September 2007 - tdwg - lists.tdwg.org

programmablebiodiversity.org ?
by Shorthouse, David 02 Oct '07

02 Oct '07

Now that GBIF is releasing lots of cool web services (thanks to Dave Martin, Tim Robertson, and others) and similar web services can be found in other organizations, ought we consider a www.programmableweb.com knock-off called something like www.programmablebiodiversity.org? This way, we can have a user-driven repository / show-and-tell for useful applications that can be built for the wider biodiversity informatics community. At the very least, this will provide some positive feedback for providers who can then point to examples of how the data can be used, mashed-up, or otherwise repurposed in imaginative ways. Plus, this could be like a communal grab-bag of tricks for organizations like EOL. If anyone wants to take the initiative on this, I'll most certainly contribute. The kinds of things I am thinking of are Rod Page's iSpecies (http://ispecies.org) or my temporary, development knock-off using nothing but JSON (http://ispiders.blogspot.com/2007/09/ispecies-clone.html) or Rod's bioGUID reference parser and my simple way to tap into this in real-time (http://tinyurl.com/ytqxo6) PygmyBrowse (http://dx.doi.org/10.1145/1125451.1125562) etc. Along the same sort of lines, the TDWG link to its "Biodiversity Projects of the World" is buried under "Activities". Shouldn't this be front and center on the TDWG homepage? Cheers, David P. Shorthouse ------------------------------------------------------ Department of Biological Sciences CW-403, Biological Sciences Centre University of Alberta Edmonton, AB T6G 2E9 mailto:dps1@ualberta.ca http://canadianarachnology.dyndns.org http://www.spiderwebwatch.org http://ispiders.blogspot.com ------------------------------------------------------

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Job - Database administrator, NMNH Smithsonian Institution
by Orrell, Thomas 26 Sep '07

26 Sep '07

SALARY RANGE: 66,767.00 - 86,801.00 USD per year SERIES AND GRADE: GS-2210-12 PROMOTION POTENTIAL: 13 ANNOUNCEMENT: 07-JB-293501-JNT-NMNH OPEN DATE: DATE: September 12, 2007 to October 5, 2007 POSITION INFORMATION: Full Time, Career/Career-Conditional DUTY LOCATIONS: 1 Vacancy - Washington, DC WHO MAY BE CONSIDERED: U.S. citizens or nationals of the United States. JOB SUMMARY: This position is a database administrator located in the Informatics Branch, Information Technology Office, of the National Museum of Natural History. The database administrator is responsible for the design, development and administration of databases related to the Research and Collections Information System (RCIS) and other research and collections-based database projects requested by other NMNH departments. As such, the database administrator is a technical resource to database development project teams. - - - - This is a new position at NMNH, and includes work on both EMu and other database projects. The full announcement is attached as a PDF. An online version of the announcement is available at: http://jobsearch.usajobs.opm.gov/ftva.asp?seeker=1&JobID=62359242 - - - - Dr. Thomas M. Orrell Research Biologist Acting Director ITIS/Informatics Branch Chief Smithsonian Institution PO Box 37012 National Museum of Natural History, W623, MRC-136 Washington, DC 20013-7012 Phone: 202 633-2151 Cell: 202-294-0514 Fax: 202-357-4122 Email: orrellt(a)si.edu URL: http://www.itis.gov For UPS and FedEx shipments please use: National Museum of Natural History, MRC-153 10th and Constitution Avenues, NW Washington, DC 20560-0153

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Software Development position for Morphbank
by Greg Riccardi 25 Sep '07

25 Sep '07

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Job advert: GBIF Web Developer
by Donald Hobern 17 Sep '07

17 Sep '07

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RE: [tdwg] Interesting example of tree navigation
by Richard Pyle 14 Sep '07

14 Sep '07

> As Rod suggested, this is pretty old news. This begs the question: has this style of user-interface failed to catch on more widely because of: 1) Technological limitations; 2) Insufficient creativity and inspiration; or 3) Insufficient usability? I'm tempted to eliminate #3 on the grounds that I don't think this style of UI has been widespread enough to have been subjected to, and then failed, some sort of usability meta-experiment. This is not to say that it won't ultimately fail such a meta-experiment -- just that it hasn't really had a chance to fail it yet. Rich

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Interesting example of tree navigation
by Rebecca Shapley 13 Sep '07

13 Sep '07

This is not only a fascinating website in general, but in one spot has a quite novel - not perfect, but nicely innovative - interaction model for a tree of information. Does a decent job of both showing the overview of information available and offering more information at various levels, in context, in response to interaction. http://www.schematic.com/#/HowWeDoIt/ProjectProcess/ -R.

