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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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Re: [tdwg] Species pages and video
by Wouter Addink 31 Aug '07

31 Aug '07

> (*)As of August 21 2007 there is no Google Scholar published API. > http://groups.google.com/group/google-help-dataapi/browse_thread/thread/96b… > ..would definitely be nice to have one. Probably some screenscraper or webbot techniques could be used to get data out of Google Scholar, but that would be odd..

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Microsoft .NET implementation of TAPIR
by Kevin Richards 30 Aug '07

30 Aug '07

Hi all I have recently completed a project funded by the TIP (TDWG Infrastructure Project) funded project that has resulted in a Microsoft .NET version of the TAPIR protocol. TAPIR (TDWG Access Protocol for Information Retrieval) is a computer protocol designed for discovery, search and retrieval of distributed data over the Internet, see http://www.tdwg.org/activities/tapir/ for more information. The .NET implementation of the TAPIR protocol provides the following functionality: All TAPIR operations (metadata, capabilities, inventory, search and ping). KVP and XML request encodings. Inventories on any mapped concepts. Searches with any output models involving concepts from mapped schemas. Response structures with basicSchemaLanguage. Multiple resources can be exposed from a single TAPIRDotNET instance. A simple client (tapir_client.aspx) for testing. OAI-PMH message handling. After mapping the OAI-PMH structure to the data source, OAI-PMH requests can be handled and valid OAI-PMH responses are retuned from the provider. The OAI-PMH message handling was a result of an investigation into the use of the generic, domain independent, protocol, OAI-PMH (http://www.openarchives.org/OAI/openarchivesprotocol.html) over TAPIR. The investigation proved to be an interesting look at integrating similar data harvesting protocols. TapirDotNET is available from http://sourceforge.net/projects/tapirdotnet/ I have also been looking at returning RDF over TAPIR for the herb IMI specimens. I will be presenting this at TDWG next month. Kevin Richards

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[Fwd: [SciVee: Pioneering New Modes of Scientific Dissemination newsletter] Announcement: New Feature Rollout]
by Timothy M. Jones 30 Aug '07

30 Aug '07

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RE: [tdwg] Species pages and video
by Richard Pyle 29 Aug '07

