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NESCent Phyloinformatics VoCamp - LAST CALL FOR PARTICIPATION
by Nico Cellinese 17 Sep '09

17 Sep '09

NESCent Phyloinformatics VoCamp LAST CALL FOR PARTICIPATION This is the second and last circular for the Phyloinformatics VoCamp event that will be co-located with the 2009 TDWG Conference. Please note that there is only 1 day left until the deadline for application, which is Friday September 18. The full Call for Participation is at http://docs.google.com/View?id=dhdjhbvd_66gr5cdqfq . The application consists of your cv and your responses to 6 questions about your experience, skills, objectives, support, and commitment to open software development through an online form at http://bit.ly/VoCamp_Form . The form is easy to fill out, so please do not let the approaching deadline deter you from applying if you are interested. We specifically encourage applications from members of under- represented groups. If you have questions, contact an organizer or write to vocamp1(a)nescent.org. Yours, The Organizing Committee Arlin Stoltzfus, Chair (University of Maryland Biotechnology Institute) Nico Cellinese (University of Florida) Karen Cranston (Field Museum of Natural History) Hilmar Lapp (NESCent) Sheldon McKay (Cold Spring Harbor Laboratory, iPlant Collaborative) Enrico Pontelli (New Mexico State University)

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NESCent Phyloinformatics VoCamp
by Nico Cellinese 09 Sep '09

09 Sep '09

NESCent Phyloinformatics VoCamp OPEN CALL FOR PARTICIPATION Integrating diverse biological data with the historical process of evolution is a grand challenge for 21st century biology. The interoperability of data from diverse fields (e.g., genetics, ecology, biodiversity, biomedicine) requires a technology infrastructure based on formalized, shared vocabularies. Developing such vocabularies is a community project. In order to build controlled vocabularies and ontologies, the National Evolutionary Synthesis Center (NESCent: http://nescent.org) is sponsoring a "Phyloinformatics VoCamp". We invite scientists from diverse sub-disciplines to apply for this event, as explained below. The application deadline is September 18, 2009. More information about motivation, plans, and preliminary ideas is available online at http://bit.ly/VoCamp_Proposal. Feel free to disseminate this notice to colleagues who may be interested.* A VoCamp (http://vocamp.org) is an intense, hands-on, working meeting with face-to-face interactions between a diverse group of people focused on vocabulary and ontology design, development and application. The Phyloinformatics VoCamp will include ontology and vocabulary developers from relevant efforts, experts on knowledge representation and reasoning, and users and developers of integrative applications that use these ontologies. This event will partially overlap with the Biodiversity Information Standards (TDWG: http://tdwg.org) Annual Conference in Montpellier, France, November 9-13, 2009. The VoCamp is an activity of the TDWG Interest Group on Phylogenetics Standards (http://wiki.tdwg.org/Phylogenetics) and is partly supported by TDWG and the Université Montpellier. GOALS AND ACTIVITIES -------------------- The objective of the event is to connect previously disparate ontology development efforts, stakeholder communities, and interoperability initiatives with shared objectives. Aside from sharing knowledge, expertise, and best practices, our goal is to build-out existing ontology resources in a hands-on manner in terms of ontological rigor, semantic richness, and modularity that supports effective reuse. We also plan to have programming expertise and activities present at the event, such as for necessary large-scale transformations, and especially for proof-of-concept applications that directly apply the ontologies being developed. On a long-term basis, we anticipate that the event, if successful, will give rise to similarly structured follow-up events organized by the participating stakeholder communities, such as TDWG, SONet (http://sonet.ecoinformatics.org), and OBO (http://www.obofoundry.org). ORGANIZATION ------------ The VoCamp will be 4 days in duration during November 7-11, 2009 and is co-located with the TDWG annual conference (http://www.tdwg.org/conference2009) in Montpellier, France. The first two days (Nov 7-8) will be dedicated entirely to VoCamp and the remainder of the event (Nov 10-11) will overlap with TDWG 'workshops days'. Participants will have the opportunity, and are encouraged, to interact with TDWG participants and attend conference sessions outside of the VoCamp. The specific vocabulary development targets will be selected by the participants partly in advance through a dedicated area on a wiki, a mailing list, and one or more conference calls, and partly on-site through an Open Space activity. The exact agenda for the event will be developed similarly, but will be largely devoted to ontology and vocabulary development time. At the event itself, participants will self-organize into small subgroups focused on particular targets. The VoCamp will conclude with a wrap-up session, and a report presented to the TDWG conference audience. We also anticipate that several "boot camps" will be needed to ensure a productive event for all participants, for example on ontology design and engineering, reasoning, and infrastructure for collaborative development of ontologies. We welcome comments and suggestions for issues in ontology development that are not explicitly addressed here or in our proposal but that could be addressed at the event. Please email the organizers at vocamp1(a)nescent.org with any suggestions. HOW TO APPLY ------------ The application consists of your cv and your responses to 6 questions about your experience, skills, objectives, support, and commitment to open software development. To apply, please fill out the online form at http://bit.ly/VoCamp_Form by September 18, and submit your CV to the organizers at vocamp1(a)nescent.org. NESCent will provide funds in support of expenses, including travel, accommodation, registration, and meals. Pending the final amount of funds available and the support requested by the participants, sponsorship may need to be capped. Logistical and travel details will be communicated to accepted and confirmed participants. We specifically encourage applications from members of under- represented groups, specifically women and minorities, and from graduate students and post-docs. If you have questions or are unsure whether to apply, please contact an organizer or write to vocamp1(a)nescent.org . Please understand that funding and space for this event are limited. We also need to balance a critical mass of expertise in specific areas with broad participation. Therefore, not all qualified applicants can be guaranteed acceptance. Yours, The Organizing Committee Arlin Stoltzfus, Chair (University of Maryland Biotechnology Institute) Nico Cellinese (University of Florida) Karen Cranston (Field Museum of Natural History) Hilmar Lapp (NESCent) Sheldon McKay (Cold Spring Harbor Laboratory, iPlant Collaborative) Enrico Pontelli (New Mexico State University) * This announcement is being sent to the following lists: evoldir, TDWG, SSB, nexml, phylows, CDAO, SONet, GBIF, Ecolog, TAXACOM.