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Species pages with video and metadata
by Timothy M. Jones 13 Sep '07

13 Sep '07

Update on Carex species pages - The pages listed below now include metadata, following Dublin Core - with a tweak or two. Time spent adding metadata to files - after template creation (2 hours), opening files, updating files, saving/closing files, uploading files to server, amounted to ~ 6 minutes per species (avg.seven files). http://utc.usu.edu/factsheets/CarexFSF/new/carex_davisii_species.htm http://utc.usu.edu/factsheets/CarexFSF/new/carex_oligosperma_species.htm http://utc.usu.edu/factsheets/CarexFSF/new/carex_communis_species.htm Other new stuff added- * Scivee for video hosting, metadata added to video as a txt file. * Vertical search engine for Carex, called specific search on the main species pages (at bottom of pages). * Synonymy through link to Tropicos * Both Google Map and Earth with GBIF * Tabbed navigation redone/easier Thanks for all the attaboys, recommendations and critiques, Tim

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RE: [tdwg] Taxi from Vienna Airport to Bratislava (Arriving Saturday 14 September)
by Richard Pyle 13 Sep '07

13 Sep '07

My turn for some "disambiguation": I actually arrive Sunday, Sept 16th -- not Sept 15th as I said in my original email. I was confused because I leave Hawaii on the 14th. I didn't realize that I have to endure TWO over-night flights.... Thanks to Kevin Richards for pointing out my error, and sorry for any confusion I may have caused! Bob -- I guess this means you are arriving Saturday the 15th (not 14th). I take full blame... Rich _____ From: Bob Morris [mailto:morris.bob@gmail.com] Sent: Monday, September 10, 2007 3:36 PM To: Richard Pyle Cc: tdwg(a)lists.tdwg.org Subject: Re: [tdwg] Taxi from Vienna Airport to Bratislava (Arriving Saturday 14 September) To remove ambiguity: I arrive on Saturday September 14 in Vienna from Atlanta, arriving 10:05 am and seek to share shuttle taxi. I am going to Hotel #16, but I think the hotels are mostly near each other. On 9/10/07, Bob Morris <morris.bob(a)gmail.com> wrote: I am on the same flight on Saturday, Sept 14 so also looking for sharing. Otherwise, I will probably take the train (14 euro from Wien Sudbahnhof) or perhaps bus from the airport. It looks like there are prearranged shuttles from the airport for about 58 euro for up to four people. http://www.bratislavahotels.com/vienna-airport-shuttle-bratislava. On 9/10/07, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hi All, I'm just now sorting out how I'm going to get from the Vienna airport to the Bratislava ( http://www.tdwg.org/conference2007/housingtravel/travel/ <http://www.tdwg.org/conference2007/housingtravel/travel/> ), and I think I'm just going to book a Taxi. I'm writing this note now to find out: 1) Whether anyone arriving at about the same time at Vienna airport would be interested in sharing a taxi ride with me; or 2) Whether anyone arriving at about the same time at Vienna airport who has already booked a taxi would be interested in having me share it with them. I arrive on Sunday (15 Sept) at 10:05am on Delta flight 40. I don't mind hanging around the airport for a few hours to synch up with others arriving later in the day, but I would like to get to Bratislava in time to attend the Literature interest group meeting at 14:30. Thanks in advance, Aloha, Rich P.S. Anyone know what style of electical outlet they have in Bratislava? Richard L. Pyle, PhD Database Coordinator for Natural Sciences and Associate Zoologist in Ichthyology Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: <chrome://skype_ff_toolbar_win/content/cb_transparent_l.gif> <chrome://skype_ff_toolbar_win/content/famfamfam/us.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/arrow.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> (808)848-4115 <chrome://skype_ff_toolbar_win/content/cb_transparent_r.gif> , Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html _______________________________________________ tdwg mailing list tdwg(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg -- Robert A. Morris Professor of Computer Science UMASS-Boston ram(a)cs.umb.edu http://bdei.cs.umb.edu/ http://www.cs.umb.edu/~ram <http://www.cs.umb.edu/%7Eram> http://www.cs.umb.edu/~ram/calendar.html <http://www.cs.umb.edu/%7Eram/calendar.html> phone <chrome://skype_ff_toolbar_win/content/cb_transparent_l.gif> <chrome://skype_ff_toolbar_win/content/famfamfam/us.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> <chrome://skype_ff_toolbar_win/content/space.gif> (+1)617 287 6466 <chrome://skype_ff_toolbar_win/content/cb_transparent_r.gif> -- Robert A. Morris Professor of Computer Science UMASS-Boston ram(a)cs.umb.edu http://bdei.cs.umb.edu/ <http://bdei.cs.umb.edu/> http://www.cs.umb.edu/~ram http://www.cs.umb.edu/~ram/calendar.html phone (+1)617 287 6466

