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[tdwg-phylo] Reminder: Student application deadline for Summer of Code 2009
by Hilmar Lapp 29 Mar '09

29 Mar '09

*** Please disseminate widely to students at your institution. *** *** Note: Phylogenetics standards are among the project ideas *** *** and members of this Interest Group are among the mentors. *** PHYLOINFORMATICS SUMMER OF CODE 2009 - STUDENT APPLICATION DEADLINE IS APRIL 3 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 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 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. Project ideas are listed on the website and range from hardware acceleration for phylogenetic inference, to support for phyloinformatics standards within the BioPerl and BioRuby toolkits, to alignment of next-gen sequencing data, to ontology term markup for biocuration, to semantic interoperability of web-services, to 3D-printing of phylogenies. 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: Instructions are at the website (see "When you apply"). You can find GSoC program rules and eligibility requirements at http://socghop.appspot.com . ***The 12-day application period for students ends on Friday, April 3rd, 2009, at 19:00 UTC (3pm EDT, 12pm PDT).*** INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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[tdwg-phylo] Summer of Code 2009
by Hilmar Lapp 19 Mar '09

19 Mar '09

*** Please disseminate widely at your local institutions *** *** so that we reach as many students as possible. *** PHYLOINFORMATICS SUMMER OF CODE 2009 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 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 hardware accerelation for phylogenetic inference, to tree visualization within a wiki, to alignment of next-gen sequencing data, to development of a reusable ontology term markup module for biocuration. 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 23rd and runs through Friday, April 3rd, 2009. 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. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/ Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/ about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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DarwinCore 1.4 & 'lots'
by Kehan Harman 09 Mar '09

09 Mar '09

Dear All, Markus has asked me to pass this on to this shiny new mailing list as it's the list that's designed for this kind of query. I'm working as part of the Scratchpads project (http://scratchpads.eu) and we're wanting to update our specimen module which is currently based on DarwinCore 1.2.1. We'd like to be able to support the concept of 'lots' within this module and were wondering whether DarwinCore and/or the curatorial extensions for it (or ABCD for that matter) support this. A 'lot' is for example a jar of specimens of n number of species, and this is often the lowest level to which specimens get curated. I'm pretty sure this is taken into account by DarwinCore but just wanted to find out if you know the mapping for this. Markus indicated that with DwC it would only support one name per record. I know that people on this list will have had to deal with this at the application level so maybe you could share how you've done it within your institutions. thanks Kehan Harman ---------- Forwarded message ---------- From: "Markus Döring (GBIF)" <mdoering_at_gbif.org> Date: Tue, Mar 3, 2009 at 5:00 PM Subject: Re: DarwinCore 1.4 & 'lots' To: Kehan Harman <kehanharman_at_gmail.com> Kehan, its not dwc specific really, the problem is known since ages also in ABCD. As far as I remember a "unit" in ABCD is anything the museum curator decides to be a unit. Basically what gets a catalog number. So a single dwc record could represent multiple specimen in case they are "hidden" behind a single catalog number. Thats what I think at least, John Wiezoreck might disagree, better ask him in person. Best would be to use the new tdwg-conten meiling list which is exactly for this. Problem with a single dwc record is of course that only one scientific name applies. Please post this problem to the list, its good for all of us to share the same idea of what a "lot" becomes. markus On Mar 3, 2009, at 17:35, Kehan Harman wrote: > Hi Markus, > Not sure how familiar you are with entomological collections, but > Simon and Vince are looking at the scratchpads specimen module > (currently based on DarwinCore 1.3) and one thing that they'd like to > know about DarwinCore (& the proposed version) is whether it supports > the concept of 'lots' out of the box. A lot is for example a jar of > specimens of n number of species, and this is often the lowest level > to which specimens get curated. I'm pretty sure this is taken into > account by DarwinCore but just wanted to find out if you know the > mapping for this (or who I should talk to to find this out)? The > reason I'm emailing you is you're one of the contributors on > http://rs.tdwg.org/dwc/index.htm. > > Cheers, > Kehan > > > -- -- kehanharman(a)gmail.com http://kehan.wordpress.com skype: kehanharman msn: kehanharman(a)gmail.com Bill Vaughan - "Suburbia is where the developer bulldozes out the trees, then names the streets after them."

