Difference between revisions of "2008 GMOD Summer School"

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<center>
<h3>July 11-13, 2008<br />
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{| style="font-size: 180%; vertical-align: middle; border: 2px solid #A6A6BC; line-height: 120%" cellpadding="10"
[http://nescent.org National Evolutionary Synthesis Center (NESCent)]<br />
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| [[Image:SummerSchoolSmall.png|center]]
Durham, North Carolina, USA</h3>
+
| valign="center" | <b>2008 GMOD Summer School</b><br /><br />July 11-13, 2008<br />[http://nescent.org National&nbsp;Evolutionary&nbsp;Synthesis<br />&nbsp;&nbsp;Center (NESCent)]<br />Durham, North Carolina, USA
 +
|-
 +
| colspan="2" | [[Image:SummerSchool2008Class2.jpg|center]]
 +
|}
 
</center>
 
</center>
  
The first annual '''GMOD Summer School''' is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components.  The course is now full.  '''However, you are still encouraged to [[GMOD Summer School Statement of Interest|submit an application]].'''  The course has a (short) waiting list and we will pull people from that list if and when openings occur.
 
 
If you have applied for the GMOD Summer School you should have received an e-mail from the [[GMOD Help Desk|Help Desk]] informing you of your admission status.
 
  
 +
The first annual [[GMOD Summer School]] was a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components such as [[Apollo]], [[Chado]], [[CMap]], and [[GBrowse]].  Participants included 25 students and 4 instructors, from 19 states and 4 countries.  It was held at the [http://nescent.org National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina, USA, July 11-13, 2008.
  
 
__TOC__
 
__TOC__
  
 
= Program =
 
= Program =
 
+
{|
The program features two and half days of hands on training starting with an overview of GMOD and then covering installation and configuration of popular GMOD tools, include [[Chado]], [[GBrowse]], [[CMap]], [[Apollo]], and the [[Community Annotation System]].
+
| The program featured two and half days of hands on training starting with an overview of GMOD and then covering installation and configuration of popular GMOD tools, include [[Chado]], [[GBrowse]], [[CMap]], [[Apollo]], and the [[Community Annotation System]].
 
+
| [[Image:SummerSchool2008GBrowse.jpg]]
== Tentative Program ==
+
|}
 
+
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
|-
 
|-
! width="10%" style="background-color: #FFBBAA" | Date
+
! width="15%" style="background-color: #FFBBAA" | Time
! width="10%" style="background-color: #FFBBAA" | Time
+
! style="background-color: #d6eee4" | Session
! style="background-color: #d6eee4" width="40%" | Session
+
 
|-
 
|-
! rowspan="7" style="background-color: #FFDDCC" | Friday<br />July 11
+
! colspan="2" style="background-color: #FFDDCC" | Friday July 11
! style="background-color: #FFCCBB" | 9am - 10am
+
| style="background-color: #d6fff5" align="center" | '''GMOD Overview'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />Introduction to 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, course overview, and installing VMware appliances on student computers.
+
 
|-
 
|-
! style="background-color: #FFCCBB" | 10am - Noon
+
! style="background-color: #FFCCBB" | 9am - 10:30am
 +
| style="background-color: #d6fff5" align="center" | '''GMOD 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, course overview, and installing VMware appliances on student computers.
 +
|-
 +
! style="background-color: #FFCCBB" | 10:30am - Noon
 
| style="background-color: #d6fff5" align="center" | '''[[Chado]]: Theory'''<br />[[User:Clements|Dave Clements]]<br />Architecture and logical design of the Chado database [[Glossary#Schema|schema]]:  Chado's modules and extensibility, how IDs and database cross references are handled, the central role of [[:Category:Ontologies|ontologies/controlled vocabularies]], and an overview of how sequence data is handled.
 
| style="background-color: #d6fff5" align="center" | '''[[Chado]]: Theory'''<br />[[User:Clements|Dave Clements]]<br />Architecture and logical design of the Chado database [[Glossary#Schema|schema]]:  Chado's modules and extensibility, how IDs and database cross references are handled, the central role of [[:Category:Ontologies|ontologies/controlled vocabularies]], and an overview of how sequence data is handled.
 