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Taxi from Vienna Airport to Bratislava
by Richard Pyle 11 Sep '07

11 Sep '07

Hi All, I'm just now sorting out how I'm going to get from the Vienna airport to the Bratislava (http://www.tdwg.org/conference2007/housingtravel/travel/) and I think I'm just going to book a Taxi. I'm writing this note now to find out: 1) Whether anyone arriving at about the same time at Vienna airport would be interested in sharing a taxi ride with me; or 2) Whether anyone arriving at about the same time at Vienna airport who has already booked a taxi would be interested in having me share it with them. I arrive on Sunday (15 Sept) at 10:05am on Delta flight 40. I don't mind hanging around the airport for a few hours to synch up with others arriving later in the day, but I would like to get to Bratislava in time to attend the Literature interest group meeting at 14:30. Thanks in advance, Aloha, Rich P.S. Anyone know what style of electical outlet they have in Bratislava? Richard L. Pyle, PhD Database Coordinator for Natural Sciences and Associate Zoologist in Ichthyology Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html

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Biodiversity Informatics Position avaiable
by Weitzman, Anna 11 Sep '07

11 Sep '07

Please respond to Anne Bruneau if your are interested in this position. Biodiversity bioinformatics network designer and manager Canadian University Biodiversity Consortium Qualifications - M.Sc. or Ph.D. in biology and university degree in computer science, with experience in both fields. The person will have sound network management skills and experience, with examples of achievements in production-level networks. Preference will be given to candidates with experience with biological collections, digitisation of collections, biodiversity, or biological software. The person will have excellent leadership qualities, networking, interpersonal skills, and a very good working knowledge of English and French. Job description - The biodiversity bioinformatics manager will design and implement the tools necessary to build a network of distributed databases that can be queried from the Web as a single entity. The person will put in place a Web-accessible portal for synthesising and displaying biodiversity data. The person will need to interact with a large community of biologists. The person will assist collections managers in the choice of software and hardware for efficient data entry, database management and digitisation of collections. The person will enable effective communication between collections managers and university information technology units. Working in concert with global biodiversity initiatives (e.g., GBIF, TDWG, etc.), the person will be knowledgeable of new bioinformatics developments related to biodiversity networks throughout the world. The biodiversity bioinformatics manager will be based at the Institut de recherche en biologie végétale, associated with the Université de Montréal and located at the Montreal Botanical Garden. The position is for five years, with possibility of renewal, starting in Fall 2007 (negotiable). Salary to be discussed. The Canadian University Biodiversity Consortium is a network of biological collections from 12 universities and five botanical gardens in Canada. One of its objectives is to put in place a network of over 30 distributed collections databases that focus on plants, fungi and insects. The project is funded by a Canadian Foundation for Innovation grant led by the Université de Montréal. The Consortium also includes researchers from the universities of British Columbia, Alberta, Saskatchewan, Manitoba, Guelph, Toronto, York, McGill, Laval and Acadia. Applicants should send a letter of interest, a complete c.v. and names of three referees (preferably by email) to: Dr. Anne Bruneau Institut de recherche en biologie végétale Université de Montréal 4101 Sherbrooke est Montréal, Québec H1X 2B2 CANADA Tel: (514)-872-7301 anne.bruneau(a)umontreal.ca Gestionnaire et designer de réseau bioinformatique sur la biodiversité Consortium des universités canadiennes sur la biodiversité Qualifications - M.Sc. ou Ph.D. en sciences biologiques et diplôme universitaire en informatique, avec de l'expérience de travail dans les deux domaines. La personne retenue aura des habilités solides en gestion de réseaux avec des réalisations concrètes de réseaux fonctionnels. Une préférence sera donnée aux candidats ayant de l'expérience de travail avec les collections biologiques, l'informatisation des collections, la biodiversité et les logiciels pertinents à la biologie. Le candidat devra avoir d'excellentes qualités de leadership, de travail en équipe et d'habilités interpersonnelles et une bonne connaissance du français et de l'anglais. Description du poste - Le gestionnaire en biodiversité bioinformatique devra concevoir et mettre en place les outils nécessaires pour établir un réseau de bases de données distribuées qui pourra être interrogé directement par le biais du Web. La personne mettra sur pied un portail Web permettant de synthétiser et rendre facilement disponibles des données sur la biodiversité. Cette personne devra interagir avec une large communauté de biologistes. Elle guidera les gestionnaires des collections dans leurs choix de logiciels et de matériel informatique pour l'entrée efficace des données, la gestion des bases de données et l'informatisation des collections. Cette personne sera responsable pour assurer une communication efficace entre les gestionnaires de collections et les services de la technologie informatique des universités. Le/la gestionnaire du réseau bioinformatique travaillera de concert avec les initiatives mondiales (ex., GBIF, TDWG,...) et sera informé sur les nouvelles initiatives et les nouveaux développements en bioinformatique de la biodiversité. Le/la gestionnaire du réseau bioinformatique sera en poste à l'Institut de recherche en biologie végétale, associé à l'Université de Montréal, et localisé au Jardin botanique de Montréal. Le poste est pour une période initiale de cinq ans, avec possibilité de renouvellement; la date de début est prévue pour l'automne 2007 (négociable). Le salaire est à discuter. Le Consortium des universités canadiennes sur la biodiversité est un réseau de collections biologiques de 12 universités et 5 jardins botaniques au Canada. Un de ses objectifs est d'établir un réseau de bases de données distribuées de 30 collections biologiques de plantes, insectes et champignons. Le projet, piloté par l'Université de Montréal, est subventionné par la Fondation canadienne pour l'innovation. Le Consortium comprend des chercheurs des universités de la Colombie Britannique, de l'Alberta, de la Saskatchewan, du Manitoba, de Guelph, de Toronto, York, McGill, Laval et Acadia. Les candidats intéressés doivent faire parvenir une lettre d'intérêt, un c.v. complet et les noms de trois références (de préférence par courrier électronique) à : Anne Bruneau, Ph.D. Institut de recherche en biologie végétale Université de Montréal 4101 Sherbrooke est Montréal, Québec H1X 2B2 CANADA Tel: (514)-872-7301 anne.bruneau(a)umontreal.ca

