W970TreeGenes: Enabling Visualization and Analysis in Forest Tree Genomics
Date: Sunday, January 10, 2016
Time: 5:50 PM
Room: California
Emily Grau
,
University of Connecticut, Storrs, CT
Steven A Demurjian Jr
,
University of Connecticut, Storrs, CT
Hans Vasquez-Gross
,
University of California Davis, Davis, CA
Damian Gessler
,
University of Arizona, Tucson, AZ
Margaret Staton
,
University of Tennessee, Knoxville, Clemson, SC
Sook Jung
,
Washington State University, Pullman, WA
Alex Feltus
,
Genetics & Biochemistry, Clemson University, Clemson, SC
Dorrie Main
,
Washington State University, Pullman, WA
Stephen P. Ficklin
,
Washington State University, Pullman, WA
David Neale
,
Dept. Plant Sciences University of California Davis, Davis, CA
Jill Wegrzyn
,
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
The TreeGenes project is a collection of web-based resources designed to support the needs of the forest tree research community. These resources include an extensive curated database as well as custom tools to manage the flood of information resulting from high-throughput genomics projects. The goal is to capture raw data and metadata from sample collection through to the final analysis stage. TreeGenes allows users to track and manage next generation sequencing and genotyping studies, query and download datasets, and perform analysis through interfaces that connect directly to high performance computing resources.
The TreeGenes database holds genetic, phenotypic, and environmental data from over 1700 forest tree species. This data is delivered to the public through taxonomy views, literature searches, genetic maps (CMap), genome browsers (Gbrowse), and custom interfaces such as CartograTree. While much of the data is curated from external repositories, advanced integration of metadata supporting genotype:phenotype and genotype:environment association studies has been developed.
To enhance the utility of this resource, TreeGenes is currently is transitioning to Tripal. This transition will allow us to take advantage of features such as improved user management, data loaders, and standardized schemas provided through Drupal and Chado. Custom development will include a new Tripal module to streamline public submission of genetic association data, which will allow for greater flexibility and improved integration. We will also discuss the challenges and benefits of transitioning a mature database and website to Chado and Tripal.