|-
 
|-
Line 40: Line 38:
 
|-
 
|-
 
! style="background-color: #FFCCBB" | 3pm  - 5pm
 
! style="background-color: #FFCCBB" | 3pm  - 5pm
| style="background-color: #d6fff5" align="center" | '''[[GBrowse]] I'''<br />[[User:Scott|Scott Cain]]<br />Overview, GBrowse installation and using [[GBrowse adaptors]]
+
| style="background-color: #d6fff5" align="center" | '''[[GBrowse]] 1'''<br />[[User:Scott|Scott Cain]]<br />Overview, GBrowse installation and using [[GBrowse adaptors]]
 
|-
 
|-
! style="background-color: #FFCCBB" | 5pm  - 6:30pm
+
! style="background-color: #FFCCBB" | 5pm  - 6pm
 +
| style="background-color: #d6fff5" align="center" | '''Social Hour'''<br />Get to know your fellow GMOD Summer School participants, the instructors, and [http://www.nescent.org/dir/ NESCent researchers].
 +
|-
 +
! style="background-color: #FFCCBB" | 6pm  - 7:30pm
 
| style="background-color: #d6fff5" align="center" | '''Dinner Break'''<br />[http://www.ninthst.com/eat.html Places to eat]
 
| style="background-color: #d6fff5" align="center" | '''Dinner Break'''<br />[http://www.ninthst.com/eat.html Places to eat]
 
|-
 
|-
! style="background-color: #FFCCBB" | 6:30pm - 9pm
+
! style="background-color: #FFCCBB" | 7:30pm - 9:30pm
| style="background-color: #d6fff5" align="center" | '''[[GBrowse]] II'''<br />[[User:Scott|Scott Cain]]<br />GBrowse Configuration: Changing defaults and displays, adding tracks, and performance tuning
+
| style="background-color: #d6fff5" align="center" |'''Open Discussion'''<br />[[User:Scott|Scott]], [[User:Clements|Dave]], [[User:Faga|Ben]], Ed, and '''''You!'''''<br />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.  We expect this to be lively.
 
|-
 
|-
! rowspan="4" style="background-color: #FFF6CC"| Saturday<br />July 12
+
! colspan="2" style="background-color: #FFF6CC"| Saturday July 12
! style="background-color: #FFE5BB" |  9am - 12:30pm
+
| style="background-color: #d6fff5" align="center" | '''[[Apollo]]'''<br />Ed Lee<br />Overview, installation, configuration, reading/writing data, setting up a Java WebStart instance.
+
 
|-
 
|-
! style="background-color: #FFE5BB" | 12:30pm - 1:30pm
+
! style="background-color: #FFE5BB" | 9am - 11:30pm
 +
| style="background-color: #d6fff5" align="center" | '''[[GBrowse]] 2'''<br />[[User:Scott|Scott Cain]]<br />GBrowse Configuration: Changing defaults and displays, adding tracks, and performance tuning
 +
|-
 +
! style="background-color: #FFE5BB" | 11:30pm - 12:30pm
 
| style="background-color: #d6fff5" align="center" |'''Lunch Break'''<br />[http://www.ninthst.com/eat.html Places to eat]
 
| style="background-color: #d6fff5" align="center" |'''Lunch Break'''<br />[http://www.ninthst.com/eat.html Places to eat]
 
|-
 
|-
!style="background-color: #FFE5BB" | 1:30pm - 5pm
+
! style="background-color: #FFE5BB" | 12:30pm - 4pm
| style="background-color: #d6fff5" align="center" | '''[[CMap]]'''<br />[[User:Faga|Ben Faga]]<br />Overview, installation, configuration and data importation.
+
| style="background-color: #d6fff5" align="center" | '''[[Apollo]]'''<br />Ed Lee<br />Overview, installation, configuration, reading/writing data, setting up a Java WebStart instance.
 +
|-
 +
! style="background-color: #FFE5BB" | 4pm - 5pm
 +
| style="background-color: #d6fff5" align="center" | '''[[CMap]] 1'''<br />[[User:Faga|Ben Faga]]<br />Overview, installation, configuration and data importation.
 +
|-
 +
! style="background-color: #FFE5BB" | 5pm - 6:30pm
 +
| style="background-color: #d6fff5" align="center" |'''Dinner Break'''<br />[http://www.ninthst.com/eat.html Places to eat]
 +
|-
 +
! style="background-color: #FFE5BB" | 6:30pm - 9pm
 +
| style="background-color: #d6fff5" align="center" | '''[[CMap]] 2'''<br />[[User:Faga|Ben Faga]]<br />Overview, installation, configuration and data importation.
 
