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Re: [Tdwg-phylo] Interest group meeting at TDWG 2018? [SEC=UNCLASSIFIED]
by Laity, Tania 15 May '18

15 May '18

Hi I would be interested, please count me in Thanks Tania From: tdwg-phylo [mailto:tdwg-phylo-bounces@lists.tdwg.org] On Behalf Of Hilmar Lapp Sent: Wednesday, 16 May 2018 8:01 AM To: TDWG IG on Phylogenetics Standards <tdwg-phylo(a)lists.tdwg.org> Subject: [Tdwg-phylo] Interest group meeting at TDWG 2018? Dear all, The Phylogenetics Standards Interest Group at TDWG hasn’t met for a number of years, and in fact neither Nico nor I could attend the 2017 conference. However, we will be at TDWG 2018, and we, together with Emily Jane McTavish (UC Merced, Open Tree of Life PI) are co-organizing a symposium: https://tdwg.github.io/conferences/2018/sessions/S14 The TDWG organizers are asking whether space should be reserved for a meeting of our IG. This would be taking place over one of the lunch breaks (as, apparently, most other IG meetings, too). If you’d be interested in coming together again for a meeting over lunch, please let me know and we’ll work with the TDWG organizers to arrange it. -hilmar -- Hilmar Lapp -:- genome.duke.edu<http://genome.duke.edu> -:- lappland.io<http://lappland.io>

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Interest group meeting at TDWG 2018?
by Hilmar Lapp 15 May '18

15 May '18

Dear all, The Phylogenetics Standards Interest Group at TDWG hasn’t met for a number of years, and in fact neither Nico nor I could attend the 2017 conference. However, we will be at TDWG 2018, and we, together with Emily Jane McTavish (UC Merced, Open Tree of Life PI) are co-organizing a symposium: https://tdwg.github.io/conferences/2018/sessions/S14 The TDWG organizers are asking whether space should be reserved for a meeting of our IG. This would be taking place over one of the lunch breaks (as, apparently, most other IG meetings, too). If you’d be interested in coming together again for a meeting over lunch, please let me know and we’ll work with the TDWG organizers to arrange it. -hilmar -- Hilmar Lapp -:- genome.duke.edu -:- lappland.io

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GBIF & GGBN survey on DNA and biodviersity
by Dmitry Schigel 06 Jun '16

06 Jun '16

Dear colleague, The Global Biodiversity Information Facility (GBIF) and the Global Genome Biodiversity Network (GGBN) are seeking expert opinions on how to link morphological and molecular biodiversity data, i.e. physical specimens, derived DNA, sequences, observations and other evidence of species' presence and abundance in space and time. This survey targets data users and providers of specimen and sequence information. We know your time is extremely valuable, this survey should take about 25 minutes. We are particularly eager to receive early responses from those who are able to complete the survey by 15 June 2016, as we plan to report on preliminary results during workshop 9 of the SPNHC/GGBN conference, Documentation of environmental samples and eDNA on 20 June 2016. To take the survey, please follow this link<https://www.surveymonkey.com/r/N2GC2KR>, or copy the URL into your browser: https://www.surveymonkey.com/r/N2GC2KR We encourage you to share the survey with your contacts and networks, especially with users and holders of molecular biodiversity data. The survey will run until 15 September 2016, and the final results will be reported at TDWG 2016 Conference in Costa Rica. If you have any questions about this survey, please contact Dmitry Schigel, dschigel(a)gbif.org<mailto:dschigel@gbif.org>. Thanks in advance for your help. Gabriele Dröge (GGBN), Siro Masinde, and Dmitry Schigel (GBIF). ***** Dmitry Schigel, PhD Programme Officer for Content Analysis and Use Global Biodiversity Information Facility (GBIF) Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK T +45 35 32 14 85 G +45 30 45 02 25 E dschigel(a)gbif.org<mailto:dschigel@gbif.org> W www.gbif.org<http://www.gbif.org/> [GBIFlogoNO_TEXT_50%]

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Postdoctoral fellow in Computable Semantics for the Tree of Life
by Cellinese,Nico 04 May '15

04 May '15

A Postdoctoral position is available to work with Hilmar Lapp and Nico Cellinese on building phyloreferences for the Tree of Life. All details can be found here: http://www.flmnh.ufl.edu/museum-voices/cellinese-lab/2015/05/03/postdoctora… Spread the word so we can start having fun asap. Thanks! Nico <><><><><><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Associate Curator, Botany & Informatics Joint Associate Professor, Department of Biology University of Florida Florida Museum of Natural History 354 Dickinson Hall, 1659 Museum Rd. Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://www.flmnh.ufl.edu/museum-voices/nico-cellinese/ Twitter @ncellinese

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Darwin Core and phylogenies
by Roderic Page 16 Apr '15

