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Special Session on Metagenomics, Barcoding, and Biodiversity at iEvoBio
by Hilmar Lapp 29 Apr '11

29 Apr '11

This year, iEvoBio will have a special focus Session on Metagenomics, Barcoding, and Biodiversity and the challenges that these new approaches raise for evolutionary informatics. We now have over 6000 genomes and vast quantities of metagenomic sequences in the public domain, primarily from bacteria and archaea from many habitats. Various short sequences (e.g. barcodes) for quick identification of eukaryotes are emerging. The availability of this sequence data and ever-cheaper methods for producing it offer exciting opportunities forunderstanding molecular evolution and biodiversity. However, the data are growing faster than the infrastructure to support it. Moreover, the eukaryotic and microbial informatics communities have independent histories and approaches, so synergy is not easy. These challenges typify the intersection of fields that are the scope of iEvoBio. Invited speakers in this special session include Neil Davies (http://moorea.berkeley.edu/aboutus/people/ndavies ) from the Moorea Biocode project, Linda Amarral-Zettler (http://amarallab.mbl.edu/ ) from the Marine Biological Laboratory Wood's Hole, and Holly Bik, from the Hubbard Center for Genome Studies at the University of New Hampshire. After the talks, there will be an open panel with all the speakers, including keynote speaker Dawn Field (http://ceh.academia.edu/DawnField ) from the Center for Ecology and Hydrology at Oxford. 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 for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow)

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Phyloinformatics Summer of Code 2011 - Call for student applications
by Hilmar Lapp 26 Mar '11

26 Mar '11

*** Please disseminate widely at your local institutions, *** *** including posting to message and job boards, so that *** *** we reach as many interested students as possible. *** PHYLOINFORMATICS SUMMER OF CODE 2011 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 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 visualizing viral epidemics to 3D protein structure evolution, rich annotation for TreeBASE content, exposing phenotype observations to the Encyclopedia of Life, to enhancing R packages for phylogenetic analysis. 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. Each organization has a slightly different application format, and ours is at http://bit.ly/PhyloSoC2011-apptemplate. The 12- day application period for students opens on Monday, March 28th, and runs through Friday, April 8th, 2011. 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. Working closely with potential mentors to develop your project proposal greatly increases your chance for acceptance. Do not underestimate the amount of time it takes to develop a competitive proposal. 2011 NESCent Phyloinformatics Summer of Code: http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs --------- Karen Cranston and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================

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Reminder: Deadline for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 24 Mar '11

24 Mar '11

This is a reminder that the deadline for submitting abstracts for full talks to the 2011 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is Friday, March 25, 2011, which is just two days away. Please see http://bit.ly/iEvoBio2011_CfA for the full Call for Abstracts and author instructions. As another reminder, full talks are only 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 also open (see http://ievobio.org/ challenge.html). Tentative submission deadlines are listed on the conference website (http://ievobio.org/program.html#dates). 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, and there is an announcement-only Google group at http://groups.google.com/group/ievobio-announce . You can use the group's RSS feed (linked from its URL), or join the group to receive announcements by email. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow)

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Deadline extension for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 15 Mar '11

15 Mar '11

The deadline for submitting abstracts for full talks to the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) has been extended by one week to Friday, March 25, 2011. We hope that this will give those interested in contributing sufficient time to do so. Please see http://bit.ly/iEvoBio2011_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 at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/ iEvoBio, and there is a Google group you can join at http://groups.google.com/group/ievobio-announce to receive announcements. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow)

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Phyloinformatics Summer of Code 2011: Call for Mentors
by Hilmar Lapp 21 Feb '11

