March 2010 - tdwg-tag - lists.tdwg.org

Re: [tdwg-tag] RDF N3
by Kevin Richards 17 Nov '10

17 Nov '10

I like the sound of the 'compactness' of the format, but I worry that there is a lack of tools that support the format (ie browsers, mainly). It is quite nice to naturally navigate the rdf world with a standard browser. But for transfer standards, I suppose this wouldn't matter. Kevin Sent from my HTC ----- Reply message ----- From: "Bob Morris" <morris.bob(a)gmail.com> Date: Sun, Jan 24, 2010 12:08 PM Subject: [tdwg-tag] RDF N3 To: "Technical Architecture Group mailing list" <Tdwg-tag(a)lists.tdwg.org> Let's make N3 be the recommended RDF representation. It is way more compact and human readable than RDF/XML. We could even specify a normative conversion tool if necessary. -- Robert A. Morris Professor of Computer Science (nominally retired) UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: ram(a)cs.umb.edu web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/FilteredPush http://www.cs.umb.edu/~ram phone (+1)617 287 6466 _______________________________________________ tdwg-tag mailing list tdwg-tag(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tag ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

4 4

Re: [tdwg-tag] Phyloinformatics Summer of Code 2010 - Call for student applications
by Hilmar Lapp 27 Mar '10

27 Mar '10

Hi all - sorry for the additional noise. The original email contained two errors: this is the 2010 program (not 2009, as the subject line said), and one URL was wrong. The corrected version is below for those who'd like to forward it on or print it out. I'd also like to take the opportunity to highlight a few of our project ideas that pertain to biodiversity informatics and phylogenetic standards: #1, NeXML support in Bioruby; #6, building geo- phylogenies in Java; #10, a UI for MIAPA, the minimum reporting standard for phylogenetic analyses; and #15, Google Earth browser interface for TreeBASE. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== *** Please disseminate widely at your local institutions, including *** *** posting to message and job boards, so that we reach as many *** *** students as possible. *** PHYLOINFORMATICS SUMMER OF CODE 2010 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from phylogenetics pipeline development to a user interface for MIAPA-driven annotation of experiments, interactive animations of gene tree evolution, and rendering phylogenies on Google Earth. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/ ), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 29th and runs through Friday, April 9th, 2010. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. 2010 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2010/faqs DataONE Summer 2010 Internship Program (managed separately, and different from GSoC; postdocs also eligible): http://d1-lab.appspot.com/ --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

1 0

Phyloinformatics Summer of Code 2009 - Call for student applications
by Hilmar Lapp 25 Mar '10

25 Mar '10

*** Please disseminate widely at your local institutions, including *** *** posting to message and job boards, so that we reach as many *** *** students as possible . *** PHYLOINFORMATICS SUMMER OF CODE 2010 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from phylogenetics pipeline development to a user interface for MIAPA-driven annotation of experiments, interactive animations of gene tree evolution, and rendering phylogenies on Google Earth. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/ ), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 29th and runs through Friday, April 9th, 2010. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. 2010 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2010 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2010/faqs DataONE Summer 2010 Internship Program (managed separately, and different from GSoC; postdocs also eligible): http://d1-lab.appspot.com/ --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

1 0

FW: Announcing PURL Federation Development Effort
by Kevin Richards 22 Mar '10

22 Mar '10

An interesting bit of GUID work... Kevin -----Original Message----- From: semantic-web-request(a)w3.org [mailto:semantic-web-request@w3.org] On Behalf Of David Wood Sent: Tuesday, 23 March 2010 7:00 a.m. To: purl-dev Cc: purl-interest; semweb-31(a)meetup.com; DCMI Architecture Forum; semantic-web; public-lod Subject: Announcing PURL Federation Development Effort Hi all, The National Center for Biomedical Ontology and Zepheira are pleased to announce work on a PURL Federation. A PURL Federation will allow multiple PURL service operators to cooperate in PURL resolutions, covering for each other in the case of service outages and allowing the persistent resolution of PURLs as funding levels and organizational details change with time. PURL Federations are intended to enhance the ability of Semantic Web and Linked Data communities to ensure the persistence of their identifiers. Prototypes of the PURL Federation code will be released occasionally in the coming months, with an Alpha version to be released in the Summer of 2010. Further announcements of releases will be made on the purl-dev mailing list and on http://purlz.org. The architecture document guiding the development of a PURL Federation is available at: http://purlz.org/project/purl/development/wiki/PURLFederationArchitecture Review and feedback on the proposed architecture is encouraged. We want to hear your use cases and good ideas. Thanks in advance. Regards, Dave -- David Wood Partner Zepheira - The Art of Data http://zepheira.com/team/dave/ Cell: +1 540 538 9137 Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

1 0

Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 03 Mar '10

03 Mar '10

The Call for Abstracts for full talks is now open for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs/index.php/ievobio/ 2010. See below for instructions. Accepted talks will be about 15-20 minutes in length and will be presented during the full talk sessions in the morning of each of the two conference days, following the day's keynote presentation. Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions consist of a title and an abstract at most 1 page long. The abstract should provide an overview of the talk's subject. As the number of program slots for full talks is limited, the abstract should give enough detail so reviewers can decide whether the submission merits a full talk or whether it should be moved to one of the lightning talk sessions. If the subject of the talk is a specific software for use by the research community, the abstract must state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. The deadline for submission is April 8, 2010. We intend to notify authors of accepted talks before early registration for iEvoBio (and Evolution) ends. Further instructions for submission are at the following URL: http://ievobio.org/ocs/index.php/ievobio/2010/information/presenters Full talks are 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Lightning talks (5 mins long), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries is already open (see http://ievobio.org/challenge.html), and information on how to contribute to the other 3 sessions is forthcoming. More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) (*) 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, if a submitted talk concerns a specific software system for use by the research community, that software 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 of full talks who cannot meet this requirement at the time of submission should state their intentions, and are advised that the requirement must be met by June 27 at the latest.

1 0

https://rs.tdwg.org/dwc/xsd/tdwg_dwcterms.xsd missing taxonAccordingTo
by Bob Morris 01 Mar '10

01 Mar '10

The current twg_dwcterms.xsd seems to be missing taxonAccordingTo Bob -- Robert A. Morris Professor of Computer Science (nominally retired) UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: ram(a)cs.umb.edu web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/FilteredPush http://www.cs.umb.edu/~ram phone (+1)617 287 6466

2 2