Difference between revisions of "2011 GMOD Spring Training"

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<center>
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[[File:2011GMODSpringTrainingLogo.png|center|600px|2011 GMOD Spring Training March 8-12, 2011]]
{| style="vertical-align: middle; border: 2px solid #A6A6BC" cellpadding="10"
+
 
| {{ImageCenter|GMODAmericas2011Logo.jpg|Part of GMOD Americas 2011|220|GMOD Americas 2011}}
+
[[File:2011GMODSpringTraining.jpg|center|600px|March 2011 GMOD Spring Training Participants, minus a few]]
| <span style="font-size: 200%; line-height: 140%"><b>2010 GMOD Spring Training</b></span><br /><br /><span style="font-size: 160%; line-height: 120%">March 8-12, 2011<br />[http://www.nescent.org/ NESCent]<br />Durham, North Carolina, United States<br /><br />Part of [[GMOD Americas 2011]]
+
</span>
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|}
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</center>
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__NOTITLE__
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{{TocRight}}
 
{{TocRight}}
The '''''2011 GMOD Spring Training''''' will be held May 8-12 at the [http://www.nescent.org National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina, as part of [[GMOD Americas 2011]].  Like previous [[GMOD Schools]], this one will focus on installing, configuring and integrating popular [[GMOD Components]].  Sessions will be taught by GMOD Component developers and GMOD staff.  There is space for 25 participants and admission is competitive.
+
The '''''2011 GMOD Spring Training''''' was held March 8-12 at the [http://www.nescent.org National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina, as part of [[GMOD Americas 2011]].  Like previous [[GMOD Schools]], this one focused on installing, configuring and integrating popular [[GMOD Components]].  Sessions were taught by GMOD Component developers and GMOD staff.  There was space for 25 participants and admission was competitive.
  
= Applications =
+
= Course Sessions &rarr; Online Tutorials =
  
'''Admission to the course is competitive and is based on the strength of the application (especially the statement of interest).'''  In [[2010 GMOD Summer School - Americas|2010]] there were over 60 applicants for 25 slots.
+
The course sessions will become online tutorials on this wiki following the course.
 
+
<div class="indent">
We will start accepting applications in early December. (Watch this space for a link.) Applications will be reviewed over the holiday break and applicants will be notified of their status in January.
+
{|
 
+
| valign="top" |
Registration fees have not been definitively set, but are likely to fall in the $225-$250 range for the course.
+
These tutorials will be updated:
 +
* [[Apollo Tutorial]]
 +
* [[Chado Tutorial]]
 +
* [[Galaxy Tutorial]]
 +
* [[GBrowse Tutorial]]
 +
* [[GBrowse_syn Tutorial]]
 +
* [[JBrowse Tutorial]]
 +
* [[MAKER Tutorial]]
 +
* [[Tripal Tutorial]]
 +
| &nbsp;&nbsp;&nbsp;
 +
| valign="top" |
 +
And these tutorials will be added:
 +
* [[InterMine 2011 Tutorial|InterMine Tutorial]]
 +
* [[SOBA 2011 Tutorial|SOBA Tutorial]]
 +
|}
 +
</div>
  
 
= Schedule =
 
= Schedule =
 
The '''''tentative''''' schedule is below.
 
  
 
<center>
 
<center>
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
|-
 
|-
! width="5%"  style="background-color: #99ccff; font-size: 140%; line-height: 130%" rowspan="13" | [[GMOD Americas 2011|G<br />M<br />O<br />D<br />&nbsp;<br />A<br />M<br />E<br />R<br />I<br />C<br />A<br />S<br />&nbsp;<br />2<br />0<br />1<br />1<br />]]
 
