GMOD

GMOD is a collection of interopable open source software components for visualizing, annotating, and managing biological data. This workshop introduces several GMOD components that are particularly useful with genomic data: MAKER, a genome anotation pipeline; Galaxy, a genome analysis workflow and publishing; JBrowse, a next generation genome viewer; Tripal, a web database construction toolkit; and GBrowse_syn, a generic synteny viewer. The goal of these sessions is to give attendees an idea of how to use GMOD tools to manage, analyze, and visualize their data. Sessions are aimed at biologists who have or soon will have genomic data. All sessions are Beginner to Intermediate. No prior knowledge of the tools is required. None of the sessions are hands-on.
Date: Wednesday, January 16, 2013
Time: 10:20 AM-5:00 PM
Room: Golden West
Organizer:
Scott Cain
10:20 AM
Introduction


PDF file
11:00 AM
W380
GMOD: A User's Perspective
Christine G. Elsik, Division of Animal Sciences, University of Missouri

PDF file
11:40 AM
W381
MAKER
Michael S. Campbell, University of Utah

PDF file
12:20 PM
W382
Tripal: a Toolkit for Construction of Genomic and Genetic Websites Using Chado and Drupal
Stephen P. Ficklin, Washington State University; Lacey-Anne Sanderson, University of Saskatchewan; Chun-Huai Cheng, Washington State University; Sook Jung, Washington State University; Kirstin Bett, University of Saskatchewan; Dorrie Main, Washington State University

PDF file
1:00 PM
Lunch


2:00 PM
W383
GBrowse_syn
Sheldon McKay, Dolan DNA Learning Center, Cold Spring Harbor Laboratory

2:40 PM
W384
JBrowse: A Next-Generation Genome Browser
Scott Cain, Ontario Institute for Cancer Research; Robert Buels, University of California, Berkeley

3:20 PM
Break


3:35 PM
W385
WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation
Ed Lee, Lawrence Berkeley National Laboratory; Gregg A Helt, Lawrence Berkeley National Laboratory; Monica C. Munoz-Torres, Lawrence Berkeley National Laboratory; Suzanna E. Lewis, Lawrence Berkeley National Laboratory; Justin Reese, Division of Animal Sciences, University of Missouri; Christopher Childers, Division of Animal Sciences, University of Missouri; Christine G. Elsik, Division of Animal Sciences, University of Missouri; Robert Buels, University of California, Berkeley; Ian Holmes, University of California, Berkeley

PDF file
4:15 PM
W386
Galaxy
Jennifer Hillman-Jackson, Pennsylvania State University

PDF file
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