2012 GMOD Summer School

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

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GMOD 2012 Summer School wiki

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

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: Apollo • MAKER • GBrowse • Chado • JBrowse • GBrowse_syn • Tripal • GFF3 • Galaxy • SOBA
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
Barry Moore	MAKER	University of Utah
Ed Lee	Apollo	Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay	GBrowse_syn, GBrowse	iPlant Collaborative, CSHL
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

Getting from Duke Tower to NESCent

While there is a shuttle mentioned below that you can take to and from Duke Tower, I will be walking to NESCent in the morning. Since we have a start time of 8:30, I was planning on leaving Duke Tower promptly at 8:00. For anybody who would like to walk with me, we'll meet in the courtyard by the tower and walk from there. On Monday morning, I'll be wearing my GMOD shirt, so I'll be easy to recognize.

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.”