29 Aug '07

Thanks Bob, I'm still waiting to hear back from them (Google) on related stuff (mostly concerning bulk uploading). I know they prefer that I upload the full-res version, even though they shrink it down when streaming. I'd actually rather them have the full-res versions, so that as future internet bandwidth paradigms allow higher-res streaming, they can automatically step it up without input from me. Of course, uploading a 178MB file compared with a 3.5MB file -- multiplied several thousand times -- is another factor that cannot be completely ignored. The ideal would be a JPEG2K-ish standard as you describe with user-specified resolution. Rather than get Google to build another stand-alone app, I'd rather see them come out with their own browser with built-in support for Earth (and customized/optimized video streaming, Google Base access, Co-op features, etc.) all built in. So far, no NDAs.... Aloha, Rich _____ From: Bob Morris [mailto:morris.bob@gmail.com] Sent: Tuesday, August 28, 2007 5:34 PM To: Richard Pyle Cc: Eamonn O Tuama; Timothy M. Jones; tdwg(a)lists.tdwg.org Subject: Re: [tdwg] Species pages and video JPEG2000 video standards---which are generally mp4--- probably address this problem, because JPEG2K can decompress at arbitrary resolution, that is you can tell the remote server what resolution you want the stuff sent at. I think, but am not certain, that this would be the case for the video standards too, since it should be doable frame at a time. Indeed, I vaguely recall a demo at a JPEG2K meeting in which video was streamed at resolutions which varied with time. There are lots of questions, but apparently few answers, of the form "does Flash support JPEG2000. Of course rendering in the current browsers remains a problem if it doesn't, though people certainly tolerate standalone Google Earth, for example---so why wouldn't they tolerate standalone video viewers. Ask your Google video pals what's up. Preferably not under an NDA. :-) Bob On 8/28/07, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Dear all, I've been meaning to jump in on this conversation several times, but I keep getting side-tracked. For over two years now, we have been developing a protocol and associated software tools (I use the pronoun "we" loosely as far as the software development goes -- that has been entirely the work of Rob Whitton) to allow us to harness the power of video for our scientific purposes. We conduct surveys of coral-reef fishes in the Pacific, and the use of hi-definition underwater video cameras allow us to make dozens of "video vouchers" (as we call them) of fish species in the context of their natural habitat on every single dive (again, I use the pronoun "we" loosely, as John Earle is the primary videographer on our surveys). Though perhaps not as ideal as specimens, the video is much better than in-situ still photos (especially at hi-def resolution), because it gives us multiple angles on the subject (increasing the probability of capturing that elusive but diagnostic small black spot near the anus), as well as behavior (which can sometimes aid in confirming identifications). And it's a LOT better than just an un-imaged observation record. It also allows us to document many more species on a given dive than we could by collecting alone. The software that Rob Whitton has developed is optimized for field-based capturing of metadata. We ( i.e., John) will generally catalog the video clips on the same day the video was taken. Metadata is robust, with full locality/habitat data (including depth and other parameters), as well as rich content cataloging (multiple identifications of the same imaged organism, etc.) At the moment, we (i.e., John & Rob) have something on the order of 7,000 video clips cataloged -- representing nearly a terabyte of video files (a mix of both standard-resolution DV and HDV). Very soon we will have an initial website online to allow searching/etc., and we have a couple of major regional checklists in the works that will cite these "video vouchers" in addition to more traditional means of documenting species at localities. So...the reason I am posting this now (rather than wait until the site is online) is to ask others who are exploring the use of video content for similar purposes how they plan to implement it. Our current plan is to maintain an archive of full-resolution digital video files on our local SAN, but the files are much too large to stream in real-time over almost any typical internet connection, and moreover would completely choke our bandwidth if the site ever became popular. For this reason, we want to use a video hosting service to stream the content, which we will link to from our own web databases (which themselves will serve only keyframes from the clips). We've been working with Google to sort out a way to do batch uploads onto Google Video. I generally prefer the Google Video environment over YouTube, but I'm not familiar with other video hosting services that are out there. Here is a sample clip: http://video.google.com/videoplay?docid=153611051098248174 Google Video allows me to dump all of the metadata into the Description field. Unfortunately, this is not very structured. However, Google Video allows you to link back to your own web page for each clip, so I can have that link go to an LSID resolver, or some other web interface where more structured metadata can be served. Another feature I like is that you can lay as many subtitle/caption files as you want. For example, if you go to the link above, in the lower right corner you'll see a little "CC" icon. Click on the drop-down button to the right of the "CC" button, and you can choose from any number of subtitle tracks. In the example above, there are two different tracks: "Audio Dialog" transcribes the spoken words you hear on the clip's soundtrack, and "Species List", which names the species as they appear in the clip. Rob Whitton is developing his software to automatically generate the text for the metadata and multiple CC tracks, so that we can (eventually) automate the upload process. The main problem -- which I think will be true of any of these video hosting services -- is the limited resoloution of the clips as they are streamed. For example, here is a frame from the original HDV clip in the above link: http://www2.bishopmuseum.org/testvideo/Frame01.jpg Here is the same frame at the resolution that the video is rendered on Google Video: http://www2.bishopmuseum.org/testvideo/Frame02.jpg Obviously, the full-resolution video contains a LOT more information. The problem is that an MPG (i.e., compressed) copy of the full-resolution HDV clip is 172MB, whereas the compressed version that Google streams is 3.5MB. The problem is not with Google Video -- it's with the internet. Most people will not have access to the badwidth necessary to stream video at the full HDV resolution. So...what we'd like is a service that will allow people to view the clips at a resolution that is reasonable to stream over the internet (Google Video, YouTube, etc.), but then have the option of downloading the full-resolution file (in this case, 178MB) if they want to see it on their own computer, and are willing to wait for the full download. Obviously, we'll have to somehow regulate the downloading so that we don't choke our bandwidth -- but we want to allow people to have access to the full-resolution imagery. My hope is that Google (or whoever) itself would offer the service of streaming content at an appropriate resolution, but then allowing people to download the full resolution clip as a file, if they want (i.e., using Google's or whoever's bandwidth, and not ours). But for the time being, we mostly see Google as a way to: 1) Manage streaming of video content at low resolution, and 2) increase visibility (through Google searches_ of the content we do have. Of course, the latter depends heavily on how well the metadata are fleshed out and structured -- which brings me back to Éamonn's post. Like him, I am very-much looking forward to conversations at the upcoming meeting in Bratislava. Meanwhile, I guess the main point of this message is to ask whether others know of analagous projects, and how they have dealt with issues of bandwidth, bulk uploading to video hosting services, and metadata structure and content. Aloha, Rich 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 > -----Original Message----- > From: tdwg-bounces(a)lists.tdwg.org > [mailto:tdwg-bounces@lists.tdwg.org] On Behalf Of Eamonn O Tuama > Sent: Tuesday, August 28, 2007 5:20 AM > To: 'Timothy M. Jones'; tdwg(a)lists.tdwg.org > Subject: RE: [tdwg] Species pages and video > > Dear Timothy, > > I think the use of video is valuable even if there is not > much motion involved - combining a series of stills with > voice over can be very effective - and the many video hosting > services makes it relatively easy to get online. However, > unlike text which can be mined for information, video (and > images) require good metadata to describe what the content is > about - to aid in searches, etc. > > Your species pages with their general facts and interactive > taxonomic keys span the task areas covered by SDD (Structure > of Descriptive Data) and SPM (Species Profile Model) TDWG > interest groups. I look forward to fruitful discussions > between the two at the forthcoming meeting in Bratislava that > will lead to standardised ways of marking up your species > content so that it is more easily discoverable, accessible > and re-usable (assuming permissions > granted) across what GBIF has labelled "The Universal > Biodiversity Data Bus". > > Best regards, > > Éamonn > > -----Original Message----- > From: tdwg-bounces(a)lists.tdwg.org > [mailto:tdwg-bounces@lists.tdwg.org] On Behalf Of Timothy M. Jones > Sent: 10 August 2007 16:48 > To: tdwg(a)lists.tdwg.org > Subject: [tdwg] Species pages and video > > Hello, > > I will not be attending the meeting this fall but thought > that this may be of interest to those interested in species > pages models. > I am working on species pages that include the use of video. > The videos were only added a month ago and are a bit > rudimentary (with budget-conscious equipment) but the > potential now seems truly limitless. > > Examples - > http://utc.usu.edu/factsheets/CarexFSF/new/carex_eburnea_species.htm <http://utc.usu.edu/factsheets/CarexFSF/new/carex_eburnea_species.htm> > > http://utc.usu.edu/factsheets/CarexFSF/new/carex_nebrascensis_ > species.htm > > http://utc.usu.edu/factsheets/CarexFSF/new/carex_mitchelliana_ > species.htm > > Comments appreciated, > Timothy M. Jones > http://utc.usu.edu/keys/Carex/Carex.html <http://utc.usu.edu/keys/Carex/Carex.html> > _______________________________________________ > tdwg mailing list > tdwg(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg <http://lists.tdwg.org/mailman/listinfo/tdwg> > > > _______________________________________________ > tdwg mailing list > tdwg(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg _______________________________________________ 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/~ram/calendar.html <http://www.cs.umb.edu/~ram/calendar.html> phone (+1)617 287 6466