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Darwin Core review
by Peter Desmet 06 Mar '09

06 Mar '09

Hi all, I had a look at the Darwin Core terms (http://rs.tdwg.org/dwc/terms/index.htm) and I have some questions and remarks. 1. The "Replaces"-links for terms in the "Complete historical record" (http://rs.tdwg.org/dwc/terms/history/index.htm) always link to themselves. See for example: HigherGeography (http://rs.tdwg.org/dwc/terms/history/index.htm#HigherGeography-2009-01-21) The "Replaces"-link links to same 2009-01-21 instead of 2007-04-17 (http://rs.tdwg.org/dwc/terms/history/index.htm#HigherGeography-2007-04-17) And this 2007-04-17 also links to 2007-04-17 instead of the older 2003-06-17. A link for "Is Replaced By" instead of text would also be useful. 2. As a result, I had some difficulties mapping the terms from DwC 1.4 (http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreDraftStandard) with the new ones. Update: Until I found the Darwin Core Versions document (http://rs.tdwg.org/dwc/terms/history/versions/index.htm) 3. Are the terms StartDayOfYear, EndDayOfYear, StartTimeOfDay, EndTimeOfDay, YearSampled, MonthOfYear, DayOfMonth necessary if you can provide this information in EarliestDateCollected, LatestDateCollected? Or is this to provide e.g. the time at which something was collected if you don't know the date (I don't know if you can express this in EarliestDateCollected)? If so, YearSampled can always be expressed in EarliestDateCollected/LatestDateCollected. 4. Is it possible to provide a different example for SampleRemarks and SamplingEventRemarks for a clearer difference between the two? Now both have "found dead on road". 5. Why is ValidDistributionFlag removed? This looked like an interesting field for all our botanical garden specimens. We now have to express this in SamplingProtocol, which will need a controlled vocabulary for sorting these out. 6. Is Behavior an attribute of a SamplingEvent or Sample? 7. I'm happy with addition of the term "PreviousIdentifications". Is it possible to provide the previous identificators and dates there as well? 8. Can you add multiple "ResourceRelationship", "SampleAttribute", "EventAttribute" to one sample? If yes, how does this work in a flat schema like DwC? 9. The name "SamplingAttributeID" (http://rs.tdwg.org/dwc/terms/index.htm#SamplingAttributeID) should probably be changed to "SampleAttributeID". 10. What terms are mandatory? Best regards, Peter -- Peter Desmet Biodiversity Informatics Manager / Directeur de l'informatique de la biodiversité Montréal Biodiversity Centre / Centre sur la biodiversité de Montréal Canadensys - www.canadensys.net Institut de recherche en biologie végétale Université de Montréal 4101, rue Sherbrooke est Montréal, Québec, H1X 2B2 Canada Télé / Phone: 514-872-5249 Télécopie / Fax: 514-872-9406 Email: peter.desmet.cubc(a)gmail.com

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[tdwg-phylo] Phyloinformatics Summer of Code 2009
by Hilmar Lapp 27 Feb '09

27 Feb '09

Hi all: NESCent is getting ready for participating in the 2009 Google Summer of Code. The skeleton for the project ideas page, along with a template for project ideas, is online: http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 A big part of the strength of our application as a participating organization comes from our project ideas and a diverse roster of primary and secondary mentors. If you have an idea for carving out a summer programming project for a student, and/or can fancy yourself mentoring a student, or are simply enthusiastic about helping out, for example as a backup mentor, please let me know, and I will send you a summary of how the Summer of Code program works in principle, as well as guidelines for how to become a mentor for us or help out in other ways. For comparison purposes, previous years' ideas pages are here: http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2008 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2007 As for supporting standards within the program, last year for example one of the funded projects was on phyloXML support in BioPerl. Cheers, -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================

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[tdwg-phylo] Evolutionary Database Interoperability Hackathon
by Hilmar Lapp 26 Jan '09