! width="12%" style="background-color: #99ccff" | Date
 
 
! width="15%"  style="background-color: #99ccff" | Time
 
! width="15%"  style="background-color: #99ccff" | Time
! width="68%" style="background-color: #99ccff" colspan="2" | Event
+
! width="80%" style="background-color: #99ccff" colspan="1" | Event
 
|-
 
|-
| colspan="4" |
+
| colspan="2" |
 +
|-
 +
! colspan="2" style="color: #aaaaaa"  | March 4
 
|-
 
|-
! rowspan="1" style="color: #aaaaaa"  | March 4
 
 
! style="color: #aaaaaa" | 7pm-9pm
 
! style="color: #aaaaaa" | 7pm-9pm
| align="center" colspan="2" | '''[[March 2011 GMOD Meeting#Introduction to GMOD|<span style="color: #aaaaff">Introduction to GMOD</span>]]'''
+
| align="center" colspan="1" | '''[[March 2011 GMOD Meeting#Introduction to GMOD|<span style="color: #aaaaff">Introduction to GMOD</span>]]'''
 
|-
 
|-
| colspan="4" |
+
| colspan="2" |
 +
|-
 +
! colspan="2" style="color: #aaaaaa"| March 5-6
 
|-
 
|-
! rowspan="1" style="color: #aaaaaa"| March 5-6
 
 
! style="color: #aaaaaa" | 9am-5pm
 
! style="color: #aaaaaa" | 9am-5pm
| align="center" colspan="2" rowspan="2" | '''[[March 2011 GMOD Meeting|<span style="color: #aaaaff">March 2011 GMOD Community Meeting</span>]]'''
+
| align="center" colspan="1" rowspan="1" | '''[[March 2011 GMOD Meeting|<span style="color: #aaaaff">March 2011 GMOD Community Meeting</span>]]'''
 
|-
 
|-
| colspan="4" |
+
| colspan="2" |
 +
|-
 +
! colspan="2" style="color: #aaaaaa" | March 7
 
|-
 
|-
! rowspan="1" style="color: #aaaaaa" | March 7
 
 
! style="color: #aaaaaa" | 8:30am-5pm
 
! style="color: #aaaaaa" | 8:30am-5pm
| align="center" | '''[[Satellite Meetings - GMOD Americas 2011|<span style="color: #aaaaff">Satellite Meetings</span>]]
+
| align="center" colspan="1" | '''[[Satellite Meetings - GMOD Americas 2011|<span style="color: #aaaaff">Satellite Meetings</span>]]
 
|-
 
|-
| colspan="4" |
+
| colspan="2" |
 
|-
 
|-
! rowspan="1" style="background-color: #ffffaa" | Tuesday<br />March 8
+
|-
! style="background-color: #ffffbb" | 8:30am-5:30pm<br />7pm-9pm
+
! colspan="2" style="background-color: #ffffaa" | Tuesday March 8 through Saturday March 12
! style="background-color: #ffffcc" align="center" rowspan="5" | '''[[2011 GMOD Spring Training]]'''
+
|-
 +
! style="background-color: #ffffbb" | 8:30am-6:00pm<br />7:30pm-9pm
 +
! colspan="1" style="background-color: #ffffcc" align="center" | '''[[2011 GMOD Spring Training]]'''
 
<div style="font-weight: normal">A week long hands-on course on GMOD Component installation, configuration, and usage.  The course will cover these components in detail:
 
<div style="font-weight: normal">A week long hands-on course on GMOD Component installation, configuration, and usage.  The course will cover these components in detail:
  
'''[[Apollo]] &bull; [[MAKER]] &bull; [[GBrowse]] &bull; [[Chado]] &bull; [[InterMine]] &bull; [[JBrowse]] &bull; [[GBrowse_syn]] &bull; [[Tripal]] &bull; [[GFF3]] &bull; [[Galaxy]]'''
+
'''[[Apollo]] &bull; [[MAKER]] &bull; [[GBrowse]] &bull; [[Chado]] &bull; [[InterMine]] &bull; [[JBrowse]] &bull; [[GBrowse_syn]] &bull; [[Tripal]] &bull; [[GFF3]] &bull; [[Galaxy]] &bull [[SOBA]]'''
 
