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

Workshop Agenda

3:50 PM W387 Introduction to the Gramene Website Ken Youens-Clark, Cold Spring Harbor Laboratory

4:10 PM W388 Plant Reactome Palitha Dharmawardhana & Justin Preece, Oregon State University

4:40 PM W389 Plant Pathways & Gene Expression Analysis in Gramene Sushma Naithani & Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University

5:10 PM W390 Browsing and Comparing Genomes Using the Gramene Ensembl Browser Joshua Stein, Cold Spring Harbor Laboratory

5:30 PM W391 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 (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.

Workshop material

Please read these important instructions:

Computers

There will be a hands-on portion of the workshop as the network connection allows. You are encouraged to bring your laptop to follow along.

Internet Access

We will provide FREE WIRELESS INTERNET for the duration of the workshop to first 100 connections. If you already have access to Internet through another arrangement, please feel free to use that; however, we will not reimburse you for buying access to the Internet.

RECOMMENDATION: Make sure the computer you are bringing has a wireless network card

Software

TBA

Annotation Exercises

PAG 2013 Workshop

Contents

Workshop Agenda

About the workshop

Workshop material

Computers

Internet Access

Software

Annotation Exercises

Exercise #1

Exercise #2

Exercise #3

Exercise Data

Acknowledgments

Sponsored by

Navigation menu

Views

Personal tools

Navigation

Search

Tools