Working Group

Evolutionary informatics: supporting interoperability in evolutionary analysis

PI(s): Arlin Stoltzfus (National Institute of Standards and Technology)
Rutger Vos (University of British Columbia)
Start Date: 1-Sep-2006
End Date: 31-Aug-2008
Keywords: database, genomics, phylogenetics, software, comparative methods

The continuing growth of bioinformatics and genomics presents an opportunity for expanding the application of evolutionary methods, with respect to both the amount and the variety of systematic comparative data. Though evolutionary biologists have developed powerful tools for inferring phylogenies, detecting selection, and so on, integrating evolutionary methodology into workflows in bioinformatics does not depend so much on the power of analysis tools as it does on a well developed informatics infrastructure: software and standards for data exchange, visualization, input-and-output, editing, control, and storage-and-retrieval. We propose a working group to facilitate (directly and indirectly) the development of this infrastructure. Through a series of four meetings, each with presentations, discussion, and actual software development, the working group will build on the foundation provided by current analysis tools and available standards. The working group will gather data sets that represent canonical use-cases; remedy inconsistencies in current NEXUS implementations, and resolve ambiguities; develop translators between NEXUS and other data formats; develop a back-end storage schema; and translate actual content from existing databases of sequence family data into a standard form. The working group will develop and implement revisions to the NEXUS standard (perhaps including an XML replacement), and will lay the ground-work for a new generation of standards by identifying different data models used in different types of evolutionary analyses, and by documenting use-cases that fall beyond the reach of current standards.

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