Difference between revisions of "2012 GMOD Summer School"

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Revision as of 20:20, 6 August 2012

2012SummerSchool400.png
2012 GMOD Summer School
August 24-29, 2012
NESCent
Durham, NC, USA

__NOTITLE__

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 period is now closed, though if you would like to be placed on a waiting list, you can still fill it out. The application is available as a Google form. The deadline is July 9.

Schedule

Friday
August 24
7:30pm-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
Wednesday
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 Project, 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
Daniel Ence MAKER University of Utah

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.

Hotel

NESCent has reserved a block of rooms at Duke Tower for participants. Mention NESCent/GMOD when booking your room. The rooms are suite-style, with a separate living room and kitchen. Some rooms have two double beds, so participants could share a room to reduce costs. There is a shuttle between NESCent and Duke Tower ($2.00 per room; per trip), or the hotel is a 25 minute walk through the lovely Trinity Park neighborhood and East Campus (I will be walking, since it is a short walk and quite pleasant--Scott). You are, of course, free to choose alternate accommodations in Durham, although most less expensive options may require a car for transportation.

Some information from the hotel:

  • Check in time is 3:00pm and check out time is 11am.
  • If you arrive after hours, you will check in with the guard by paging him from the telephone located near the office door. There are posted instructions for the paging system. The guard will meet you at the office and give you your key.
  • Please be sure to bring all personal toiletries, we supply only small bars of soap. There is no hairdryer in the unit.
  • There is a full kitchen including a coffee maker and filters, but we do not supply coffee.
  • There is wired high-speed internet access in all units at no charge. You may borrow an Ethernet cable from the business office.
  • There is a coin-operated laundry here on the property. You may exchange dollars for quarters with us in the office.
  • The Tower Cafe is open For Continental Breakfast - $5.00 Per Adult.

Feedback

Previous GMOD Schools Feedback
“I would whole-heartedly recommend this course to others! It was extremely informative.”
“Overall it was exceptional.”
“Great job!”
“Overall this course was essential for me to be able to go forward and implement the GMOD tools.”
“Instructors and participants were all bright, articulate, and interesting. The days were long but the pace was reasonable. Overall, this was one of the best ongoing education experiences I have ever had.”
“The speakers were really good.”
  
“It was an amazing course.”
“The amount of information presented was terrific and the online course material was very well done. I learned a lot!”
“It was definitely a very informative course.”
“This class held me riveted for 4 days straight.”
“Really good organization and atmosphere. I loved the use of the wiki and the idea of building up a community. You are doing a great job!”
“Having the wiki ROCKS.”