PAG 2013 Workshop

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Gramene Project Workshop
Event Info
PAG 2013
Tuesday, 15 January 2013, 3:50 PM - 6:00 PM
Town & Country Hotel, California Room
Marcela Karey Monaco & Doreen Ware

Workshop Agenda

Click HERE for slides and videorecordings for the talks outlined below.

3:50 PM - Introduction to the Gramene Website

Ken Youens-Clark, Cold Spring Harbor Laboratory

4:10 PM - Plant Reactome

Palitha Dharmawardhana & Justin Preece, Oregon State University

4:40 PM - Plant Pathways & Gene Expression Analysis in Gramene

Sushma Naithani & Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University

5:10 PM - Browsing and Comparing Genomes Using the Gramene Ensembl Browser

Joshua Stein, Cold Spring Harbor Laboratory

5:30 PM - Analyzing the Barley genome

Paul J. Kersey, EMBL-EBI; Dan Bolser, EMBL-EBI; Arnaud Kerhornou, EMBL-EBI; Chuang Kee Ong, EMBL-EBI

About the workshop

The Gramene database ( 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.

Workshop material

Please read these important instructions:

Internet Access

High speed internet access will be available in the PAG Computer Room, and in the conference/registration area. There will be a hands-on portion of the workshop as the network connection allows. We will provide hand outs and post lectures and exercises in this page.

Workshop Exercises

Gene Expression Exercises

Gramene FTP site

Annotation Exercises

File:Gramene gene exercise 1.doc

File:Gramene gene exercise 2.doc

File:Gramene adding data track exercise 3.doc

Annotation Exercise Data


The Gramene Project is a collaboration between Cold Spring Harbor Laboratory (CSHL), Oregon State University (OSU), the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL - EBI), the Ontario Cancer Research Institute (OCIR), and the American Society of Plant Biologists (ASPB).

The Gramene Project is funded by the NSF award IOS:1127112 (IPGA: Gramene - Exploring Function through Comparative Genomics and Network Analysis). Partial support comes from the USDA and USDA-ARS.