|-
 
|-
! style="background-color: #FFE5BB" | 5pm - 6pm
+
! colspan="2" style="background-color: #FFF6DD" | Sunday July 13
| style="background-color: #d6fff5" align="center" |'''Social Hour'''<br />Get to know your fellow GMOD Summer School attendees and instructors.
+
 
|-
 
|-
! rowspan="2" style="background-color: #FFF6DD" | Sunday<br />July 13
 
 
! style="background-color: #FFE5CC" | 9am - 12:30pm
 
! style="background-color: #FFE5CC" | 9am - 12:30pm
 
| style="background-color: #d6fff5" align="center" |'''[[Community Annotation System]]'''<br />[[User:Scott|Scott Cain]]<br>How to install and configure the GMOD Community Annotation System, an integrated package of GMOD components (including all the ones covered in this course) that reduces much of the installation, integration, and configuration work of doing each component individually.
 
| style="background-color: #d6fff5" align="center" |'''[[Community Annotation System]]'''<br />[[User:Scott|Scott Cain]]<br>How to install and configure the GMOD Community Annotation System, an integrated package of GMOD components (including all the ones covered in this course) that reduces much of the installation, integration, and configuration work of doing each component individually.
 
|-
 
|-
 
! style="background-color: #FFE5CC" | 12:30 - 1pm
 
! style="background-color: #FFE5CC" | 12:30 - 1pm
| style="background-color: #d6fff5" align="center" |'''Wrapup and Resources'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />This joint session will describe the resources available to GMOD users and attempt to bring the course to a coherent close.
+
| style="background-color: #d6fff5" align="center" |'''Wrapup and Resources'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />Describe the resources available to GMOD users and attempt to bring the course to a coherent close.
 
|}
 
|}
 
  
 
== Instructors ==
 
== Instructors ==
  
Sessions will be taught by experienced GMOD personnel, including:
+
Sessions were taught by experienced GMOD personnel, including:
  
 
* [[User:Scott|Scott Cain]] - GMOD Project Coordinator
 
* [[User:Scott|Scott Cain]] - GMOD Project Coordinator
 
* [[User:Clements|Dave Clements]] - [[GMOD Help Desk]]
 
* [[User:Clements|Dave Clements]] - [[GMOD Help Desk]]
* [[User:Faga|Ben Faga]] - [[CMap]] (and other GMOD components) developer
+
* [[User:Faga|Ben Faga]] - [[CMap]] and [[GBrowse]] developer
 
