Gramene Project

The Gramene database (http://www.gramene.org) is a curated, open-source, web-accessible data resource for comparative genome analysis in plants. The database provides agricultural researchers and plant breeders with very valuable biological and genomic information on several crops and model plant species. Gramene's web interface provides information on genetic and physical maps, sequences, genes, RNA-seq/microarray expression data, proteins, genetic markers, mutants, QTLs, controlled vocabularies and scientific citations, genetic variation data, biological pathways, and provides displays and tools that integrate these various types of information, so that the user may visually make comparisons between the diverse genomes. This workshop will review the available data sets at Gramene and provide demonstration of how to use our tools to answer various biological and research questions. Attendees will learn about the types of data available at Gramene, get tips on navigating the website, and use the database and tools to find data for their own projects. The workshop will feature a demo session on barley, a uniquely organized genome, as well as introduce the new Plant Reactome, a platform for the comparative analysis of plant metabolic and regulatory networks. The workshop is geared for the community of plant researchers and breeders; beginners, as well as frequent users of the Gramene database alike. Attendees may also wish to bring their own data to work with during the workshop.
Date: Tuesday, January 14, 2014
Time: 1:30 PM-3:40 PM
Room: California
Organizers:
Marcela Karey Monaco and Doreen Ware
1:30 PM
Introduction to the Gramene Website
Ken Youens-Clark, Cold Spring Harbor Laboratory

1:50 PM
Plant Reactome
Vindya Amarasinghe, Dept. of Botany & Plant Pathology, Oregon State University; Justin Preece, Dept. of Botany & Plant Pathology, Oregon State University; Palitha Dharmawardhana, Dept. of Botany & Plant Pathology, Oregon State University; Guanming Wu, Ontario Institute for Cancer Research; Sushma Naithani, Dept. of Botany & Plant Pathology, Oregon State University; Peter D'Eustachio, NYU School of Medicine; Marcela Karey Monaco, Cold Spring Harbor Laboratory; Dylan Beorchia, Oregon State University; Alex Roos, Oregon State University; Kindra Amoss, Oregon State University; David Croft, European Bioinformatics Institute; Robin Haw, Ontario Institute for Cancer Research; Henning Hermjakob, European Bioinformatics Institute; Lincoln Stein, Ontario Institute for Cancer Research; Doreen Ware, Cold Spring Harbor Laboratory, Cold Spring Harbor; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University

2:10 PM
Gramene's Plant Pathways Databases & Analysis of User-Defined Expression Data Sets
Sushma Naithani, Dept. of Botany & Plant Pathology, Oregon State University; Vindya Amarasinghe, Dept. of Botany & Plant Pathology, Oregon State University; Palitha Dharmawardhana, Dept. of Botany & Plant Pathology, Oregon State University; Justin Preece, Dept. of Botany & Plant Pathology, Oregon State University; Doreen Ware, USDA ARS NAA Robert W. Holley Center; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University

2:30 PM
Browsing and Comparing Genomes Using the Gramene Ensembl Browser
Joshua Stein, Cold Spring Harbor Laboratory; Sharon Wei, Cold Spring Harbor Laboratory; Marcela Karey Monaco, Cold Spring Harbor Laboratory; Ken Youens-Clark, Cold Spring Harbor Laboratory; Andrew Olson, Cold Spring Harbor Laboratory; Sunita Kumari, Cold Spring Harbor Laboratory; Jerry Lu, Cold Spring Harbor Laboratory; Jim Thomason, Cold Spring Harbor Laboratory; Dan Bolser, EMBL -The European Bioinformatics Institute; Arnaud Kerhornou, EMBL-The European Bioinformatics Institute; Paul J. Kersey, EMBL - The European Bioninformatics Institute; Doreen Ware, USDA ARS NAA Robert W. Holley Center

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