Using Gramene: A genomics and genetics resource for rice and other grasses.

Tuesday - January 16, 2006, 3:50 pm - 6:00 pm

There is an enormous amount of scientific information available on plant genetics, but accessing that information is not as easy at it may seem at first. This workshop will review the available datasets at Gramene and provide in-depth hands-on experience with using Gramene tools. Attendees will learn about the types of data available at Gramene (www.gramene.org), get tips on navigating the website, and use the database and tools to find data for their own projects.

Organizers:

Organizers: Claire Hebbard, Immanuel Yap, Gramene

Audience:

This workshop is geared for the beginning or intermediate cereal researcher or breeder who may or may not be familiar with Gramene. Attendees may also wish to bring their own data to work with in the workshop.

Agenda

In this workshop you will have the opportunity to:

Get an overview of basic Gramene website navigation, datasets, and query tools, including the new Diversity and the new Pathways datasets.
Get hands-on experience using Gramene, including:

Working with maps and graphical displays:

Use the Ensembl genome browser to locate and display markers, ESTs, gene models, and other features identified on the rice, maize, and arabidopsis genomes.
Use the CMap comparative map viewer to view mapped genes, markers, QTL and clones on various types of genetic, physical, and sequence maps from different cereal crops.
Compare maps and examine co-linearity between species.

Researching genomic detailed information for the grasses:

Locate a marker based upon name, type or species; and view its information.
Learn which trait is associated with a QTL.
Learn about genes and alleles associated with important phenotypes and functions.
Determine structured controlled vocabularies for plant structure, growth stages, traits, function, process, cellular component, environment and taxonomy.
Search for grain citations; find articles about genes, proteins, QTL, markers, or ontologies.
Determine a protein's location, function, and protein family.
Fine-tune search parameters.

Working with sequences:

Find a protein and its sequence.
Search for sequence similarity matches.

Learn about Gramene tutorials and help docs.
Get assistance on applying Gramene resources to your research.
Learn how to contribute to the database.
Learn about upcoming changes anticipated in the database.

Learn how to contribute to the database.

Gramene is a curated, open-source, web-accessible data resource for comparative genome analysis in the grasses, with a focus on rice. The database provides agricultural researchers and plant breeders with invaluable biological and genomic information on rice and other grasses. Gramene's web interface provides information on genetic and physical maps, sequences, genes, proteins, genetic markers, mutants, QTLs, controlled vocabularies and scientific citations, and provides displays and tools that integrate these various types of information so the user may visually make comparisons between the genomes of grass species. Gramene is accessed by researchers in over 100 countries around the world.

The database and the curated datasets are freely available for local use and installation. Quarterly releases provide researchers with up-to-date and new information and tools. There are many opportunities for seeking assistance on using the database, including help documents, FAQ's, tutorials, exercises, a mailing list, and a "feedback" button.

The Gramene project (www.gramene.org) is a collaborative effort between the Cold Spring Harbor Laboratory (www.cshl.edu), the Department of Plant Breeding and Genetics at Cornell University (http://plbrgen.cals.cornell.edu/) and various national and international projects dedicated to cereal genomics and genetics research.

Created on ... November 8, 2006