16 Apr '15

My apologies in advance if this has come up before. Historically it seems that phylogenetics and classical biodiversity informatics live in separate worlds, for a bunch of reasons. One area they clearly intersect though is “phylogeography” or “geophylogenies”. I’ve been playing simple ways to create and visualise geophylogenies (e.g., http://iphylo.blogspot.co.uk/2015/01/geojson-and-geophylogenies.html ) and it occurs to me that it might be useful to have a Darwin Core-style way of encoding these. Phylogenetic data is typically stored very differently from the simple row-based approach adopted by Darwin Core (e.g., NEXUS format, XML [yuck], or JSON [sometimes yucky if it’s full of XML-style baggage, but I digress]). This makes it a challenge to integrate phylogenetic data with projects such as GBIF. This lack of integration is regrettable, anyone looking at the rise of phylogeography and DNA barcoding will recognise that many classically-defined species are poor representations of actual biodiversity, even in taxa that we think we know quite well (e.g., vertebrates). Given that we can encode a phylogenetic tree as a set of rows, each one representing an edge in the tree (what those of a certain age would call and "ancestor function”), it would be easy to have a Darwin Core extension that had one row per node in the tree, optionally with branch lengths, and leaf nodes also labelled by occurrence id (the same id used in the standard occurrence table, where ideally most if not all would be georeferenced). In this way we could add geophylogenies to Darwin Core archives, and existing tools for importing these (e.g., GBIF) could simply ignore the phylogeny until such times as they can handle them, but other tools could read the trees and display them. Is anyone doing something along these lines? Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: Roderic.Page(a)glasgow.ac.uk<mailto:Roderic.Page@glasgow.ac.uk> Tel: +44 141 330 4778 Skype: rdmpage Facebook: http://www.facebook.com/rdmpage LinkedIn: http://uk.linkedin.com/in/rdmpage Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com ORCID: http://orcid.org/0000-0002-7101-9767 Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ ResearchGate https://www.researchgate.net/profile/Roderic_Page

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symposium and workshop at TDWG 2013
by Hilmar Lapp 03 Oct '13

03 Oct '13

If you haven't been aware yet, the Phylogenetics IG at TDWG, together with Rutger Vos (NCB Naturalis Museum, Leiden), will be holding a combined symposium and workshop with the title "Sharing and delivery of reusable phylogenetic knowledge". The event aims to present and put to the test recent community progress towards effective sharing and reuse of expert phylogenetic knowledge, a key ingredient to addressing comparative research questions across biology. Even though many researchers would rather reuse a quality phylogeny than try to build it themselves, in practice it is difficult and often enough impossible to find suitable phylogenies, to evaluate their fitness for purpose, and to access them in a format suitable for analysis. To mitigate these obstacles, an interdisciplinary grassroots network has begun to develop solutions that include data standards, metadata ontologies, a decoupled architecture, and community-building hackathons. Aside from presenting the results of these efforts and showcasing diverse applications for phylogeny reuse, the event will allow participants to inform these efforts so they respond to biodiversity science needs. Finally, the event is designed to catalyze new collaborations by providing ample room for interactive demonstrations using participant-contributed research problems. The event will take place in the morning of Thursday, Oct 31. Speakers: * Ross Mounce, University of Bath, UK: Sharing phylogenetic data: even more vital for morphological data * Jonathan Rees, National Evolutionary Synthesis Center (NESCent), USA: Assembling a draft overall tree of life from phylogenetic trees and taxonomic databases * Rutger Vos, NCB Museum Naturalis, Netherlands: PhyloTastic - names-based phyloinformatic data integration * Saverio Vicario, Institute for Biomedical Technologies, Italy: Numerical tree representations and their application to MCMC phylogenetic inference, phylogenetic signal, and ... database query * Alexandre Antonelli, University of Gothenburg, Sweden: SUPERSMART: Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa * Suzanna Lewis, Lawrence Berkeley National Laboratory, USA: Quest for Orthologs: anchoring comparative biology research Full details are on our IG wiki: http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/PhyloSharingWorkshop2013 We hope to see as many of you there as possible. -Hilmar, Nico, and Rutger -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================

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symposium/workshop at the 2013 TDWG conference
by Hilmar Lapp 20 Aug '13

20 Aug '13

As some of you might have noticed in the workshop program for the 2013 TDWG Conference that just went online, the Phylogenetics Standards IG will be holding a half-day symposium/workshop combination there. The title of the event is "Sharing and delivery of reusable phylogenetic knowledge". There's now an initial website for the event on our wiki: http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/PhyloSharingWorkshop2013 If you have any feedback, ideas (including for symposium speakers(*)), or other input for the workshop, please don't hesitate to let us know. -Hilmar, Nico, & Rutger (*) At Nico's behest, all speakers must agree to give their talks in Italian ;) -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================

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by admin HC 15 Jul '12

15 Jul '12

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Last reminder: Deadline for iEvoBio Challenge Competitions is approaching
by Hilmar Lapp 11 Jun '12

11 Jun '12

The deadline for submissions to the yearly iEvoBio Challenge is June 25, 2012, and is rapidly approaching! This is our last reminder. This year’s theme is "Synthesizing Phylogenies," and further information on criteria for challenge entries, how to submit them, and award amount can be found at http://ievobio.org/challenge.html. Also, Biomatters Ltd is running the Geneious Challenge alongside iEvoBio’s competition. The goal of this challenge is to develop a new and exciting visualization or analysis plugin to Geneious Pro, using the public API. See http://ievobio.org/geneious_challenge.html for more information. The deadline for this competition is also June 25. More details about the iEvoBio conference and program are available at 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 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 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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Mentorship program at the 2012 iEvoBio conference
by Hilmar Lapp 16 May '12

16 May '12

The iEvoBio Mentorship Program pairs undergraduate and graduate students with faculty who have extensive experience in evolution, systematics, biodiversity, mathematics and/or software development to enhance their experience at iEvoBio 2012. Mentors will guide participants in collaborative and networking opportunities throughout the two-day conference. If you would like to gain the wisdom of your colleagues' experiences by participating in this program, please email the iEvoBio 2012 organizing committee at committee(a)ievobio.org by June 1, indicating if you have any activities you would like to be included in the mentorship program, or a particular field of interest. You can find more information about the meeting and registration at http://ievobio.org/. 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 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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