Difference between revisions of "2010 GMOD Summer School - Americas"

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| [[Image:2010SummerSchoolAmericas300.png|center]]
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| [[File:2010SummerSchoolAmericas300.png|center]]
| <span style="font-size: 200%; line-height: 120%"><b>2010 GMOD Summer School - Americas</b><br />6-9 May, 2010<br />[http://www.nescent.org/ NESCent]<br />Durham, NC, USA</span>
+
| <span style="font-size: 200%; line-height: 120%"><b>2010 GMOD Summer School - Americas</b><br />6-9 May, 2010<br />[http://www.nescent.org/ NESCent]<br />Durham, NC, USA</span><br />
 
|}
 
|}
 
</center>
 
</center>
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{{TocRight}}
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[[File:2010GMODSummerSchoolAmParticipants.jpg|center|500px]]
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The '''''2010 GMOD Summer School - Americas''''' was held 6-9 May at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina.  Like previous [[GMOD Summer School|GMOD Summer Schools]], this course focused on installing, configuring and integrating popular [[GMOD Components]].  Sessions were taught by GMOD Component developers and GMOD staff.  There was space in the course for 25 participants, and admission was competitive.
 
The '''''2010 GMOD Summer School - Americas''''' was held 6-9 May at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina.  Like previous [[GMOD Summer School|GMOD Summer Schools]], this course focused on installing, configuring and integrating popular [[GMOD Components]].  Sessions were taught by GMOD Component developers and GMOD staff.  There was space in the course for 25 participants, and admission was competitive.
  
<div class="emphasisbox">
+
: '''All of the sessions from this school have now been moved to this website, where they are available as [[Training and Outreach#Online Tutorials|Online Tutorials]].'''
At some point during June or July of 2010, the sessions from this year's course will be moved to this wiki, where they will become ''Tutorials''.  Until that happens, you can still access the tutorials from the 2009 courses.
+
 
</div>
+
  
 
== Applications ==
 
== Applications ==
 
'''The deadline for applying to the summer school has now passed.'''
 
'''The deadline for applying to the summer school has now passed.'''
  
== Tentative Program ==
+
== 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 program featured 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]].
 
+
''This schedule is subject to change. ''
+
  
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
|-
 
|-
! width="10%" style="background-color: #99ccff" | Date
 
 
! width="7%"  style="background-color: #99ccff" | Time
 
! width="7%"  style="background-color: #99ccff" | Time
! width="83%" style="background-color: #99ccff" | Session
+
! width="93%" style="background-color: #99ccff" | Session
 +
|-
 +
| colspan="2" |
 
|-
 
|-
| colspan="3" |
+
! colspan="2" style="background-color: #bbffff" | Thursday May 6
 
|-
 
|-
! rowspan="8" style="background-color: #bbffff" | Thursday<br />May 6
 
 
! style="background-color: #ccffff" | 8:45am
 
! style="background-color: #ccffff" | 8:45am
 
| style="background-color: #ddffff" align="center" | '''Introduction and Overview'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />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
 
| style="background-color: #ddffff" align="center" | '''Introduction and Overview'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />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
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| style="background-color: #ddffff" align="center" | Day ends
 
| style="background-color: #ddffff" align="center" | Day ends
 
|-
 
|-
| colspan="3" |
+
| colspan="2" |
 +
|-
 +
! colspan="2" style="background-color: #bbffcc" | Friday May 7
 
|-
 
|-
! rowspan="5" style="background-color: #bbffcc" | Friday<br />May 7
 
 
! style="background-color: #ccffdd" | 8:45am
 
! style="background-color: #ccffdd" | 8:45am
 
| style="background-color: #ddffdd" align="center" |'''[[GBrowse Tutorial|GBrowse]]'''<br />[[User:Scott|Scott Cain]]<br />
 
| style="background-color: #ddffdd" align="center" |'''[[GBrowse Tutorial|GBrowse]]'''<br />[[User:Scott|Scott Cain]]<br />
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|-
 
|-
 
! style="background-color: #ccffdd" | 2:00pm
 
! style="background-color: #ccffdd" | 2:00pm
| style="background-color: #ddffdd" align="center" |'''[[Galaxy]]'''<br />[[User:JamesTaylor|James Taylor]]<br />Introduction; Installation and configuration of Galaxy; Defining your own tools; ...
+
| style="background-color: #ddffdd" align="center" |'''[[Galaxy Tutorial|Galaxy]]'''<br />[[User:JamesTaylor|James Taylor]]<br />Introduction; Installation and configuration of Galaxy; Defining your own tools; ...
 