* Ed Lee - [[Apollo]] developer
 
* Ed Lee - [[Apollo]] developer
  
= Who Should Attend? =
+
= Who Attended? =
  
The GMOD Summer School is for both the people who implement GMOD at your organization, and for Principal Investigators who would benefit from having their organizations use GMOD.
+
[[Image:SummerSchool2008Class.jpg|right]]
 +
The GMOD Summer School was attended by people implementing GMOD at their organizations, and by Principal Investigators whose organizations have adopted GMOD.  The course went into detail about how to install and configure GMOD components.  It was aimed primarily at [[Computing Requirements|GMOD System Administrators]], the people who actually implement and manage a GMOD installation on a day to day basis.  This course was for organizations either planning to use GMOD components, or in the early phases of implementing GMOD.
 +
<center>
 +
{| class="wikitable"
 +
! Participant
 +
! Affiliation
 +
|-
 +
|Feseha Abebe-Akele
 +
|University of New Hampshire
 +
|-
 +
|Parker Antin
 +
|University of Arizona
 +
|-
 +
|Burcu Bakir-Gungor
 +
|Medical College of Wisconsin, RGD
 +
|-
 +
|[[User:Scott|Scott Cain]]
 +
|CSHL
 +
|-
 +
|[[User:Clements|Dave Clements]]
 +
|NESCent
 +
|-
 +
|Matthew Conte
 +
|Howard Hughes Medical Institute
 +
|-
 +
|Sean Davey
 +
|University of Arizona, BirdBase
 +
|-
 +
|Victor de Jager
 +
|Radboud University Nijmegen Medical Centre
 +
|-
 +
|Jason Dzurisin
 +
|University of Notre Dame
 +
|-
 +
|[[User:Faga|Ben Faga]]
 +
|CSHL
 +
|-
 +
|Bob Freeman
 +
|Harvard University Medical School
 +
|-
 +
|Jean-Pierre Gauthier
 +
|INRA
 +
|-
 +
|Glenn Harris
 +
|Virgina State University
 +
|-
 +
|Erik Hom
 +
|Harvard University
 +
|-
 +
|Zhiliang Hu
 +
|Iowa State University
 +
|-
 +
|Li Jin
 +
|University of Delaware
 +
|-
 +
|Ed Johnson
 +
|University of Georgia
 +
|-
 +
|Ed Lee
 +
|BBOP
 +
|-
 +
|Fabrice Legeai
 +
|INRA
 +
|-
 +
|Xianhua Liu
 +
|NESCent
 +
|-
 +
|Prashanti Manda
 +
|Mississippi State University
 +
|-
 +
|Tom McNeill
 +
|Syngenta Biotechnology
 +
|-
 +
|Christos Noutsos
 +
|University of Chicago
 +
|-
 +
|Jason Phillips
 +
|University of North Carolina
 +
|-
 +
|Joan Pontius
 +
|National Cancer Institute
 +
|-
 +
|Sarah Richardson
 +
|Johns Hopkins University
 +
|-
 +
|Stéphanie Sidibe-Bocs
 +
|CIRAD
 +
|-
 +
|Brett Whitty
 +
|Michigan State University
 +
|-
 +
|Andy Wu
 +
|Washington State University
 +
|-
 +
|}
 +
</center>
  
The course goes into detail about how to install and configure GMOD components.  It is aimed primarily at [[Computing Requirements|GMOD System Administrators]], the people who actually implement and manage a GMOD installation on a day to day basis.  This course is for organizations that are either planning to use GMOD components, or are in the early phases of implementing GMOD.
+
= Prerequisites =
  
== 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 Install HOWTO|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.
 
+
''The course requires a minimal level of Linux systems administration knowledge'' (see [[Computing Requirements]]).  Attendees without that minimal level of knowledge will likely be lost for most of the course.
+
 
+
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 Install HOWTO|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.  This is a non-trivial task for beginning Linux sys admins, but if you can do this successfully then you will likely fully participate in the course.  If you can't then the course will be, at best, frustrating for you.
+
  
 
== System Requirements ==
 
== System Requirements ==
  
{|
+
{{Template:2009SummerSchoolSystemOptions}}
| <span class="plainlinks">[http://www.vmware.com http://gmod.org/wiki/images/e/ec/VmwareLogoSmall.jpg]</span>
+
|''Participants are required to bring their own laptops, and those laptops must already be capable of running a [http://www.vmware.com VMware] system image.''
+
|}
+
Each session will start with different VMware image that was built specifically for that session.  Some VMware images will incorporate work covered in earlier sessions.  For example, the image used in the [[GBrowse]] session will already have [[PostgreSQL]] and [[Chado]] installed and Chado will be preloaded with example data.
+
  
=== VMware on Windows and Linux ===
+
= Cost and Registration =
  
{|
+
There was no tuition cost for the GMOD Summer School. Participants were responsible for their own travel, lodging and meal expenses.
| <span class="plainlinks">[http://www.microsoft.com/ http://gmod.org/wiki/images/a/a5/WindowsLogoSmall.jpg]</span>
+
| [[Image:LinuxLogoSmall.jpg]]
+
|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.
+
|}
+
  
=== VMware on Mac OS X ===
+
The course was full with a waiting listDue to last minute cancellations and the flexibility of applicants we were able to get everyone who applied into the course (and we still had a full course).
 
