2010 GMOD Summer School - Americas
This page or section is under construction.
We expect this page to be done, and to start taking applications on January 29, 2010.
2010 GMOD Summer School - Americas 6-9 May, 2010 NESCent Durham, NC, USA |
__NOTITLE__
The 2010 GMOD Summer School - Americas will be held 6-9 May at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like previous GMOD Summer Schools, this course will focus on installing, configuring and integrating popular GMOD Components. Sessions will be taught by GMOD Component developers and GMOD staff. There is space in the course for 25 participants, and admission is competitive.
Applications
We are now accepting applications for this course. Admission to the course is competitive and is based on the application (especially the statement of interest) that is submitted with the application. Last year there were over 50 applications for the 25 slots. The application deadline is the end of Friday, February 19. Any applications received after February 19 will be automatically put on the waiting list. Applicants will be notified of admission status by February 26. |
Tentative Program
The program will feature 4 full days of hands-on training starting with an overview of GMOD, and then covering the installation, configuration, and administration of several popular GMOD Components.
The 2010 program will be very similar to what was offered in 2009. A few things will change, but the core will stay the same.
Date | Time | Session |
---|---|---|
Thursday May 6 |
8:45am | Introduction and Overview Scott Cain and Dave Clements Participant and instructor introductions, how the GMOD project works, what software tools are available in GMOD, how they interoperate, what resources are needed to get a GMOD installation up and running, and course overview |
10:25am | VMware and BioPerl Setup Everyone Get the GMOD Summer School VMware image up and running on your laptop, and then finish installation of BioPerl. | |
12:15pm | Lunch on your own | |
1:15pm | MAKER I Carson Holt MAKER overview, installation, and basic configuration for annotating genomic sequence | |
4:30pm | Social Hour w/ NESCent Staff and then Dinner on your own | |
6:30pm | MAKER II Carson Holt Advanced MAKER configuration, re-annotation options, and improving annotation quality | |
7:30pm | JBrowse Mitch Skinner JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse. | |
9:00pm | Day ends | |
Friday May 7 |
8:45am | GBrowse Scott Cain |
1:00pm | Lunch on your own | |
2:00pm | Galaxy Anton Nekrutenko and James Taylor Introduction; Installation and configuration of Galaxy; Defining your own tools; ... | |
6:00pm | Open Discussion and User Presentations Everyone This session is open to any and all questions you have on the GMOD Project, GMOD Components, and GMOD users. The instructors will come with their knowledge of GMOD and their opinions on the project's strengths, weaknesses, and future directions. Students will also have the opportunity to share work from their projects with the rest of the group. We expect this session to be lively. | |
7:30pm | Day ends | |
Saturday May 8 |
8:45am | Chado I Scott Cain and Dave Clements |
1:00pm | Lunch on your own | |
2:00pm | Chado II Scott Cain and Dave Clements | |
3:00pm | Apollo Ed Lee Overview, basic installation, basic configuration, reading/writing data, and remote analyses. Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance. | |
7:30pm | Day ends | |
Sunday May 9 |
8:45am | GBrowse_syn Sheldon McKay |
12:30pm | Lunch on your own | |
1:30pm | Tripal Stephen Ficklin Tripal is a web front end to Chado databases built on Drupal. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration. | |
6:00pm | Wrapup and Resources Dave Clements and Scott Cain | |
6:30pm | Summer School Ends |
Instructors
The tentative list of instructors includes
Instructor | GMOD Affiliation | Affiliation |
---|---|---|
Scott Cain | GMOD Project Coordinator; Chado, GBrowse | Ontario Institute for Cancer Research |
Dave Clements | GMOD Help Desk | National Evolutionary Synthesis Center (NESCent) |
Stephen Ficklin | Tripal | Clemson University Genomics Institute |
Carson Holt | MAKER | University of Utah |
Ed Lee | Apollo developer | Berkeley Bioinformatics Open-source Projects (BBOP) |
Sheldon McKay | GBrowse_syn, GBrowse | Cold Spring Harbor Laboratory |
Anton Nekrutenko | Galaxy | Penn State |
Mitch Skinner | JBrowse | University of California, Berkeley |
James Taylor | Galaxy | Emory University |
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
- Comfortable with the Linux command line interface, and
- 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
VMware | http://www.vmware.com}} | Participants are required to bring their own laptops, already capable of running a VMware system image. |
The course starts with getting a VMware image (built specifically for the course) up and running on your machine. We then build upon that image in each succeeding session.
- VMware on Windows and Linux
Windows | http://www.microsoft.com/}} | Linux}} | A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it. There are multiple versions. Be sure to download a version that can run on your laptop. |
- VMware on Mac OS X
Participants can also bring newer Macs with Intel processors. The Intel processor is a requirement for all the packages discussed below.
Apple | http://www.apple.com/macosx/}} | There is no free VMware player that runs directly under Mac OS X. However, there are several other options, all of which require an Intel Mac: |
- VMware Fusion
Fusion | http://www.vmware.com/products/fusion/}} | VMware Fusion ($80/corporate, $40/Academic) allows you to run VMware images (as well as Windows and Linux) under Mac OS. We recommend this option for Mac users. There is a fully functional, 30 day free trial version of VMware Fusion available for download. |
- VirtualBox
VirtualBox is free and open source, and runs on Intel Macs (and Windows, Linux and Solaris too). It claims to be capable of running VMware images, but we have not tested this with our images. |
Cost
This course is free thanks to NIH grant 1R01HG004483-01 under Ian Holmes, and to the grants of the individual instructors.
Travel, Lodging and Food
The course will be held at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. The closest airport is Raleigh-Durham International Airport (RDU), a 30 minute drive from NESCent.
Participants will be responsible for their own travel, lodging and some meal costs. We will offer a block of rooms in a local hotel at a discounted rate of (probably around $85/night, including tax). Participants can share a room to further reduce their costs. The hotel is within walking distance and also will have a free shuttle service to NESCent.
A light breakfast will be provided everyday. For other meals, NESCent is adjacent to Durham's 9th Street District, which offers many dining options, and a grocery store.