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Interest Group Charter: Need feedback
by Hilmar Lapp 06 Sep '09

06 Sep '09

Hi all, as I'm sure you've noticed already, the 2009 TDWG Conference is coming up and only about 2 months away. Nico and I hope to see as many of you there as possible! As the one remaining TODO needed to complete the formal establishment of our TDWG Interest Group, we need to get the group's charter written, finalized, and approved. Nico and I have now written a draft charter here: http://docs.google.com/View?id=dhdjhbvd_65ff7bp3dn Since in order to be approved by the executive committee in time for the 2009 conference it needs to be submitted rather soon. So, we'd be much obliged if you can review the draft and give us feedback, comments, and suggestions by Friday, Sep 11, so we can incorporate it in time for submitting the final version on Monday, Sep 14. FYI, there'll likely be significant activities of our group at the event, the announcements and Calls for Participation for which will be posted here over the coming week. Pending final approval for funding and logistics, one of these will be a VoCamp; check out http://evoinfo.nescent.org/VoCamp1_Proposal if you're curious. Cheers, Hilmar & Nico

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NSF INTEROP proposal
by Hilmar Lapp 31 Jul '09

31 Jul '09

FYI, a group of collaborators (Arlin Stoltzfus, Karen Cranston, Sheldon McKay, Enrico Pontelli, Nico Cellinese, and myself) under the leadership of Arlin recently pulled together a grant application for the NSF Interop solicitation. The ideas for the grant emerged mostly from the recent Database Interoperability Hackathon (for which I posted the announcement and Call for Participation here back in Jan). Proposal summary and full text are public at the following URL: http://evoinfo.nescent.org/NSF_Interop_Proposal It was submitted July 22. If funded, TDWG and this Interest Group will play a significant role in the proposed activities. We probably won't hear about reviews or funding before Feb/March next year, so keep fingers crossed until then. Cheers, -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : ===========================================================

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phylogenetic tree data
by Yose Widjaja 04 Jun '09

04 Jun '09

Hi, I was just wondering, is it possible to obtain, somewhere from the net, the full phylogenetic tree for life on earth? How big would the data be? How many nodes are there (counting a species, and every split in the graph, as a node)? I'm thinking of fitting it inside the interatctorium (www.interactorium.net) Cheers -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Yose Widjaja Supreme Emperor @ Jormy Games www.jormy.com yose(a)jormy.com -- -- -- -- -- -- -- -- -- -- -- -- -- --

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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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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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Phyloinformatics Summer of Code 2009
by Hilmar Lapp 26 Feb '09

26 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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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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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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