+
{|
+
| <span class="plainlinks">[http://www.apple.com/macosx/ http://gmod.org/wiki/images/8/82/AppleSmall.gif]</span>
+
| 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'':
+
|}
+
 
+
; Mac OS 10.5 (Leopard) and Boot Camp
+
{|
+
| <span class="plainlinks"> [http://www.apple.com/macosx/features/bootcamp.html http://gmod.org/wiki/images/0/09/AppleBootCampLogo.jpg]</span>
+
| The [http://www.apple.com/macosx/ latest release of Mac OS (10.5, Leopard)] includes [http://www.apple.com/macosx/features/bootcamp.html Boot Camp], a feature that allows you to boot your Mac into another operating system, including Windows or LinuxFrom there you can install the VMware player for your OS.*
+
|}
+
 
+
; VMware Fusion
+
{|
+
| <span class="plainlinks"> [http://www.vmware.com/products/fusion/ http://gmod.org/wiki/images/0/02/VMWareFusionsLogo.jpg]</span>
+
| VMware's [http://www.vmware.com/products/fusion/ Fusion] product ($79.99) allows you to run Windows or Linux under Mac OS.  From there you can install the VMware player for your OS.  [[User:Scott|Scott]] uses Fusion on a regular basis and is pretty happy with it (though he paid half price for it when it came out).
+
|}
+
 
+
; Parallels Desktop for Mac
+
{|
+
| <span class="plainlinks"> [http://www.parallels.com/en/products/desktop/ http://gmod.org/wiki/images/5/51/ParallelsDesktopLogo.gif]</span>
+
| Another option is [http://www.parallels.com/en/products/desktop/ Parallels Desktop for Mac] ($79.99).  Like Fusion, Parallels allows you to run Windows and Linux under Mac OS.  And once again, from there you can install the VMware player for your OS.  This requires two 'levels' of virtualization: Parallels to get Windows or Linux and then VMware Player to run the course Linux.*
+
|}
+
 
+
{|
+
| valign="top" | '''*'''
+
| ''This is how they are supposed to work anyway!  We haven't tested these options all the way through yet.  We will update this page as we try them.''
+
|}
+
 
+
= Cost =
+
 
+
There is no tuition cost for the GMOD Summer School.  It's free.  Participants are responsible for their own travel, lodging and meal expenses.  Assistance is available for travel and living expenses to participants from underrepresented groups; please contact the [[GMOD Help Desk]] for more information.
+
 
+
= Registration =
+
 
+
The course is now full.  '''However, you are encouraged to [[GMOD Summer School Statement of Interest|submit an application]].'''  The course has a short waiting list and we will pull people from that list as openings occur.
+
 
+
If you have applied for the GMOD Summer School you should have received an e-mail from the [[GMOD Help Desk|Help Desk]] informing you of your admission status.
+
 
+
= Location =
+
 
+
{|
+
| <span class="plainlinks"> [http://www.nescent.org http://gmod.org/wiki/images/c/c7/NESCentMainPageIcon.png]</span>
+
| The GMOD Summer School will be held at the [http://nescent.org National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina, United States.
+
|}
+
Transportation and lodging information will be added here as the course draws nearer.
+
  
 
= Transportation, Lodging, and Meals =
 
= Transportation, Lodging, and Meals =
  
[http://www.rdu.com/ Raleigh-Durham International Airport (RDU)] is 30 minutes from NESCent.  Cheaper flights are sometimes available into [http://www.flyfrompti.com/ Piedmont Triad International Airport] near Greensboro which is about 90 minutes from Durham.  See [http://www.nescent.org/about/directions.php Directions to NESCent] for more.
+
Participants were responsible for their own transportation, lodging and meals.  Everyone who flew, came in through [http://www.rdu.com/ Raleigh-Durham International Airport (RDU)], a 30 minute drive from NESCent.  Most participants stayed at [http://www.millenniumhotels.com/millenniumdurham/index.html Millennium Hotel Durham], which provided a free shuttle to and from NESCent.
  
NESCent visitors usually stay at [http://www.millenniumhotels.com/millenniumdurham/index.html Millennium Hotel Durham].  The NESCent visitor room rate is currently around $114 per night and there is a free shuttle between the hotel and NESCent.  The Millennium also offers a shuttle between the airport and the hotel for $24 each way.  We are currently investigating other lower cost housing options.
+
NESCent is adjacent to [http://www.ninthst.com/ Durham's 9<sup>th</sup> Street District] where participants ate most of their meals.
 