21 Feb '11

(Apologies if you receive multiple copies.) Over the next 3 weeks we will be pulling together NESCent's application to the 2011 Google Summer of Code as a mentoring organization. This is a call for all prospective mentors, primary and secondary, to step forward. Participating as an organization is competitive. Over the last years the acceptance rate for organizations has been around 30-35%. The most important component of organization applications is the Ideas page, and specifically the quality and suitability of the project ideas. These project ideas are contributed by you, our mentors. In the past we have had a strong, diverse and well-documented portfolio of ideas with different degrees of difficulty, from different participating open-source projects, using different programming languages. If you can fancy yourself serving as a mentor, or helping someone else mentoring a student as a secondary mentor, or would like to help out in other capacities, please contact us as soon as you can at phylosoc-admin(a)nescent.org . If you have not been a mentor with us in previous years, we'll send you guidance on what doing so involves, and how you can contribute to our participation. We will also add everyone who is interested in serving to our (private) mentors mailing list (at least those who aren't already). If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor for us, don't hesitate to ask questions or to contact previous mentors (see URLs below for projects that got selected). Being a mentor does require time (see http://bit.ly/soc2011-mentortime) , but our past mentors have pretty much unanimously found it a fun and rewarding experience. That's aside from the code a student could contribute to your project, and, possibly most important of all in the long run, the chance to gain a new developer. The initial skeleton of our 2011 Ideas page is now up here and ready for adding project ideas and mentors(*). http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 We will send further guidance on drafting project ideas, but for now you can see examples of the format and scope of project ideas on the Ideas pages from previous years (click on "Ideas"): http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 Dates: ====== Submission of organization applications starts Feb 28 and closes on March 11. For project ideas to contribute to the strength of our application they must be in reasonable shape by the morning of March 11. *If* we are accepted, ideas can be refined (or added) between March 18-27. Students apply March 28-April 8, and selected students are announced April 25. The coding period runs from May 23 to August 22. See http://bit.ly/soc2011-timeline for a full timeline of the whole program. Cheers, and we look forward to hearing from you! Karen Cranston Hilmar Lapp (*) Editing content on the NESCent Informatics wiki (f.k.a. Hackathon wiki) requires you to login. We had to disable local account creation due to spam getting out of control. The wiki is still open, though - just login with your OpenID. If you don't have an OpenID, the "Login with OpenID" page has information on you can easily get one, and if you have a Google account, you're all set to go.

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Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 16 Feb '11

16 Feb '11

(Apologies if you get multiple copies of this.) The Call for Abstracts for full talks is now open for the 2011 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs/index.php/ievobio/2011. 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 component 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 March 18, 2011. 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/2011/schedConf/cfp 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). The calls for contribution to the other 3 sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. 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 , or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) (*) 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 19, 2011, at the latest.

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How can we engage the wider non-tech research community?
by Ross Mounce 08 Feb '11

08 Feb '11

Dear list, Having already noted on Twitter that this list is rather quiet, I thought I'd post something to (hopefully) generate debate: As a student primarily concerned with palaeo-morpho-phylo data, I'm rather disheartened by the lack of progress in data archiving and publishing standards, particularly in the palaeontological research community. What's worse is. I get the feeling (some) people just don't care. They can seem oblivious to the benefits. Ignorant to the lost re-purposing potential. A tiny few evolution and ecology journals have recently changed editorial policy for the better -> So what? These journals are a just a drop in the ocean of what's out there that publish phylogenetic analyses, particularly palaeo-phylo analyses. How many systematic palaeontologists know or care about ontologies and/or XML-schema? It's all fine and well creating wonderfully clever linked architectures for data, but if the primary data-producers don't know about them, nor want the additional 'hassle' (no matter how little hassle it is), these brilliant data-networks may remain relatively empty. Community-change is needed, first-and-foremost I argue. The question I ask is how? Regards, Ross PS I find it gratingly ironic that Palaeontologists have an extremely faithfully updated public database for taxonomic and stratigraphic occurrence records: http://paleodb.org/ Why are MorphoBank and/or TreeBASE not as popular? -- -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/- Ross Mounce PhD Student Fossils, Phylogeny and Macroevolution Research Group University of Bath 4 South Building, Lab 1.07 http://bit.ly/rossmounce http://www.citeulike.org/user/rossmounce -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-

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survey & report (publishing trees) - nearing release, need collaborators
by Arlin Stoltzfus 03 Feb '11

