PhylotasticiEvoBio

instructions

from the email and web site:

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 revised deadline for submission is April 9, 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

The abstract should be uploaded as a file in Portable Document Format (PDF, strongly preferred) or plain text format. The uploaded document should include title, authors, author affiliations, and references as applicable.

title

Making the Tree of Life Phylotastic!

contributors

(add your name and affiliation here in alphabetical order)

• Karen Cranston (karen.cranston@nescent.org, National Evolutionary Synthesis Center, 2024 W. Main St, A200, Durham, NC, 27705)
• Luke J. Harmon (lukeh@uidaho.edu, University of Idaho, Department of Biological Sciences, Campus Box 3051, Moscow, ID 83844)
• Enrico Pontelli (epontell@cs.nmsu.edu, New Mexico State University, Department of Computer Science, Box 30001, MSC CS, Las Cruces, NM 88003)
• Brian Sidlauskas (brian.sidlauskas@oregonstate.edu, Oregon State University, Department of Fisheries and Wildlife, 104 Nash Hall, Corvallis, OR, 97331)
• Arlin Stoltzfus (arlin@umd.edu; NIST and IBBR, 9600 Gudelsky Drive, Rockville, MD 20850)
• Rutger Vos (NCB Naturalis)

abstract

Phylogenies provide a central conceptual framework for comparative analysis in evolution and ecology, but only rarely do researchers reuse and share them. In fact, the vast majority of published phylogenies are unavailable in a computable format (e.g., because they are published simply as images), and few tools exist to facilitate reuse of phylogenies by the broader community. What new biological insights would result if any researcher or educator could obtain a current phylogeny linking any given set of taxa?

The Phylotastic project aims to develop an open architecture providing this functionality, addressing a community need for the functionality of Phylomatic (an installable package that offers pruning and grafting of an angiosperm megatree), but implemented as a set of web services providing access to all available megatrees. The Phylotastic project will use available megatrees in the design and implementation of a software system that provides the operations of pruning, grafting, name-reconciliation, and so on, that are necessary to leverage these megatrees, making the Tree of Life accessible to researchers. The main challenge of the project is to develop this “back-end” functionality. However, in order to show the potential of such a system, and to inspire others to add to the open framework as which Phylotastic is designed, the project also aims to create a few "front-end" tools that create mash-ups and leverage existing visualization tools.

This project is being organized by NESCent's HIP (Hackathons, Interoperability, Phylogenetics) working group, which aims to use hackathons to augment an emerging network of interoperable informatics resources in evolutionary science. The Phylotastic hackathon is the first of 3 hackathons planned by HIP. While previous NESCent hackathons used Open Space principles to facilitate multiple participant-initiated projects, the HIP leadership team designed the Phylotastic hackathon so that all participants would be working towards a coordinated solution to a single problem. Using an open call for participation, the leadership team recruited 19 highly qualified applicants to build Phylotastic at NESCent, in the week of June 4 to 8, 2012. A satellite hackathon with a half-dozen additional participants was organized at the University of Idaho.

This talk will describe both the process and the products of the Phylotastic project. Key elements of the process include how the community need for Phylotastic was identified, how the organizers recruited participants, and how the participants collaborated before and during the event. The key products to be described will be use-case examples and visualizations illustrating how research scientists can leverage available megatrees.