26 Jan '09

(Note that the issue we are trying to address and the standards we try to bring to bear here are closely related to what we discussed at the workshop and the conference session in Perth. If you are interested in participating, I'd encourage you to apply! -hilmar) NESCent Hackathon on Evolutionary Database Interoperability OPEN CALL FOR PARTICIPATION The National Evolutionary Synthesis Center (NESCent; http:// nescent.org) is sponsoring an "Evolutionary Database Interoperability" hackathon aimed at enhancing the value (and raising the profile) of important community resources for evolutionary and biodiversity data by increasing their accessibility to users and software. We are broadly soliciting applications for participation from the community. More information about the event is available online at http://evoinfo.nescent.org/Database_Interop_Hackathon . A hackathon is an event at which a group of programmers who otherwise do not have the opportunity to interact on a routine basis meet with users and domain experts to collaboratively develop working code that is of utility to the community as a whole. The Database Interoperability Hackathon will bring together developers from a number of emerging standards for evolutionary data exchange (NeXML; http://nexml.org ), data and metadata semantics (CDAO; http://www.evolutionaryontology.org ), and programmatic access of evolutionary data providers (PhyloWS; http://evoinfo.nescent.org/PhyloWS) with database programmers and metadata experts from a variety of evolutionary and biodiversity community resources. In addition, the mix of people will include programmers of embeddable widgets, mash-up and aggregation applications that can showcase the value of the effort for research applications. We also welcome comments and suggestions for issues in database interoperability that could be addressed at the event but are not yet on our radar. Please email the organizers at hackathon3(a)nescent.org with any suggestions you have. GOALS AND ACTIVITIES The focus of the programming aspect of the meeting will be to promote interoperability among online evolutionary databases through the following core set of activities. 1) Mapping the data and operation semantics of the participating online resources to an ontology, CDAO. 2) Implement a NeXML transformation for participating online resources as a formally defined query input and data output. 3) Implementation of programmable web-service interfaces following the emerging PhyloWS standard. 4) Showcase some of the possibilities that can arise from achieving data provider interoperability through small integration and/or mash- up oriented prototype applications. Supporting activities will include discussing input from end-users, discussing compliance with emerging reporting standards (MIAPA) and documentation of solutions and open problems on the hackathon wiki. ORGANIZATION The event will be 5 days in duration and will take place at NESCent in Durham, North Carolina, on March 9-13, 2009. Participant travel, accommodation, expenses for meals, etc, will be paid by NESCent. Logistical and travel details will be communicated to accepted and confirmed participants. The specific development targets will be selected by the participants through a hackathon wiki, a mailing list, and one or more conference calls. The exact agenda for the event will be developed similarly, but will be largely devoted to coding time. At the event itself, participants will self-organize into small subgroups (of 2-5) focused on particular targets. The NeXML, CDAO, and PhyloWS standards are products of the Evolutionary Informatics working group (http://evoinfo.nescent.org) under the auspices of whom this event is being organized. CALL FOR PARTICIPATION We invite all individuals interested in attending to apply by responding to the questions below. We specifically encourage applications from members of underrepresented groups, specifically women and minorities, and from graduate students and postdocs. 1. Please indicate if you would be available for all or only for part of the March 9-13 time period. 2. All code and documentation produced at the event is to be made available immediately under an OSI-approved open-source license or a Creative Commons license. Please indicate if this would pose any difficulty for your participation. 3. Please briefly describe your qualifications (programming languages, metadata standards, experience with data schemas, web-service programming, mash-up programming, etc). 4. Please state what you would most like to accomplish at the hackathon, given your current understanding. If you would not be writing software at the event, please state how you would like to contribute and how you would expect to benefit. 5. Please indicate if you are a member of an underrepresented group (including women, persons with disabilities, and any of the following minorities: African American, Hispanic, American Indian, Alaska Native, Native Hawaiian, and Pacific Islander). To apply, please enter your personal information and your responses by February 5 into the online form at http://spreadsheets.google.com/viewform?key=p6ikV0To6fXpJ369ozyNSSw&hl=en In addition, if possible please email a CV to the organizers at hackathon3(a)nescent.org by the same deadline. If you are interested in participating but are unable to respond in full by that deadline, please let us know as soon as possible. Please understand that the funds as well as the space for this event are limited. We also need to balance a critical mass of developers in certain areas of expertise with a broad participation of different data providers, and so not all qualified applicants can be guaranteed acceptance. Yours, The Organizing Committee Arlin Stoltzfus, Rutger Vos (Evolutionary Informatics Working Group) Hilmar Lapp, Todd Vision (NESCent) Katja Schulz (Tree of Life)

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[tdwg-phylo] Welcome
by Hilmar Lapp 26 Jan '09