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RE: [tdwg] Species pages and video
by Emery, Rob 29 Aug '07

29 Aug '07

Hello Everyone, More and more we are using very high quality auto montage stills to provide diagnostic images with almost unlimited depth of field e.g. http://www.padil.gov.au/viewPestDiagnosticImages.aspx?id=677 It only occurred to us recently when presenting to farmers that these images, while spectacular, are not much use in helping them identify farm pests by eye or with a hand lens. We decided to take video of the pests because it gives farmers a better idea of what they are looking for. The movement of the insects can help distinguish them as can a backdrop of the environment where they are likely to be found. We have now incorporated mpeg video into a number of our database-driven species profile pages. One of the links below has the video pop up in the player and the other should run embedded in the web page. The range of stored grain protectants in Australia have varying efficacy against species so we expect farmers to be able to perform some rudimentary identification when deciding on a treatment. We recently uploaded these videos to YouTube because... well... we could. http://agspsrv34.agric.wa.gov.au/ento/agird/pestweb/Query1_1.idc?ID=-991 113051 http://agspsrv34.agric.wa.gov.au/ento/pestweb/Query1_1.idc?ID=904621453 Regards, Rob -------------------------------------------------- Rob Emery (Mr) (Senior Entomologist) ph: 61 8 9368 3247 Fax: 61 8 9368 3223 Mob: 0404 819 601 <mailto:remery@agric.wa.gov.au> <http://www.agric.wa.gov.au/ento> Department of Agriculture and Food Western Australia 3 Baron-Hay Court, _-_|\ South Perth, 6151 / \ Western Australia --> \_.-._/ v This e-mail and files transmitted with it are privileged and confidential information intended for the use of the addressee. The confidentiality and/or privilege in this e-mail is not waived, lost or destroyed if it has been transmitted to you in error. If you received this e-mail in error you must (a) not disseminate, copy or take any action in reliance on it; (b) please notify the Department of Agriculture and Food, WA immediately by return e-mail to the sender; (c) please delete the original e-mail. This email has been successfully scanned by McAfee Anti-Virus software. Department of Agriculture and Food WA

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Species pages and video
by Timothy M. Jones 28 Aug '07

28 Aug '07

Hello, I will not be attending the meeting this fall but thought that this may be of interest to those interested in species pages models. I am working on species pages that include the use of video. The videos were only added a month ago and are a bit rudimentary (with budget-conscious equipment) but the potential now seems truly limitless. Examples - http://utc.usu.edu/factsheets/CarexFSF/new/carex_eburnea_species.htm http://utc.usu.edu/factsheets/CarexFSF/new/carex_nebrascensis_species.htm http://utc.usu.edu/factsheets/CarexFSF/new/carex_mitchelliana_species.htm Comments appreciated, Timothy M. Jones http://utc.usu.edu/keys/Carex/Carex.html

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