+
NESCent is adjacent to [http://www.ninthst.com/ Durham's 9<sup>th</sup> Street District] which offers many  [http://www.ninthst.com/eat.html places to eat]. The [http://www.millenniumhotels.com/millenniumdurham/index.html Millennium Hotel] also has a [http://www.millenniumhotels.com/millenniumdurham/restaurant/index.html restaurant].  Meals are not provided as part of the summer school.
+
  
 
= Posters and Fliers =
 
= Posters and Fliers =
 +
 +
'''Note:''' Both of these posters are now out of date.  The PI Track has now been combined with the Implementation track, and the schedule details shown on the second one have now changed.
  
 
{| class="wikitable" width="60%"
 
{| class="wikitable" width="60%"
| valign="top" | <span class="plainlinks">[http://gmod.org/wiki/images/7/75/SummerSchoolPoster2008.pdf http://gmod.org/wiki/images/8/80/SummerSchoolPoster2008Thumb.png]</span>
+
| valign="top" align="center" | [[File:SummerSchoolPoster2008Thumb.png|Media:SummerSchoolPoster2008.pdf|Poster 1]]<br />[[Media:SummerSchoolPoster2008.pdf|Download]]<br />A poster (US Letter size) announcing the 2008 GMOD Summer School.
<br />A [[Media:SummerSchoolPoster2008.pdf|poster]] (US Letter size) announcing the 2008 GMOD Summer School is available for [[Media:SummerSchoolPoster2008.pdf|download]].
+
| valign="top" align="center" | [[File:SummerSchoolFlier2008.png|:Media:GMODSummerSchoolFlier2008.pdf|Poster 2]]<br />[[Media:GMODSummerSchoolFlier2008.pdf|Download]]<br />A flier with the schedule on it also available.
| valign="top" | <span class="plainlinks">[http://gmod.org/wiki/images/3/30/GMODSummerSchoolFlier2008.pdf http://gmod.org/wiki/images/c/c9/SummerSchoolFlier2008.png]
+
<br />A flier with the schedule on it also available for [[Media:GMODSummerSchoolFlier2008.pdf|download]].
+
 
|}
 
|}
  
Please post these at your organization.
+
= Acknowledgments and Feedback =
 
+
= Acknowledgements =
+
  
The GMOD Summer School is funded by [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].
+
The 2008 GMOD Summer School was funded by [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].
  
[[Image:SummerSchoolSmall.png|center]]
+
{{Template:2008GMODSummerSchoolFeedback‎}}
  
 
[[Category:GMOD Community]]
 
[[Category:GMOD Community]]
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Latest revision as of 22:11, 16 April 2014

SummerSchoolSmall.png
2008 GMOD Summer School

July 11-13, 2008
National Evolutionary Synthesis
  Center (NESCent)

Durham, North Carolina, USA
SummerSchool2008Class2.jpg


The first annual GMOD Summer School was a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components such as Apollo, Chado, CMap, and GBrowse. Participants included 25 students and 4 instructors, from 19 states and 4 countries. It was held at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, July 11-13, 2008.

Program

The program featured two and half days of hands on training starting with an overview of GMOD and then covering installation and configuration of popular GMOD tools, include Chado, GBrowse, CMap, Apollo, and the Community Annotation System. SummerSchool2008GBrowse.jpg
Time Session
Friday July 11
9am - 10:30am GMOD 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, course overview, and installing VMware appliances on student computers.
10:30am - Noon Chado: Theory
Dave Clements
Architecture and logical design of the Chado database schema: Chado's modules and extensibility, how IDs and database cross references are handled, the central role of ontologies/controlled vocabularies, and an overview of how sequence data is handled.
Noon - 1pm Lunch Break
Places to eat
NESCent is adjacent to Durham's 9th Street District.
1pm - 3pm Chado: Practice
Scott Cain
Using Chado: Installation, importing and exporting data, and a complete worked example of loading example sequence data.
3pm - 5pm GBrowse 1
Scott Cain
Overview, GBrowse installation and using GBrowse adaptors
5pm - 6pm Social Hour
Get to know your fellow GMOD Summer School participants, the instructors, and NESCent researchers.
6pm - 7:30pm Dinner Break
Places to eat
7:30pm - 9:30pm Open Discussion
Scott, Dave, Ben, Ed, and You!
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. We expect this to be lively.
Saturday July 12
9am - 11:30pm GBrowse 2
Scott Cain
GBrowse Configuration: Changing defaults and displays, adding tracks, and performance tuning
11:30pm - 12:30pm Lunch Break
Places to eat
12:30pm - 4pm Apollo
Ed Lee
Overview, installation, configuration, reading/writing data, setting up a Java WebStart instance.
4pm - 5pm CMap 1
Ben Faga
Overview, installation, configuration and data importation.
5pm - 6:30pm Dinner Break
Places to eat
6:30pm - 9pm CMap 2
Ben Faga
Overview, installation, configuration and data importation.
Sunday July 13
9am - 12:30pm Community Annotation System
Scott Cain
How to install and configure the GMOD Community Annotation System, an integrated package of GMOD components (including all the ones covered in this course) that reduces much of the installation, integration, and configuration work of doing each component individually.
12:30 - 1pm Wrapup and Resources
Scott Cain and Dave Clements
Describe the resources available to GMOD users and attempt to bring the course to a coherent close.