|-
 
|-
 
! style="background-color: #ccffdd" | 6:00pm
 
! style="background-color: #ccffdd" | 6:00pm
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| style="background-color: #ddffdd" align="center" |Day ends
 
| style="background-color: #ddffdd" align="center" |Day ends
 
|-
 
|-
| colspan="3" |
+
| colspan="2" |
 +
|-
 +
! colspan="2" style="background-color: #ffffaa"| Saturday May 8
 
|-
 
|-
! rowspan="5" style="background-color: #ffffaa"| Saturday<br />May 8
 
 
! style="background-color: #ffffbb" | 8:45am
 
! style="background-color: #ffffbb" | 8:45am
 
| style="background-color: #ffffcc" align="center" | '''[[Chado Tutorial|Chado I]]'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]
 
| style="background-color: #ffffcc" align="center" | '''[[Chado Tutorial|Chado I]]'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]
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| style="background-color: #ffffcc" align="center" | Day ends
 
| style="background-color: #ffffcc" align="center" | Day ends
 
|-
 
|-
| colspan="3" |
+
| colspan="2" |
 +
|-
 +
! colspan="2" style="background-color: #ffccaa" | Sunday May 9
 
|-
 
|-
! rowspan="5" style="background-color: #ffccaa" | Sunday<br />May 9
 
 
! style="background-color: #ffddcc" | 8:45am
 
! style="background-color: #ffddcc" | 8:45am
 
| style="background-color: #ffeedd" align="center" |'''[[GBrowse_syn Tutorial|GBrowse_syn]]'''<br />[[User:Mckays|Sheldon McKay]]
 
| style="background-color: #ffeedd" align="center" |'''[[GBrowse_syn Tutorial|GBrowse_syn]]'''<br />[[User:Mckays|Sheldon McKay]]
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== Instructors ==
 
== Instructors ==
 
The instructors were
 
  
 
<center>
 
<center>
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|-
 
|-
 
| [[User:Elee|Ed Lee]]
 
| [[User:Elee|Ed Lee]]
| [[Apollo]] developer
+
| [[Apollo]]
 
| [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)]
 
| [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)]
 
|-
 
|-
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== System Requirements ==
 
== System Requirements ==
  
{{ImageRight|VmwareLogoSmall.jpg|VMware||http://www.vmware.com}}
+
[[File:VmwareLogoSmall.jpg|right|link=http://www.vmware.com|VMware]]
 
<span style="font-size: 110%">'''Participants are required to bring their own laptops, already capable of running a [[VMware]] system image.'''</span>
 
<span style="font-size: 110%">'''Participants are required to bring their own laptops, already capable of running a [[VMware]] system image.'''</span>
  
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=== VMware on Windows and Linux ===
 
=== VMware on Windows and Linux ===
  
{|
+
[[File:WindowsLogoSmall.jpg|right|link=http://www.microsoft.com/|Windows]] [[File:LinuxLogoSmall.jpg|right|Linux]]
| {{#icon: WindowsLogoSmall.jpg|Windows||http://www.microsoft.com/}}
+
A free VMware player is available for [[:Category:Windows|Microsoft Windows]] and [[:Category:Linux|Linux]] [[Glossary#Operating System|operating systems]] from [http://vmware.com/products/player/ 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.
| {{#icon: LinuxLogoSmall.jpg|Linux}}
+
|A free VMware player is available for [[:Category:Windows|Microsoft Windows]] and [[:Category:Linux|Linux]] [[Glossary#Operating System|operating systems]] from [http://vmware.com/products/player/ 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 ===
 
=== VMware on Mac OS X ===
  
{|
+
[[File:AppleSmall.gif|right|link=http://www.apple.com/macosx/|Apple]]
| {{#icon: AppleSmall.gif|Apple||http://www.apple.com/macosx/}}
+
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 [[:Category:Mac OS X|Mac OS X]].  However, there are several other options, '''all of which require an Intel Mac''':
| 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 [[:Category:Mac OS X|Mac OS X]].  However, there are several other options, '''all of which require an Intel Mac''':
+
|}
+
  
; VMware Fusion
+
; [[File:VMWareFusionsLogo.jpg|right|link=http://www.vmware.com/products/fusion/|Fusion]]VMware Fusion
{|
+
:[http://www.vmware.com/products/fusion/ VMware Fusion] ([http://www.vmware.com/a/buylink/10 $80/corporate], [http://www.vmware.com/vmwarestore/academicstore.html $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.'''
| {{#icon: VMWareFusionsLogo.jpg|Fusion||http://www.vmware.com/products/fusion/}}&nbsp;
+
| [http://www.vmware.com/products/fusion/ VMware Fusion] ([http://www.vmware.com/a/buylink/10 $80/corporate], [http://www.vmware.com/vmwarestore/academicstore.html $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
+
; [[File:VirtualBox-logo.png|right]]VirtualBox
{|
+
:[http://www.virtualbox.org/wiki/Downloads 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.''
| [[Image:VirtualBox-logo.png]]
+
| [http://www.virtualbox.org/wiki/Downloads 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.''
+
|}
+
  
