W391 Tools and Resources in Gramene Diversity

Date: Tuesday, January 17, 2012
Time: 4:50 PM
Room: California
Jon Zhang , Cornell University, Ithaca, NY
Genevieve DeClerck , Cornell University/Gramene.org, Ithaca, NY
Athikkattuvalasu Karthikeyan , Cornel University, Wheeling, IL
Shuly Avraham , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Terry Casstevens , Cornell University, Apex, NC
Charles Chen , Cornell University, Ithaca, NY
Jer-Ming Chia , Cold Spring Harbor Labs, Cold Spring Harbor, NY
Ken Youens-Clark , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Aaron Chuah , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Paul Derwent , European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
Shiran Pasternak , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Liya Ren , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
William Spooner , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Joshua Stein , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Jim Thomason , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Qi Sun , Cornell University, Ithaca, NY
Sharon Wei , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Pankaj Jaiswal , Oregon State University, Corvallis, OR
Doreen Ware , Cold Spring Harbor Laboratory-USDA-ARS, Cold Spring Harbor, NY
Edward S. Buckler , USDA-ARS-Cornell University, Ithaca, NY
Susan McCouch , Cornell University, Ithaca, NY
With the increasing number of high-throughput sequencing technologies, a bottleneck has formed associating this data with phenotypic variation. The Gramene Diversity Module is designed to help overcome this bottleneck. Using Genomic Diversity and Phenotype Data Model (GDPDM;maizegenetics.net/gdpdm), this module is able to compress genotype data by several orders of magnitude facilitating integration and analysis of genotypic and phenotypic data. Currently, Diversity hosts a number of important variation datasets for rice, maize, Arabidopsis, sorghum, and wheat. In addition Diversity offers a set of tools to help the plant research community analyze this data including TASSEL, GWAS visualization tool (www.gramene.org/db/jshc2010), and phenotype query tool. Diversity is updated twice a year as part of the biannual Gramene release, the latest of which (Build 34) was in the Fall of 2011.