</div>
 
</div>
|-
 
! rowspan="1" style="background-color: #ffffaa" | Wednesday<br />March 9
 
! style="background-color: #ffffbb" | 8:30am-5:30pm<br />7pm-9pm
 
|-
 
! rowspan="1" style="background-color: #ffffaa" | Thursday<br />March 10
 
! style="background-color: #ffffbb" | 8:30am-5:30pm<br />7pm-9pm
 
|-
 
! rowspan="1" style="background-color: #ffffaa" | Friday<br />March 11
 
! style="background-color: #ffffbb" | 8:30am-5:30pm<br />7pm-9pm
 
|-
 
! rowspan="1" style="background-color: #ffffaa" | Saturday<br />March 12
 
! style="background-color: #ffffbb" | 8:30am-5:30pm<br />7pm-9pm
 
 
|}
 
|}
 
</center>
 
</center>
 
+
Most sessions lasted half a day.  We tried something new this year:  Each night the instructors for that day's topics were available to answer questions and help participants use the tools with their data.
This schedule will become more definitive in the next few weeks.
+
  
 
= Instructors =
 
= Instructors =
  
Sessions will be taught by experienced component developers and GMOD project staff, including:
+
Sessions were taught by experienced component developers and GMOD project staff:
  
 
<center>
 
<center>
Line 99: Line 97:
 
| Alex Kalderimis
 
| Alex Kalderimis
 
| [[InterMine]]
 
| [[InterMine]]
| [http:flymine.org FlyMine]
+
| [http://flymine.org FlyMine]
 
|-
 
|-
| Barry Moore
+
| [[User:Bmoore|Barry Moore]]
 
| [[MAKER]]
 
| [[MAKER]]
 
| [http://www.utah.edu University of Utah]
 
| [http://www.utah.edu University of Utah]
Line 130: Line 128:
 
= 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 virtual system (e.g. [[VMware]]) image.'''</span>
 
<span style="font-size: 110%">'''Participants are required to bring their own laptops, already capable of running a virtual system (e.g. [[VMware]]) image.'''</span>
  
Line 138: Line 136:
  
 
{|
 
{|
| {{#icon: WindowsLogoSmall.jpg|Windows||http://www.microsoft.com/}}
+
| [[File:WindowsLogoSmall.jpg|link=http://www.microsoft.com/|Windows]]
| {{#icon: LinuxLogoSmall.jpg|Linux}}
+
| [[File: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.
 
|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.
 
|}
 
|}
Line 147: Line 145:
  
 
{|
 
{|
| {{#icon: AppleSmall.gif|Apple||http://www.apple.com/macosx/}}
+
| [[File:AppleSmall.gif|link=http://www.apple.com/macosx/|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 [[: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''':
 
|}
 
|}
Line 153: Line 151:
 
; VMware Fusion
 
; VMware Fusion
 
{|
 
{|
| {{#icon: VMWareFusionsLogo.jpg|Fusion||http://www.vmware.com/products/fusion/}}&nbsp;
+
| [[File:VMWareFusionsLogo.jpg|link=http://www.vmware.com/products/fusion/|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.'''
 
| [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.'''
 
|}
 
|}
Line 162: Line 160:
 
| [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.''
 
| [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.''
 
|}
 
|}
 +
 +
= Applications =
 +
 +
'''The application deadline was January 7, 2011.''' However, late applications were accepted until March 1, and were automatically placed on the waiting list, and considered as cancellations occured.  Applicants were notified of admission status by January 21.
 +
 +
'''Admission to the course was competitive and was based on the strength of the application (especially the statement of interest).'''  In [[2010 GMOD Summer School - Americas|2010]] there were over 60 applicants for 25 slots.
  
 
= Costs =
 
= Costs =
  
There will be a registration fee for the course to pay instructor costs and incidentals.  We will post that information here as soon as we have it.
+
The tuition is $265 for the course (less than $55 per day) to pay instructor costs and incidentals.
  