 
== Costs ==
 
== Costs ==
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== Sponsor ==
 
== Sponsor ==
  
{|
+
[[File:NESCentLogo152.jpg|right|140px|link=http://nescent.org|NESCent]]
| We would like to thank the [http://nescent.org National Evolutionary Synthesis Center (NESCent)] for hosting and financially supporting this course.  Travel awards are entirely funded by NESCent, as part of its [http://www.nescent.org/eog/ Education and Outreach] effort.  NESCent's [http://www.nescent.org/eog/ Education and Outreach Group] is committed to sharing the exciting evolutionary biology research occurring at NESCent and elsewhere.  In addition, NESCent is interested in outreach to groups who are underrepresented in evolutionary biology and improving evolution education, and offers resources for scientists, educators, and the general public that meet these goals.
+
We would like to thank the [http://nescent.org National Evolutionary Synthesis Center (NESCent)] for hosting and financially supporting this course.  Travel awards are entirely funded by NESCent, as part of its [http://www.nescent.org/eog/ Education and Outreach] effort.  NESCent's [http://www.nescent.org/eog/ Education and Outreach Group] is committed to sharing the exciting evolutionary biology research occurring at NESCent and elsewhere.  In addition, NESCent is interested in outreach to groups who are underrepresented in evolutionary biology and improving evolution education, and offers resources for scientists, educators, and the general public that meet these goals.
| {{#icon: NESCentLogo152.jpg|NESCent|140|http://nescent.org}}
+
|}
+
  
 
== Travel, Lodging and Food ==
 
== Travel, Lodging and Food ==
Line 221: Line 207:
  
 
Participants are responsible for their own travel, lodging and some meal costs.
 
Participants are responsible for their own travel, lodging and some meal costs.
 +
 +
== Feedback ==
 +
 +
22 of 25 participants filled out the post-course feedback form.
 +
 +
{|
 +
| valign="top" width="45%" | '''Would you recommend GMOD Summer School to others?'''
 +
|
 +
| valign="top" | '''Please rate the quality of the course overall.'''
 +
|-
 +
| valign="top" |
 +
{| class="wikitable"
 +
!
 +
! colspan="2" | %
 +
|-
 +
| Yes
 +
{{SurveyValue|96}}
 +
|-
 +
| Yes, with reservations
 +
{{SurveyValue|4}}
 +
|-
 +
| No
 +
{{SurveyValue|0}}
 +
|}
 +
| &nbsp;&nbsp;
 +
|
 +
{| class="wikitable"
 +
|-
 +
!
 +
! colspan="2" | %
 +
|-
 +
| 5 (very good)
 +
{{SurveyValue|86}}
 +
|-
 +
| 4
 +
{{SurveyValue|14}}
 +
|-
 +
| 3 (average)
 +
{{SurveyValue|0}}
 +
|-
 +
| 2
 +
{{SurveyValue|0}}
 +
|-
 +
| 1 (very poor)
 +
{{SurveyValue|0}}
 +
|}
 +
|}
 +
 +
{{2010GMODCourseFeedback|Comments on the 2010 GMOD Summer School - Americas}}
  
 
[[Category:Education and Outreach]]
 
[[Category:Education and Outreach]]
 +
[[Category:Events]]
 +
[[Category:GMOD Schools]]

Latest revision as of 22:14, 16 April 2014

2010SummerSchoolAmericas300.png
2010 GMOD Summer School - Americas
6-9 May, 2010
NESCent
Durham, NC, USA


2010GMODSummerSchoolAmParticipants.jpg


The 2010 GMOD Summer School - Americas was held 6-9 May at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like previous GMOD Summer Schools, this course focused on installing, configuring and integrating popular GMOD Components. Sessions were taught by GMOD Component developers and GMOD staff. There was space in the course for 25 participants, and admission was competitive.

All of the sessions from this school have now been moved to this website, where they are available as Online Tutorials.


Applications

The deadline for applying to the summer school has now passed.

Program

The program featured 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.

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, basic configuration for annotating genomic sequence, re-annotation options, and improving annotation quality
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 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.

8:30pm Day ends
Friday May 7
8:45am GBrowse
Scott Cain
1:00pm Lunch
on your own
2:00pm Galaxy
James Taylor
Introduction; Installation and configuration of Galaxy; Defining your own tools; ...
6:00pm JBrowse
Mitch Skinner
JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse.
8:00pm 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

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 Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay GBrowse_syn, GBrowse Cold Spring Harbor Laboratory
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

  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

VMware

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
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

Apple

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:

Fusion
VMware 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-logo.png
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.

Costs

This course is free thanks to

NESCent

We would like to thank the National Evolutionary Synthesis Center (NESCent) for hosting and financially supporting this course. Travel awards are entirely funded by NESCent, as part of its Education and Outreach effort. NESCent's Education and Outreach Group is committed to sharing the exciting evolutionary biology research occurring at NESCent and elsewhere. In addition, NESCent is interested in outreach to groups who are underrepresented in evolutionary biology and improving evolution education, and offers resources for scientists, educators, and the general public that meet these goals.

Travel, Lodging and Food

The course was 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 are responsible for their own travel, lodging and some meal costs.

Feedback

22 of 25 participants filled out the post-course feedback form.

Would you recommend GMOD Summer School to others? Please rate the quality of the course overall.
 %
Yes  96% 
Yes, with reservations  4% 
No  0% 
  
 %
5 (very good)  86% 
4  14% 
3 (average)  0% 
2  0% 
1 (very poor)  0% 
Comments on the 2010 GMOD Summer School - Americas
“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.”