03 Feb '11

Dear all-- After months of effort by a dedicated few (Jamie Whitacre & I), we are near to releasing a preliminary report on current best practices for publishing phylogenetic trees (1), and a survey designed to complete the report and assess user needs (2). The draft report is a product of the TDWG phylogenetic standards interest group, while the survey is from the MIAPA list participants. Its a great time to be doing this. Ready or not, in the next few years, the phylogenetics community is going to be forced (by journal policies) to archive tens of thousands of trees. Ideally, we can use this opportunity to catch a wave of interest in archiving, synthesis, and integration, and leverage the power of this wave to gain funding and to energize a community effort. But, to be successful, this is going to require more of a team effort. I'm excited about this project, but before I will commit to going ahead with it, I need commitments from 6 people, each one willing to dedicate 15 hours (over the next 6 weeks) to disseminate the survey, analyze results, and follow up on feedback and queries. These 6 people will be authors on the final published report on best practices for publishing a phylogenetic tree, and will have any other advantages that accrue from being part of this effort. Let me know if you want to be one of those people. Regards, Arlin (1) http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010 (2) https://spreadsheets.google.com/viewform?hl=en&pli=1&formkey=dHhZa0xMQTJuR0… #gid=0 ------- Arlin Stoltzfus (arlin(a)umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org

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Registration Open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 02 Feb '11

02 Feb '11

Registration is now open for the conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/register.html . iEvoBio aims to be a forum bringing together biologists working in evolution, systematics, and biodiversity, with software developers and mathematicians. The goal of iEvoBio is both to catalyse the development of new tools, and to increase awareness of the possibilities offered by existing technologies (ranging from standards and reusable toolkits to mega-scale data analysis to rich visualization). The inaugural meeting in 2010 (see http://ievobio.org/2010) attracted over 300 participants. The 2-day meeting will take place June 21-22, 2011, in Norman, OK, jointly with the 2011 Evolution Meetings as a satellite conference. The event will feature traditional elements, including a keynote presentation at the beginning of each day and contributed talks, as well as more dynamic and interactive elements, including a challenge, lightning talk-style sessions, a software bazaar, and Birds-of-a- Feather gatherings. The topic of this year's challenge is Data Integration. Cash prizes will be awarded for first place ($1,000) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. More details about the challenge will be provided in a separate announcement. Attendees can register jointly for Evolution and iEvoBio at a discount, or only for the iEvoBio conference. For more information about registration, venue, travel, or accommodations please visit the Evolution 2011 website at http://www.evolution2011.ou.edu/. 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 , or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-Chair) Cynthia Parr (Encyclopedia of Life) (Co-Chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow)

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update on "Current Best Practices for Publishing a Phylogenetic Tree" project
by Arlin Stoltzfus 24 Nov '10

24 Nov '10

To all those interested in archiving, sharing, re-use, etc of trees (w data & metadata)-- At the TDWG meeting in Woods Hole 2 months ago, the phylogenetic standards interest group spawned a sub-group (Dan Rosauer, Torsten Eriksson, Jamie Whitacre, Elena Herzog and myself) committed to a project to assess current best practices for publishing a phylogenetic tree electronically. This project is very timely as several major evolution journals have now announced that in January 2011 they will require archiving of data including phylogenetic trees. Since then, we've done a considerable amount of work that is reflected in drafts of an online report, and of a user survey. Our intention is to release a preliminary report, send out the survey to get systematic feedback from a broad community of tree-makers and tree-users, then write a more complete report for publication. The draft report and survey are available here: http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010 https://spreadsheets.google.com/viewform?formkey=dHhZa0xMQTJuR0ZCZWxoV2JSTG… At present, it does not seem that this will be done in time to release the report in 2010. However, delaying until January will give us time to improve the report. Please let me know if you have suggestions about how to improve the report, or if you would like to contribute more directly (i.e., by joining the project and doing some research and writing). By way of fair warning, currently this is a "TDWG phylogenetic standards interest group" project, but if there is not enough energy in our interest group to finish this in a timely manner-- and so far there isn't-- I'm inclined to peddle this project more widely to get collaborators. Thanks for your time, Arlin ------- Arlin Stoltzfus (arlin(a)umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org

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