= Sponsor =
+
= Sponsors =
  
{|
+
[[File:NESCentLogo152.jpg|100px|right|link=http://nescent.org|NESCent]]
| The [http://nescent.org National Evolutionary Synthesis Center (NESCent)] is hosting this course and all other [[GMOD Americas 2011]] events.  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.
+
The [http://nescent.org National Evolutionary Synthesis Center (NESCent)] is hosting this course and all other [[GMOD Americas 2011]] events.  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}}
+
 
|}
+
[[File:GalaxyLogoBoxed.png|left|130px|Galaxy]]
 +
The [[Galaxy|Galaxy Project]] is also sponsoring this course and all other [[GMOD Americas 2011]] events.  Galaxy is a analysis and data integration framework that enables biologists to both analyze their data, and to archive those analyses (including data sets and program parameters) for future reference.  Galaxy is developed at Penn State and Emory University.
 +
 
 +
Finally, course tuition would be much, much higher without the financial support of the [[#Instructors|instructor's]] projects and institutions.  Please thank them and their projects profusely for sponsoring their participation in this event.
 +
 
 +
= Get the Word Out! =
 +
 
 +
[[File:GMODAmericas2011FlierThumb.png|right|link=:Image:GMODAmericas2011Flier.pdf|GMOD Americas 2011 Flier]]
 +
 
 +
Help spread the word about GMOD Spring Training and other [[GMOD Americas 2011]] events by posting and distributing [[:Image:GMODAmericas2011Flier.pdf|this flier]], or the [[GMOD News#GMOD Spring Training: Apply Now |event announcements]] to your communities, mailing lists, and organizations.
 +
 
 +
There are many organizations out there that are struggling to cope with the volume of data that have and will continue to get in the future.  GMOD is an excellent option for helping these groups get a grip on and exploit their data.
  
 
= Travel, Lodging and Meals =
 
= Travel, Lodging and Meals =
Line 180: Line 195:
 
= Feedback =
 
= Feedback =
  
GMOD solicits input at the end of every event.  We'll post the feedback for this course short after it finishes.
 
  
In the meantime:
+
{|
 +
| 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|83}}
 +
|-
 +
| Yes, with reservations
 +
{{SurveyValue|17}}
 +
|-
 +
| No
 +
{{SurveyValue|0}}
 +
|}
 +
| &nbsp;&nbsp;
 +
|
 +
{| class="wikitable"
 +
|-
 +
!
 +
! colspan="2" | %
 +
|-
 +
| 5 (very good)
 +
{{SurveyValue|73}}
 +
|-
 +
| 4
 +
{{SurveyValue|23}}
 +
|-
 +
| 3 (average)
 +
{{SurveyValue|5}}
 +
|-
 +
| 2
 +
{{SurveyValue|0}}
 +
|-
 +
| 1 (very poor)
 +
{{SurveyValue|0}}
 +
|}
 +
|}
  
{{2010GMODCourseFeedback}}
+
The "Yes, with reservations" responses were:
 +
* This workshop is meant more for bioinformaticians than for biologists. That would be my 'reservation'.
 +
* This is an amazing course.  I learned more than I expected and all the instructors were great.
 +
* I was actually surprised at how many of the researchers in the room were comfortable with the somewhat involved installations. You definitely have to be comfortable not just with command line, but with a lot of Unix concepts... This course would not be for someone shackled to Mac or Win and clicky interfaces, I don't think...  Conversely, an IT person with no biology background might also get a bit overwhelmed...
 +
* I feel some sessions need more time.
  
 
[[Category:Events]]
 
[[Category:Events]]
 
[[Category:Education and Outreach]]
 
[[Category:Education and Outreach]]
 +
[[Category:2011 Spring Training]]
 +
[[Category:GMOD Schools]]

Revision as of 22:14, 16 April 2014

2011 GMOD Spring Training March 8-12, 2011
March 2011 GMOD Spring Training Participants, minus a few

The 2011 GMOD Spring Training was held March 8-12 at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as part of GMOD Americas 2011. Like previous GMOD Schools, this one focused on installing, configuring and integrating popular GMOD Components. Sessions were taught by GMOD Component developers and GMOD staff. There was space for 25 participants and admission was competitive.

