Difference between revisions of "2012 GMOD Summer School"

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Revision as of 23:04, 25 June 2012

Snazzy logo here!
2012 GMOD Summer School, August 24-29, 2012

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Introduction

The GMOD Summer School is a five day course that covers the use of several widely used GMOD components in the context of a organism or clade database. The course is taught by members of the projects' development teams. Applications are competitive, since we generally receive many more applications that we have slots.

Application

The application is available as a Google form. The deadline is July 9.

Schedule

Friday
August 23
7:30am-9:00pm Optional introductory session
Saturday
August 25
8:30am-6:00pm
7:30pm-9pm
2012 GMOD Summer School
A 5 day hands-on course on GMOD Component installation, configuration, and usage. The course will cover these components in detail:

ApolloMAKERGBrowseChadoInterMineJBrowseGBrowse_synTripalGFF3GalaxySOBA

Sunday
August 26
8:30am-6:00pm
7:30pm-9pm
Monday
August 27
8:30am-6:00pm
7:30pm-9pm
Tuesday
August 28
8:30am-6:00pm
7:30pm-9pm
Friday
August 29
8:30am-6:30pm

Most sessions will last half a day. Each night the instructors for that day's topics will be available to answer questions and help participants use the tools with their data.

Instructors

Sessions are taught by experienced component developers and GMOD project staff:

Instructor GMOD Affiliation Affiliation
Scott Cain GMOD Project Coordinator; Chado, GBrowse Ontario Institute for Cancer Research
Dave Clements Galaxy Galaxy, Emory University
Stephen Ficklin Tripal Washington State University
Alex Kalderimis InterMine FlyMine
Barry Moore MAKER University of Utah
Ed Lee Apollo Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay GBrowse_syn, GBrowse iPlant Collaborative
Robert Buels JBrowse University of California, Berkeley

Prerequisites

The course requires a minimal level of Linux systems administration knowledge (see Computing Requirements). By "a minimal level of Linux systems administration knowledge" we mean that participants should be

  1. Comfortable with the Linux command line interface, and
  2. Comfortable installing packages under Linux.

A good benchmark for this level of knowledge is that you should be able to get a basic GBrowse installation (that is, GBrowse without MySQL) up and running with the example GBrowse data. This also requires installing Apache, and BioPerl and all its dependencies.

System Requirements

Previous incarnations of this course used VMware images. The 2012 instance will use the Amazon Web Service (aka, the cloud). The only software required to be on students' laptops is a ssh client (like putty for Windows, or the builtin ssh client in the Mac OS), a web browser (preferably up to date (and avoiding Internet Explorer is a good idea)), and possibly (depending on what we do) Java.

Costs

There will be a tuition of $300 charged for the course to cover expenses, primarily instructor travel expenses.

Travel, Lodging and Meals

Suggestions for travel into the Durham, NC area will be forthcoming, as well as a suggested hotel.