Difference between revisions of "2009 GMOD Summer School - Americas"
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! rowspan="7" style="background-color: #ffffaa" | Saturday<br />July 18 | ! rowspan="7" style="background-color: #ffffaa" | Saturday<br />July 18 | ||
! style="background-color: #ffffbb" | 8:45am | ! style="background-color: #ffffbb" | 8:45am | ||
− | | style="background-color: #ffffcc" align="center" |'''[[GBrowse]] I'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon | + | | style="background-color: #ffffcc" align="center" |'''[[GBrowse]] I'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]<br /> |
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! style="background-color: #ffffbb" | 12:30pm | ! style="background-color: #ffffbb" | 12:30pm | ||
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! style="background-color: #ffffbb" | 1:30pm | ! style="background-color: #ffffbb" | 1:30pm | ||
− | | style="background-color: #ffffcc" align="center" |'''[[GBrowse]] II'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon | + | | style="background-color: #ffffcc" align="center" |'''[[GBrowse]] II'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]] |
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! style="background-color: #ffffbb" | 2:30pm | ! style="background-color: #ffffbb" | 2:30pm | ||
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! rowspan="5" style="background-color: #ffccaa" | Sunday<br />July 19 | ! rowspan="5" style="background-color: #ffccaa" | Sunday<br />July 19 | ||
! style="background-color: #ffddcc" | 8:45am | ! style="background-color: #ffddcc" | 8:45am | ||
− | | style="background-color: #ffeedd" align="center" |'''[[GBrowse_syn]]'''<br />[[User:Mckays|Sheldon | + | | style="background-color: #ffeedd" align="center" |'''[[GBrowse_syn]]'''<br />[[User:Mckays|Sheldon McKay]] |
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! style="background-color: #ffddcc" | 1:30pm | ! style="background-color: #ffddcc" | 1:30pm | ||
− | | style="background-color: #ffeedd" align="center" |'''[[User:Sficklin#Tripal|Tripal]]'''<br />[[User:sficklin|Stephen Ficklin]] | + | | style="background-color: #ffeedd" align="center" |'''[[User:Sficklin#Tripal|Tripal]]'''<br />[[User:sficklin|Stephen Ficklin]]<br />Tripal is a web front end to [[Chado]] databases built on [http://www.drupal.org/ Drupal]. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration. |
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! style="background-color: #ffddcc" | 6:00pm | ! style="background-color: #ffddcc" | 6:00pm | ||
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| [http://www.genome.clemson.edu/ Clemson University Genomics Institute] | | [http://www.genome.clemson.edu/ Clemson University Genomics Institute] | ||
|- | |- | ||
− | | Ed Lee | + | | [[User:Elee|Ed Lee]] |
| Lead [[Apollo]] developer | | Lead [[Apollo]] developer | ||
| [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)] | | [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)] | ||
|- | |- | ||
− | | [[User:Mckays|Sheldon | + | | [[User:Mckays|Sheldon McKay]] |
| Lead [[GBrowse_syn]] developer, [[GBrowse]] developer | | Lead [[GBrowse_syn]] developer, [[GBrowse]] developer | ||
| [http://cshl.edu Cold Spring Harbor Laboratory] | | [http://cshl.edu Cold Spring Harbor Laboratory] |
Revision as of 03:43, 13 March 2009
2009 GMOD Summer School - Americas 16-19 July, 2009 NESCent Durham, NC, USA |
__NOTITLE__
The 2009 GMOD Summer School - Americas will be held 16-19 July at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like the 2008 GMOD Summer School, this course will focus on installing, configuring and integrating popular GMOD Components.
Another GMOD Summer School is being offered in Oxford, UK in August, as part of the GMOD Europe 2009 week.
Template:2009SummerSchoolApplicationBlurb
Contents
Draft 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.
Date | Time | Session |
---|---|---|
Thursday July 16 |
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 Mark Yandell or Barry Moore | |
4:30pm | Social Hour w/ NESCent Staff and then Dinner on your own | |
6:30pm | MAKER II Mark Yandell or Barry Moore | |
7:30pm | JBrowse Scott Cain or Dave Clements JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse. | |
9:00pm | Day ends | |
Friday July 17 |
8:45am | Chado I Scott Cain, Joshua Orvis, and Dave Clements |
12:30pm | Lunch on your own | |
1:30pm | Chado II Scott Cain, Joshua Orvis, and Dave Clements | |
3:00pm | Apollo I Ed Lee Overview, basic installation, basic configuration, reading/writing data, and remote analyses. | |
5:30pm | Dinner on your own | |
7:00pm | Apollo II Ed Lee Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance. | |
9:00pm | Day ends | |
Saturday July 18 |
8:45am | GBrowse I Scott Cain and Sheldon McKay |
12:30pm | Lunch on your own | |
1:30pm | GBrowse II Scott Cain and Sheldon McKay | |
2:30pm | BioMart Junjun Zhang Introduction; exploring over 20 public databases through BioMart central portal; system installation; accessing BioMart server via API, webservice and DAS; configuration of BioMart server including federation; demonstration of creating data mart. | |
6:00pm | Dinner on your own | |
7:30pm | Open Discussion and User Presentations Everyone This optional 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. | |
9:00pm | Day ends | |
Sunday July 19 |
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 |
Tentative Instructors
Instructor | GMOD Affiliation | Affiliation |
---|---|---|
Scott Cain | GMOD Project Coordinator | Ontario Institute for Cancer Research |
Dave Clements | GMOD Help Desk | National Evolutionary Synthesis Center (NESCent) |
Stephen Ficklin | Lead Tripal developer | Clemson University Genomics Institute |
Ed Lee | Lead Apollo developer | Berkeley Bioinformatics Open-source Projects (BBOP) |
Sheldon McKay | Lead GBrowse_syn developer, GBrowse developer | Cold Spring Harbor Laboratory |
Joshua Orvis | Lead Ergatis developer and power Chado user | Institute for Genome Sciences |
Mark Yandell (or Barry Moore) | MAKER PI (or developer) | University of Utah |
Junjun Zhang | BioMart developer | Ontario Institute for Cancer Research |
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 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.
Getting a basic GBrowse up and running on your system will be assigned as homework to be done prior to the course's start.
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
- 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.
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
- Mac OS 10.5 (Leopard) and Boot Camp
The Leopard release of Mac OS (10.5) includes Boot Camp, a feature that allows you to boot your Mac into another operating system, including Windows or Linux. From there you can install the VMware player for your OS.*
* Apple tells you that you can partition your disk drive at any time using Boot Camp. In practice, this appears to only work easily when you first get your system.
Applications
Template:2009SummerSchoolApplicationStatus
Cost
This course will be free thanks to NIH grant 1R01HG004483-01 under Ian Holmes, and to the grants of the individual instructors.
Participants are responsible for their own travel, lodging, and living expenses. Some travel scholarships are available for participants from underrepresented groups. Please indicate on your application if you would like to be considered for this option.
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 $79/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.
Some meals are included in the summer school. For meals that aren't, NESCent is adjacent to Durham's 9th Street District, which offers many dining options.
“This was a very smooth course. All of the programs were focused, and well prepared. The instructions on the wiki were clear and the support from the instructors was very lively.” | “Great job everybody!” “Overall an exceptional experience!” |
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“Well done!” “Great job all around.” |
“I was very impressed by everyone involved in putting on the school. It was very apparent that they had gone the extra mile and really cared about the quality of the classes.” |
“Thank you very much for this first GMOD Summer School.” | “The course was what I was expecting and more.” |