26 Jan '09

Hi Everyone, it's been a while since the TDWG Meeting and workshop in Perth. Many of you on this list have participated in the workshop, and it was great to meet you there. I found the workshop to be productive and very encouraging towards forming this Interest Group in a way that has unique value. You may have noticed that we have our own TDWG wiki site at http://wiki.tdwg.org/Phylogenetics/ You can navigate there easily manually by going to the TDWG home page (http://tdwg.org ), then click 'Wiki' in the left hand navigation bar, then 'Phylogenetics'. I've put up already last year some minimal initial content about what we are about, and I also put up information about and notes from our Perth workshop: http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/PhylogeneticsStandardsWor… While there hasn't been much activity since on the charter and the BioSynC proposal due to the I guess all too familiar year-end frenzy, this will change over the next few months. Stay tuned, we'll keep you in the loop. Also, this is meant to be a discussion much more than an announcement forum, so if you have any suggestions, concerns, or thoughts, please don't hesitate to voice them here. Speaking of keeping in the loop, I'll shortly forward a call for participation in a NESCent-organized event that is very closely aligned with the phylogenetics standards and targeted at the interoperability issues we were talking about in Perth. As for Markus' email, I don't know to what extent you have been part of the respective discussion but I wasn't. While I see the possible benefits of better avoiding the reinventing the wheel, I find the question of merging with another and much larger community when we aren't one really yet a bit premature, and I am concerned that the loss of focus might cause some to tune out or ignore the list (more than they might otherwise), which I find the much bigger risk than reinventing as the latter can be prevented by cross-talk and subscribing to multiple lists (which I'm used to, but again maybe not everyone is). That's just my opinion though - please don't hesitate to voice yours, especially if you feel differently. Cheers, -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : ===========================================================

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[tdwg-geospatial] new tdwg-content mailing list
by "Markus Döring (GBIF)" 25 Jan '09

25 Jan '09

Dear TDWG groups, I would like to inform you about a new TDWG mailing list that was created today for discussing any TDWG standard definitions on a non technical level. The new list was created to help cross pollination of ideas between the different TDWG groups and avoid the frequent duplication of work that we have encountered so often in the past years. Every subgroup is free to decide whether they want to freeze their existing mailing list and migrate discussions to the central tdwg- content list. If you want to take this step, please let me know and I will take the required actions. A frozen mailing list will disallow any new posts or member subscriptions, but the existing archive will continue to be publicly available. An autoresponder will also be configured to inform future users of the new content list. By default I will transfer all existing subscriptions to the new list, so people don't have to subscribe again. You can also subscribe manually to the new mailing list here: http://lists.tdwg.org/mailman/listinfo/tdwg-content In addition to that, the 3 existing mailing lists that deal with technical issues have already decided to hold all discussions from now on on the technical architecture group (TAG) list. The existing guid and tapir mailing lists have been frozen today. Best wishes, Markus Döring

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[tdwg-geospatial] Centroids for level 4 areas (TDWG/Brummitt 2001 map)
by sampsa lommi 08 Oct '08

08 Oct '08

Hi, are there any centroid data available for TDWG map level 4 areas with abbreviations as an ID field? A simple CSV table with ID, lat, lon would be sufficient for my purposes. Just asking if somebody has done this already or could easily do that. Thanks in advance! Sampsa Lommi Helsinki, Finland

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[tdwg-geospatial] TDWG 2008 Conference - seeking wild ideas
by Markus Döring 05 Aug '08

05 Aug '08

[ our apologies should you receive this message more than one time ] ************************************************************** Biodiversity Information Standards (TDWG) 2008 Conference Friday 24th October 2008 Session 20: Wild Ideas http://www.tdwg.org/conference2008/ ************************************************************** "Wouldn't it be cool if we had a tool to do...." "Why don't we serve data like...." "Check out this non OGC GIS system...." "We need to copy the ideas of community...." "This online data curation site is awesome...." "Check what I can do with my super computer other than play World of Warcraft...." "Cloud computing is allowing me to...." "Google / Facebook / Flickr process data like this .... why don't we?" We all have them - wild ideas - and now we all want to hear them. Have you an idea that you could present for 15 minutes at the 2008 TDWG conference in Perth? Perhaps you have something that goes beyond the usual schemas, the usual harvesting model, the usual processing or visualisation? There are no limitations, no boundaries other than it must relate somehow to biodiversity informatics. Who knows, maybe you can generate some interest, start a working group and next year we'll be presenting a new working method. If you have an idea, please mail Tim and Markus on trobertson(a)gbif.org and mdoering(a)gbif.org with a brief outline and we'll get back to you. And if you have a presentation to give, but can't be there in person, maybe we can hook up a video link, you can ask someone else to present it for you or submit a video presentation? Cheers Markus and Tim

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