Instructors

Sessions were taught by experienced GMOD personnel, including:

Who Attended?

SummerSchool2008Class.jpg

The GMOD Summer School was attended by people implementing GMOD at their organizations, and by Principal Investigators whose organizations have adopted GMOD. The course went into detail about how to install and configure GMOD components. It was aimed primarily at GMOD System Administrators, the people who actually implement and manage a GMOD installation on a day to day basis. This course was for organizations either planning to use GMOD components, or in the early phases of implementing GMOD.

Participant Affiliation
Feseha Abebe-Akele University of New Hampshire
Parker Antin University of Arizona
Burcu Bakir-Gungor Medical College of Wisconsin, RGD
Scott Cain CSHL
Dave Clements NESCent
Matthew Conte Howard Hughes Medical Institute
Sean Davey University of Arizona, BirdBase
Victor de Jager Radboud University Nijmegen Medical Centre
Jason Dzurisin University of Notre Dame
Ben Faga CSHL
Bob Freeman Harvard University Medical School
Jean-Pierre Gauthier INRA
Glenn Harris Virgina State University
Erik Hom Harvard University
Zhiliang Hu Iowa State University
Li Jin University of Delaware
Ed Johnson University of Georgia
Ed Lee BBOP
Fabrice Legeai INRA
Xianhua Liu NESCent
Prashanti Manda Mississippi State University
Tom McNeill Syngenta Biotechnology
Christos Noutsos University of Chicago
Jason Phillips University of North Carolina
Joan Pontius National Cancer Institute
Sarah Richardson Johns Hopkins University
Stéphanie Sidibe-Bocs CIRAD
Brett Whitty Michigan State University
Andy Wu Washington State 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 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 on Windows and Linux
Windoze
Linux
A free VMware player is available for Microsoft Windows and Linux operating systems from VMware. You will need to register to download it.


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
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
VMWareFusionsLogo.jpg
VMware Fusion ({{{1}}}) allows you to run VMware images, 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.


Mac OS 10.5 (Leopard) and Boot Camp
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.

Cost and Registration

There was no tuition cost for the GMOD Summer School. Participants were responsible for their own travel, lodging and meal expenses.

The course was full with a waiting list. Due to last minute cancellations and the flexibility of applicants we were able to get everyone who applied into the course (and we still had a full course).

Transportation, Lodging, and Meals

Participants were responsible for their own transportation, lodging and meals. Everyone who flew, came in through Raleigh-Durham International Airport (RDU), a 30 minute drive from NESCent. Most participants stayed at Millennium Hotel Durham, which provided a free shuttle to and from NESCent.

NESCent is adjacent to Durham's 9th Street District where participants ate most of their meals.

Posters and Fliers

Note: Both of these posters are now out of date. The PI Track has now been combined with the Implementation track, and the schedule details shown on the second one have now changed.

Poster 1
Download
A poster (US Letter size) announcing the 2008 GMOD Summer School.
Poster 2
Download
A flier with the schedule on it also available.

Acknowledgments and Feedback

The 2008 GMOD Summer School was funded by NIH grant 1R01HG004483-01 under Ian Holmes.

Comments on the 2008 GMOD Summer School
“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!”
“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.”