March 2012 - tdwg-phylo - lists.tdwg.org

Call for student applications: PhyloSoC 2012
by Hilmar Lapp 24 Mar '12

24 Mar '12

*** Please disseminate widely at your local institutions, including *** *** posting to message and job boards, so that we reach as many *** *** students as possible *** Are you a student interested in evolutionary biology and open-source software development? PHYLOINFORMATICS SUMMER OF CODE 2012 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2012 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 receive a stipend from Google (and the coveted T-shirt upon completion!), and work from their home, or home institution, for the duration of the 3 month program. You will have the opportunity to collaborate with our enthusiastic mentor community, and will have at least one dedicated mentor to help you complete your project. We are particularly targeting students interested in both evolutionary biology and software development. Our website, above, lists potential projects. Projects include many programming languages (e.g. C/C++, Java, Perl, R) and cover subjects ranging from visualization to algorithm implementation to data interoperability. You don't need to be an expert in either evolutionary biology or software development - find a project idea that interests you, and we can work with you to develop a proposal that fits your skills. We also welcome novel project ideas apart from those already on the list. INTERESTED? Contact us 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. Admission is competitive, and we want plenty of time to work with you to develop a great project proposal. TO APPLY: Apply online at the Google Summer of Code website: http://www.google-melange.com/gsoc/homepage/google/gsoc2012 where you will also find GSoC program rules and eligibility requirements. The 14-day application period for students opens on Monday March 26th and runs through Friday, April 6th, 2012. Google Summer of Code FAQ: http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc20… Karen Cranston and Jim Proctor National Evolutionary Synthesis Center http://nescent.org

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Call for Challenge entries for conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 21 Mar '12

21 Mar '12

Many trees enter. Fresh analysis ensues. New insights emerge. The conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is again holding a Challenge competition in 2012, on the theme "Synthesizing Phylogenies". Somewhere, buried in large sets of trees, lies a stunning new revelation, a baffling discovery, the answer to a longstanding controversy, or simply something not obvious to the naked eye. The mission of the 2012 iEvoBio challenge is to find those revelations, discoveries and answers within your own data and/or within one of the datasets provided by the challenge. What new scientifically interesting results can you pull from these trees, using any combination of techniques at your disposal? Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Selected candidates will make short oral presentations to demonstrate their work in a "Challenge session" at the conference, and if suitable will automatically be entered into the Software Bazaar track of the conference. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. Alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The Geneious Challenge has the same open and closing dates as the iEvoBio Challenge. See http://ievobio.org/geneious_challenge.html for more information. Separate from iEvoBio, the Encyclopedia of Life (EOL) is leading a Phylogenetic Tree challenge to encourage not only the development of large phylogenies, but their practical use. Together with the Global Names project they will choose two winning entries: one for the best large tree and one for the most promising but not necessarily large tree -- both in Darwin Core Archive format suitable for use in major biodiversity websites such as EOL. The two winners will receive paid trips to the 2012 iEvoBio conference. See http://eol.org/info/tree_challenge for more information. 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 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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Call for Lightning Talks now open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 13 Mar '12

13 Mar '12

The Call for Lightning Talks is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions. Lightning talks are short presentations of 5 minutes. They are ideal for drawing the attention of the audience to new developments, tools, and resources, or to subsequent events where more in-depth information can be obtained. Please also see our FAQ for more information (http://ievobio.org/faq.html#lightning). Lightning talks will be part of the more interactive program elements on both conference days. 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 should be 1 page long at most and include a title, a list of contributors, and an abstract. The abstract should provide an overview of the talk's subject. Reviewers will judge whether a submission is within scope of the conference (see above). If applicable, the abstract must also state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. Review and acceptance of lightning talks will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (July 10), but see below. Further instructions for submission are at the following URL: http://ievobio.org/ocs2/index.php/ievobio/2012/schedConf/cfp Please make sure to choose the Lightning Talks track for your submission. Note that the number of lightning talk slots is finite and that therefore the track may fill up early. We cannot accept lightning talks until the open-source requirements are met, and so waiting with that until the deadline risks that the track is full by that time. We ask all submitters of lightning talks to be willing to also serve as reviewers of such, as described above. Lightning talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (open until April 2), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries remains open (see http://ievobio.org/challenge.html). The calls for contribution to the other two sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. In addition, 2012 iEvoBio sponsor Biomatters Ltd will be running the Geneious Challenge alongside this year’s iEvoBio Challenge, see http://ievobio.org/geneious_challenge.html for more information. More details about the 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 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 and Florida Museum of Natural History 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 (*) 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.

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Applications open for iEvoBio 2012 Travel Awards
by Hilmar Lapp 12 Mar '12

12 Mar '12

The 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is offering limited funds for travel expenses for the 2012 iEvoBio meeting in Ottawa, Canada. Preference will be given to participants lacking sources of funding for meeting attendance, such as graduate students, emerging professionals, and participants from underrepresented groups and countries. Please explain in an attached document the need for funding, the benefit that attending iEvoBio will afford you and how you will contribute to the meeting (max 350 words). We are looking for do-ers! A brief letter of support from your advisor, supervisor, or professional mentor should be submitted to the organizing committee (electronically), together with the application headed by the information below, to travelaward(a)ievobio.org by the deadline of 15 April 2012. Participants are required to make all their own travel arrangements, including visas and lodging, if required. Application format: Name: Contact information (address/phone/email): Academic Institution: Role (student, researcher, etc.): Origination of travel (if different from home institution) and estimated travel expenses: Explain the benefit that attending iEvoBio will afford you and what you will bring to the meeting (350 words or less):

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Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 03 Mar '12

03 Mar '12

The Call for Abstracts for full talks is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. See below for instructions. Accepted talks will be 15 minutes in length and will be presented during the full talk session of the conference. Because the number of program slots for full talks is limited, some talks may be moved to the Lightning Talk session (5 minutes in length). 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 should be 1 page long at most and include a title, a list of contributors, and an abstract. The abstract should provide an overview of the talk's subject, and give enough detail to allow reviewers to decide whether the submission merits a full talk, or whether it should be moved to a Lightning Talk session. 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 April 2, 2012. 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/ocs2/index.php/ievobio/2012/schedConf/cfp Full talks are one of the five kinds of contributed content that feature in iEvoBio. The other four 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 three sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. In addition, 2012 iEvoBio sponsor Biomatters Ltd will be running the Geneious Challenge alongside this year’s iEvoBio Challenge, see http://ievobio.org/geneious_challenge.html for more information. More details about the 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 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 and Florida Museum of Natural History 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 (*) 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 July 9, 2012, at the latest.

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iEvoBio conference, July 10-11, 2012
by Nico Cellinese 02 Mar '12

02 Mar '12

Dear All, The official website of iEvoBio 2012 is now open (www.ievobio.org). The 2 days conference will be held in conjunction with the annual Evolution meeting in Ottawa on the 10-11 July, 2012. Note that the program includes two exciting challenges and much more! We hope to see you in Canada! Cheers, NIco <><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Botany & Informatics Adjunct Assistant Professor, Department of Biology Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://cellinese.blogspot.com/

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