered, it's mostly a matter of joining the dots. Note that these wiki pages already have more information than either iSpecies ( http://ispecies.org/?q=Chromis+circumaurea ) or EOL (http://www.eol.org/pages/209986 ) This example has been assembled by hand, but much of the data required can be entered automatically (e.g., for sequences, specimens, publications, etc.), and tools such as text mining or XML markup (e.g., TaxonX) could be easily exploited. I also realise that the demos as it stands as very limited information about the organism itself, but I don't this this as intractable. If we could build things like this (and I believe we can, with a lot less effort than might be thought), is this the kind of "species page " that would be useful? Regards Rod PS If you're curious about the ideas behind this wiki, you'l find some background at http://iphylo.blogspot.com/search?q=wiki --------------------------------------------------------- Roderic Page Professor of Taxonomy DEEB, FBLS Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.p ... @bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodp ... @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 _______________________________________________ Taxacom Mailing List Taxa ... @mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/taxacom The entire Taxacom Archive back to 1992 can be searched with either of these methods: http://taxacom.markmail.org Or use a Google search specified as: site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here Name: TorK Version: 0.31 Type: KDE Networking Tool Depend: KDE 3.5.x License: GPL Homepage: http://tork.sf.net More Info: http://www.kde-apps.org/content/show.php?content=39442 Description: TorK is an Anonymity Manager for KDE. For information about Tor: http://tor.eff.org TorK allows you to configure, run and update Tor. It also allows you to view the Tor network and choose how you would like to interact with the network. TorK contains a number of unique/useful features: * A graph of your tor and non-tor traffic. * A quickstart page for launching torified applications.         See https://sourceforge.net/project/screenshots.php?group_id=159836 * A hidden services wizard that allows you to create and publish hidden services. * A drag-and-drop view of the Tor network. Create, modify and close circuits. Attach and detach streams manually from circuits. Click on servers to view their full details. * Exit node blocking/preferring by country and server name.  See https://sourceforge.net/project/screenshots.php?group_id=159836&ssid=45119 * Tor and Non-Tor traffic logs - showing you the traffic that is going through Tor and the traffic that is not. The Tor traffic log maintains a record of the circuit you used for each connection. Both logs are maintained in memory only and can be flushed by the user at any time. * A turn-on-and-off-able mini-view that shows you the traffic currently going through Tor - including destination, status, and exit node's name and country. * Passive pop-ups alerting you to important Tor events, such as changes to  your server status, DNS leaks, errors reported by Tor. * Quick configuration - six default configurations available for getting Tor running the simple and easy way. * Full access to all Tor configuration options. Changelog: 2008-01-29 Robert Hogan TorK 0.31 Bug Fixes/Feature Fixes o Major update to German Translation from Hans-J. Ullrich o Boilerplate Greek Translation o Boilerplate Spanish Translation o Allow proxy ports up to 99999. Bug reported by anonym. o Allow MapAddress configurations to apply properly. o Modify 18x12 icons to 16x16 and so prevent packaging violations in Debian and Suse. Thanks to Marek Stopka and Patrick Matthai for pointing this out. o Fix so that downloading of experimental vs stable tor works properly again. o Don't crash if /dev/*/statistics/read does not exist. o Always update new server info o Fallback to default ORPort and Dirport if UPNP configured but unavailable o Prevent Tor from reloading torrc on sighup. 2008-10-21 Robert Hogan TorK 0.30 Bug Fixes/Feature Fixes o If firstrun wizard cancelled, then cancel out of TorK and re-run it next time Tor is run. o Detect netfilter properly on more recent linux kernels. o German Translation updated by "Hans-J. Ullrich" o Remove 'Change Identity' from main toolbar. It's available in the OSD and the systray menu instead. o Always de-configure server if 'Client' option selected. o Wait twenty seconds before assuming there is a problem connecting to Tor. o Improve the handling of tor installations in the first run wizard o Make stream-handling much more efficient for heavy loads o Fix http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=502155 Minor Features o Add warning when tork is configured to expect privoxy to be running at startup but there is no sign of it o Add feature to let Tor shut down gracefully. o Ensure server settings are set correctly when launching Tor from Tork (as opposed to just connecting). o Add option to toggle between display of IP address and server name in server list. o Only display konqueror in application list if it exists. Known Bug Not Fixed Yet: o If router discovered and connecting to remote/local tor, server settings may be applied even if user requests not to. _______________________________________________ Kde-announce-apps mailing list Kde- ... @kde.org https://mail.kde.org/mailman/listinfo/kde-announce-apps