PAG 2013 Workshop
- 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
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 (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.
Please read these important instructions:
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.
Gene Expression Exercises
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.