Course Sessions → Online Tutorials

The course sessions will become online tutorials on this wiki following the course.

Schedule

Time Event
March 4
7pm-9pm Introduction to GMOD
March 5-6
9am-5pm March 2011 GMOD Community Meeting
March 7
8:30am-5pm Satellite Meetings
Tuesday March 8 through Saturday March 12
8:30am-6:00pm
7:30pm-9pm
2011 GMOD Spring Training
A week long hands-on course on GMOD Component installation, configuration, and usage. The course will cover these components in detail:

ApolloMAKERGBrowseChadoInterMineJBrowseGBrowse_synTripalGFF3Galaxy &bull SOBA

Most sessions lasted half a day. We tried something new this year: Each night the instructors for that day's topics were available to answer questions and help participants use the tools with their data.

Instructors

Sessions were 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 GMOD Help Desk National Evolutionary Synthesis Center (NESCent)
Stephen Ficklin Tripal Washington State University
Alex Kalderimis InterMine FlyMine
Barry Moore MAKER University of Utah
Ed Lee Apollo Berkeley Bioinformatics Open-source Projects (BBOP)
Sheldon McKay GBrowse_syn, GBrowse iPlant Collaborative
Mitch Skinner JBrowse University of California, Berkeley

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 virtual system (e.g. VMware) image.

The course starts with getting a virtual system image (built specifically for the course) up and running on your machine. We then build upon that image in each succeeding session. We will probably use VMware for the course:

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:
VMware Fusion
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-logo.png 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.

Applications

The application deadline was January 7, 2011. However, late applications were accepted until March 1, and were automatically placed on the waiting list, and considered as cancellations occured. Applicants were notified of admission status by January 21.

Admission to the course was competitive and was based on the strength of the application (especially the statement of interest). In 2010 there were over 60 applicants for 25 slots.

Costs

The tuition is $265 for the course (less than $55 per day) to pay instructor costs and incidentals.

Sponsors

NESCent

The National Evolutionary Synthesis Center (NESCent) is hosting this course and all other GMOD Americas 2011 events. 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.

Galaxy

The Galaxy Project is also sponsoring this course and all other GMOD Americas 2011 events. Galaxy is a analysis and data integration framework that enables biologists to both analyze their data, and to archive those analyses (including data sets and program parameters) for future reference. Galaxy is developed at Penn State and Emory University.

Finally, course tuition would be much, much higher without the financial support of the instructor's projects and institutions. Please thank them and their projects profusely for sponsoring their participation in this event.

Get the Word Out!

GMOD Americas 2011 Flier

Help spread the word about GMOD Spring Training and other GMOD Americas 2011 events by posting and distributing this flier, or the event announcements to your communities, mailing lists, and organizations.

There are many organizations out there that are struggling to cope with the volume of data that have and will continue to get in the future. GMOD is an excellent option for helping these groups get a grip on and exploit their data.

Travel, Lodging and Meals

See the GMOD Americas 2011 page for details.

Feedback

Would you recommend GMOD Summer School to others? Please rate the quality of the course overall.
 %
Yes  83% 
Yes, with reservations  17% 
No  0% 
  
 %
5 (very good)  73% 
4  23% 
3 (average)  5% 
2  0% 
1 (very poor)  0% 

The "Yes, with reservations" responses were:

  • This workshop is meant more for bioinformaticians than for biologists. That would be my 'reservation'.
  • This is an amazing course. I learned more than I expected and all the instructors were great.
  • I was actually surprised at how many of the researchers in the room were comfortable with the somewhat involved installations. You definitely have to be comfortable not just with command line, but with a lot of Unix concepts... This course would not be for someone shackled to Mac or Win and clicky interfaces, I don't think... Conversely, an IT person with no biology background might also get a bit overwhelmed...
  • I feel some sessions need more time.