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Literature Interest Group approved
by Weitzman, Anna 10 Sep '07

10 Sep '07

The Literature Interest Group and Charter has now been approved by the TDWG Executive. The group's web site is at: http://www.tdwg.org/activities/literature/. A brief description of the goals of the group follows below. More information is available in the charter and on the Wiki. Please join the mailing list using the link on that web page if you are interested. The group will hold a meeting on Sunday, 16 September 2007 from 2:30-5:00 pm in Bratislava. The meeting will be held at the Faculty of Science. Please contact me for directions, maps and details if you plan to attend. Summary Due to the international calls for greater availability of biodiversity data, an increasing number of institutions, especially the Biodiversity Heritage Library project (BHL) are digitising taxonomic literature and making these materials freely available on the World Wide Web. Most of the digitally available literature is in the form of image files and to a lesser extent, text files generated, sometimes very imperfectly, using optical character recognition (OCR). These are the two forms planned by the BHL. In a few cases text or metadata are searchable, but those are idiosyncratically formatted, marked up or split into fields. An increasing number of institutions, publishers and funding bodies are however showing interest in making full text of portions of the taxonomic literature available. Having standards in place will facilitate their work and encourage them to make the literature data interoperable with other pertinent data. Becoming Involved The Literature group welcomes participation from all interested parties with biological, library, and publishing backgrounds. Members of the group are interested in standards and technologies for analysing biodiversity data from taxonomic literature and combining them with knowledge from other biodiversity data sets. Participants in other TDWG groups that work on data included in taxonomic literature are strongly encouraged to participate. This participation is vital to ensure the standards are compatible and interoperable. The TDWG process requires that new Task Groups be launched through an Interest Group. The Literature group can facilitate establishment of new Task Groups that relate to taxonomic literature standards. Please contact the Convener or Core members to discuss potential projects or join existing Task Groups. Anna L. Weitzman, PhD Botanical and Biodiversity Informatics Research National Museum of Natural History Smithsonian Institution office: 202.633.0846 mobile: 202.415.4684 weitzman(a)si.edu

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Job opening in Canada
by Baillargeon, Guy 06 Sep '07

06 Sep '07

Please circulate to interested colleagues and graduate students approaching completion of their Ph.D. GB-)

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TDWG 2007: not too late to register
by Adrian Rissone 03 Sep '07

03 Sep '07

Dear Colleague, It's not too late to register for TDWG 2007 in Bratislava, Slovakia (16-22 September 2007). http://www.tdwg.org/conference2007/registration/ With only 2 weeks until the start of the Conference it would help us with organisation if registrations can be complete by Friday 7 September. Please contact me directly if you are hoping to attend but unable to register before then. Mr Adrian Rissone Executive Secretary E-mail: A.Rissone(a)nhm.ac.uk <mailto:A.Rissone@nhm.ac.uk>

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