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The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem Nature Precedings
Todd Vision.
Here we describe the motivation and workings of Dryad, a digital repository for data underlying published articles in the biosciences, that grew out of a grassroots effort to support a joint data archiving policy adopted by a consortium of journals in ecology and evolutionary biology.
Tipo: Manuscript Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4595/version/1
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Comparative methods in R hackathon Nature Precedings
Brian O'Meara; Michael Alfaro; Charles Bell; Benjamin Bolker; Marguerite Butler; Peter Cowan; Damien de Vienne; Richard Desper; Joseph Felsenstein; Luke Harmon; Christoph Heibl; Andrew Hipp; Gene Hunt; Thibaut Jombart; Steve Kembel; Hilmar Lapp; Scott Loarie; Wayne Maddison; Peter Midford; David Orme; Emmanuel Paradis; Sam Price; Dan Rabosky; Brian Sidlauskas; Stacey Smith; Dave Swofford; Todd Vision; Peter Waddell; Amy Zanne; Derrick Zwickl.
The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative methods to understand the evolution of organismal traits and diversification. A hackathon was organized to bring together active R developers as well as end-users working on the integration of comparative phylogenetic methods within R to actively address issues of data exchange standards, code interoperability, usability, documentation quality, and the breadth of functionality for comparative methods available within R. Outcomes included a new base package for phylogenetic trees and data, a public wiki with tutorials and overviews of existing packages, code to allow Mesquite and R to interact, improvement of existing packages, and increased...
Tipo: Poster Palavras-chave: Ecology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2126/version/1
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Phenoscape: Ontologies for Large Multi-species Phenotype Datasets Nature Precedings
Peter Midford; Paula Mabee; Todd Vision; Hilmar Lapp; Jim Balhoff; Wasila Dahdul; Cartik Kothari; John Lundberg; Monte Westerfield.
The Phenoscape project is developing ontologies and tools to integrate morphological and genomic data to address comparative questions in evolutionary biology. We are currently curating 81 publications describing ~5000 phenotypic characters in 4,000 species of Ostariophysian fishes, and will be making our database of ontology-based annotations concurrently with this meeting via a web-based interface at "http://kb.phenoscape.org":http://kb.phenoscape.org.
Tipo: Poster Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3594/version/1
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