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

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| <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 />
 
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The '''''2010 GMOD Summer School - Americas''''' will be 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 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.
+
[[File:2010GMODSummerSchoolAmParticipants.jpg|center|500px]]
  
  
== Applications ==
+
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.
{|
+
| valign="top" align="center" |
+
<div class="plainlinks" style="float: right; margin: 0.5em; padding: 0.5em; border: gray 2px solid; background-color: #ffeedd; font-size: 160%; line-height: 140%;">[http://nescent.org/courses/apply Apply Now]</div>
+
|
+
'''We are now [http://nescent.org/courses/apply accepting applications] for this course.'''
+
  
'''Admission to the course is competitive and is based on the application (especially the statement of interest).''' Last year there were over 50 applications for the 25 slots.  The application deadline is the end of Friday, February 22.  Any applications received after February 22 will be automatically put on the waiting list.  Applicants will be notified of admission status by March 1.
+
: '''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]].'''
|}
+
  
== 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]].
+
== Applications ==
 +
'''The deadline for applying to the summer school has now passed.'''
  
''This schedule is subject to change. ''
+
== 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]].
  
 
{| 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="6" 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
Line 47: Line 41:
 
|-
 
|-
 
! style="background-color: #ccffff" | 1:15pm
 
! style="background-color: #ccffff" | 1:15pm
| style="background-color: #ddffff" align="center" | '''[[MAKER Tutorial|MAKER]]'''<br />[[User:Carsonholt|Carson Holt]]<br />[[MAKER]] overview, installation, basic configuration for annotating genomic sequence, re-annotation options, and improving annotation quality
+
| style="background-color: #ddffff" align="center" | '''[[MAKER Tutorial|MAKER I]]'''<br />[[User:Carsonholt|Carson Holt]]<br />[[MAKER]] overview, installation, basic configuration for annotating genomic sequence, re-annotation options, and improving annotation quality
<!--
+
 
|-
 
|-
 
! style="background-color: #ccffff" | 4:30pm
 
! style="background-color: #ccffff" | 4:30pm
Line 55: Line 48:
 
! style="background-color: #ccffff" | 6:30pm
 
! style="background-color: #ccffff" | 6:30pm
 
| style="background-color: #ddffff" align="center" | '''[[MAKER Tutorial|MAKER II]]'''<br />[[User:Carsonholt|Carson Holt]]<br />Advanced [[MAKER]] configuration, re-annotation options, and improving annotation quality
 
| style="background-color: #ddffff" align="center" | '''[[MAKER Tutorial|MAKER II]]'''<br />[[User:Carsonholt|Carson Holt]]<br />Advanced [[MAKER]] configuration, re-annotation options, and improving annotation quality
-->
 
|-
 
! style="background-color: #ccffff" | 5:30pm
 
| style="background-color: #ddffff" align="center" | '''[[JBrowse Tutorial|JBrowse]]'''<br />[[User:MitchSkinner|Mitch Skinner]]<br />[[JBrowse]] installation, configuration and administration; converting [[GFF3]] to [[Glossary#JSON|JSON]] and loading it into JBrowse.
 
 
|-
 
|-
 
! style="background-color: #ccffff" | 7:30pm
 
! style="background-color: #ccffff" | 7:30pm
 +
| style="background-color: #ddffff" align="center" |'''Open Discussion''' and '''User Presentations'''<br />Everyone<br />This session is open to any and all questions you have on the [[Main Page|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''.
 +
|-
 +
! style="background-color: #ccffff" | 8:30pm
 
| 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 />
Line 73: Line 67:
 
|-
 
|-
 
! style="background-color: #ccffdd" | 2:00pm
 
! style="background-color: #ccffdd" | 2:00pm
| style="background-color: #ddffdd" align="center" |'''[[Galaxy]]'''<br />Anton Nekrutenko and 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
| style="background-color: #ddffdd" align="center" |'''Open Discussion''' and '''User Presentations'''<br />Everyone<br />This session is open to any and all questions you have on the [[Main Page|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.
+
| style="background-color: #ddffdd" align="center" | '''[[JBrowse Tutorial|JBrowse]]'''<br />[[User:MitchSkinner|Mitch Skinner]]<br />[[JBrowse]] installation, configuration and administration; converting [[GFF3]] to [[Glossary#JSON|JSON]] and loading it into JBrowse.
We expect this session to be ''lively''.
+
 
|-
 
|-
! style="background-color: #ccffdd" | 7:30pm
+
! style="background-color: #ccffdd" | 8:00pm
 
| 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]]
Line 100: Line 94:
 
| 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]]
Line 121: Line 116:
  
 
== Instructors ==
 
== Instructors ==
 
The ''tentative'' list of instructors includes
 
  
 
<center>
 
<center>
Line 147: Line 140:
 
|-
 
|-
 
| [[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)]
 
|-
 
|-
Line 153: Line 146:
 
| [[GBrowse_syn]], [[GBrowse]]
 
| [[GBrowse_syn]], [[GBrowse]]
 
| [http://cshl.edu Cold Spring Harbor Laboratory]
 
| [http://cshl.edu Cold Spring Harbor Laboratory]
|-
 
| Anton Nekrutenko
 
| [[Galaxy]]
 
| [http://www.psu.edu Penn State]
 
 
|-
 
|-
 
| [[User:MitchSkinner|Mitch Skinner]]
 
| [[User:MitchSkinner|Mitch Skinner]]
Line 162: Line 151:
 
| [http://berkeley.edu University of California, Berkeley]
 
| [http://berkeley.edu University of California, Berkeley]
 
|-
 
|-
| James Taylor
+
| [[User:JamesTaylor|James Taylor]]
 
| [[Galaxy]]
 
| [[Galaxy]]
 
| [http://www.emory.edu Emory University]
 
| [http://www.emory.edu Emory University]
Line 179: Line 168:
 
== 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>
  
Line 186: Line 175:
 
=== 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.''
+
|}
+
  
== Cost ==
+
== Costs ==
  
This course is ''free'' thanks to [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7234938&p_grant_num=1R01HG004483-01&p_query=&ticket=&p_audit_session_id=&p_keywords= NIH grant 1R01HG004483-01] under [http://biowiki.org/IanHolmes Ian Holmes], and to the grants of the individual instructors.
+
This course is ''free'' thanks to
 +
* [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7234938&p_grant_num=1R01HG004483-01&p_query=&ticket=&p_audit_session_id=&p_keywords= NIH grant 1R01HG004483-01] under [http://biowiki.org/IanHolmes Ian Holmes]
 +
* Financial support from [http://nescent.org NESCent]
 +
* The grants of the individual instructors
 +
 
 +
== 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.
  
 
== Travel, Lodging and Food ==
 
== Travel, Lodging and Food ==
  
The course will be held at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina, United States.  The closest airport is [http://www.rdu.com/ Raleigh-Durham International Airport (RDU)], a 30 minute drive from NESCent.
+
The course was held at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina, United States.  The closest airport is [http://www.rdu.com/ 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.
+
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}}
 +
|}
 +
|}
  
A light breakfast will be provided everyday.  For other meals, NESCent is adjacent to [http://www.ninthst.com/ Durham's 9<sup>th</sup> Street District], which offers many dining options, and a grocery store.
+
{{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.”