April 2012 - tdwg-content - lists.tdwg.org

Call for Software Bazaar entries open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity
by Cellinese,Nico 24 Apr '12

24 Apr '12

The Call for Software Bazaar entries is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions. The Software Bazaar features presenters demonstrating their software live on a laptop. At iEvoBio, this session takes the place of a poster session, and will be approximately 2.0 hours in duration. Conference attendees will be able to walk from one demonstration to the next and talk with the presenters. Please also see our FAQ (http://ievobio.org/faq.html). Entries should be software aimed at advancing research in phylogenetics, evolution, and biodiversity, and can include interactive visualizations that have been pre-computed (such as SVGs, or Google Earth-compatible KML files). Note that commercial marketing activities are not permitted - presenters wishing to promote commercial or proprietary services or products should contact the Evolution conference about exhibitor space (http://www.confersense.ca/Evolution2012). Submissions consist of a title, which will typically be the name of the software (or visualization method) being presented, the URL of a website where more information can be obtained, and the license under which the source code is available. The website must contain a link to where the source code (and possibly binaries) can be downloaded. If it is not obvious from the website, the submission must describe what the software does. Reviewers will judge whether a submission is within scope of the conference (see above), and need to be able to verify whether the open-source requirement(*) is met. Presenters are expected to bring their own laptops for presentation, and any auxiliary devices necessary (such as a mouse). Power will be available at the presentation tables (110V/60Hz, US-style plugs; international presenters need to bring a suitable adaptor). Please let the organizing committee know as much in advance as possible if you expect to have unusually high demands for wireless network bandwidth, a large display, or other hardware. Review and acceptance of Software Bazaar submissions will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (July 10), but, because space for Software Bazaar presentations is finite, we cannot guarantee the availability of slots for late submissions. We cannot accept submissions until the open-source requirements are met. Software Bazaar demonstrations are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Challenge entries, and 4) Birds-of-a-Feather gatherings. The Calls for Challenge entries (http://ievobio.org/challenge.html) and Lightning Talks (same submission URL as above) remain open, and the Birds-of-a-Feather call is forthcoming. More details about the conference and program are available at http://ievobio.org<http://ievobio.org/>. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, software to be demonstrated to conference attendees must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. Authors are advised that non-compliant submissions must be revised to meet the requirement by July 8 at the latest, and in the event that presentation slots run out, precedence is established by the date they are first found in compliance, not the date of submission. _______________________________________________

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Semantics of Biodiversity Workshop
by John Deck 06 Apr '12

06 Apr '12

Following is a workshop of broad interest to many of you. If you are interested in attending or have further questions, please contact John Deck (jdeck(a)berkeley.edu). Note that there is a limited time in which to make your guaranteed hotel reservations at the The Oread hotel in Lawrence, under the "Biodiversity Semantics Workshop", which must be done before April 15th to get the reserved rate. Feel free to forward or post. Cheers, John ******* Google Doc link describing workshop and agenda: https://docs.google.com/document/d/1Z-RytvBlinIcSD3ctK1kiWUs2rr4TOxijT2TQb9… Text Description of above google doc link: Semantics of Biodiversity Workshop May 16 - 18, 2012 University of Kansas Biodiversity Institute -- Lawrence, Kansas Sponsored by RCN4GSC, Morphbank, Kansas University Biodiversity Informatics Center, and BiSciCol in collaboration with the National Center for Biomedical Ontology ** ABOUT THE SPEAKER ** Barry Smith is a prominent contributor to ontology research in biomedical and other domains. He is one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, a PI on the Protein Ontology and Infectious Disease Ontology projects, and one of the founders of the Open Biomedical Ontologies (OBO) Foundry initiative. TOPICS ** The Semantics of Biodiversity Workshop will explore terms used to describe biological collection objects and their derivatives using the Darwin Core standard as a starting point. The goal is to enable linking data across domains and to produce a deeper understanding of our planet’s biodiversity. For example, by linking information about the ecosystem (both gross and micro-habitat) and the geospatial environment to tissue samples and derived sequences, we can better understand population dynamics, ecosystem gene expression, and the significance of biodiversity in different environments. While the biodiversity informatics community has made much progress in standardizing terms over the last 20 years, specific problem areas are encountered both within and between relevant standards domains. Drawing on community discussions from the TDWG and GSC communities, and using the experiences of OBO in integrating information, Smith will guide a discussion of term clarification for the Darwin Core standard. Some example discussion topics are: - How do samples and occurrences relate to each other? - How can we best distinguish between collection objects, observations, and individuals? - What is the nature of the relationship between habitats, environments, and environmental materials? - What is the difference between a set, a lot, and a collection? - How to deal with taxonomic names associated with collection objects? Much of the workshop will be devoted to these and other discussion topics that will be introduced by attendees. Come prepared with your topics and/or important darwin core terms and be able to introduce them. It will be helpful to indicate before the workshop what topic you can introduce at the meeting by emailing jdeck(a)berkeley.edu. ** ** Day 1 (Wednesday, May 16th) 9am - 5:30pm Coffee & treats Wednesday and Thursday hosted by KU Breakfast at Hotel all 3 days Lunch and dinner on your own, with plenty of options within walking distance Background and problem statement (Wednesday) - Review successful examples from other communities - Getting clear on the distinctions between objects, data, and metadata - Contrasting annotation with metadata - Relationship expressions. - Tracking Identifiers to refer to objects or classes uniquely. Applying ontological principles to our subject domain (Wednesday and Thursday) - Interactive review of 10 or so of the most important Darwin core terms from the ground up. Participants will be describing terms and the intention behind their original formation. Come prepared to discuss your term(s) of interest. 6pm- 7:30pm Reception hosted by Kansas University’s Biodiversity Institute Day 2 (Thursday, May 17th) 9am - 5:30pm Solutions for the future (Thursday) - Enabling linked data - Pitfalls, traps, and planning - Creating a sociology so people can re-use ontologies Planning the 3rd Day discussions (4-5:30pm on Thursday) - Barry will be departing at 4pm on Thursday and so we will use the remainder of day to plan our discussion for Friday. ** Day 3 (Friday, May 19th) 9am - Noon We will be collecting discussion topics on Thursday afternoon for our Friday discussion. Some possible topics include: - Develop concrete proposals for Darwin Core term clarification - Do we need a new namespace for Darwin Core (for enforcing URIs)? - Implications for MIxS Standard - Implications for the Darwin Core Archive Format - Recommendations to the TDWG-RDF Group -- John Deck (541) 321-0689

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Deadline extension for full talk abstracts for Conference on Informatics
by Cellinese,Nico 03 Apr '12

03 Apr '12

The deadline for submitting abstracts for full talks to the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) has been extended to Monday, April 9, 2012. We hope that this will give those interested in contributing sufficient time to do so. Please see http://bit.ly/iEvoBio2012_CfA for the full Call for Abstracts and author instructions. We still expect to be able to notify accepted talks in time for the early registration deadline of iEvoBio (and Evolution). More details about the program and guidelines for contributing content are available athttp://ievobio.org<http://ievobio.org/>. You can also find continuous updates on the conference's Twitter feed (http://twitter.com/iEvoBio) or Google Plus page (http://bit.ly/iEvoBio-on-Gplus), and there is a Google group you can join at http://groups.google.com/group/ievobio-announce to receive announcements. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign

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