Difference between revisions of "2008 GMOD Summer School"

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m (GMOD Summer School moved to 2008 GMOD Summer School: Event has gone from pending to past. Page describes event that happened in 2008. Will eventually replace it with the 2009 Summer School page.)
m (Changed tense from pending to past, droppd a bunch of stuff. Not finished with changes yet.)
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{| style="font-size: 180%; vertical-align: middle; border: 2px solid #A6A6BC; line-height: 120%" cellpadding="20"
 
{| style="font-size: 180%; vertical-align: middle; border: 2px solid #A6A6BC; line-height: 120%" cellpadding="20"
 
| [[Image:SummerSchoolSmall.png|center]]
 
| [[Image:SummerSchoolSmall.png|center]]
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| valign="center" | <b>GMOD Summer School</b><br /><br />July 11-13, 2008<br />[http://nescent.org National Evolutionary Synthesis<br />&nbsp;&nbsp;Center (NESCent)]<br />Durham, North Carolina, USA
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| valign="center" | <b>2008 GMOD Summer School</b><br /><br />July 11-13, 2008<br />[http://nescent.org National Evolutionary Synthesis<br />&nbsp;&nbsp;Center (NESCent)]<br />Durham, North Carolina, USA
 
|}
 
|}
 
</center>
 
</center>
 
__NOTITLE__
 
__NOTITLE__
  
−
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 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.
−
 
+
−
'''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 any 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.
+
−
 
+
  
 
__TOC__
 
__TOC__
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= 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]].
−
 
+
−
== Tentative Program ==
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{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
 
{| class="wikitable" border="1" cellpadding="5" cellspacing="0"
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| 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.
 
| 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.
 
|}
 
|}
−
''Last changed 2008/05/12''
 
  
 
== 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.
+
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.
−
 
+
−
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]]).  Attendees without that minimal level of knowledge will likely be lost for most of the course.
+
''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.
−
 
+
−
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 ==
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{|
 
{|
 
| <span class="plainlinks">[http://www.vmware.com http://gmod.org/wiki/images/e/ec/VmwareLogoSmall.jpg]</span>
 
| <span class="plainlinks">[http://www.vmware.com http://gmod.org/wiki/images/e/ec/VmwareLogoSmall.jpg]</span>
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|''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.''
+
|''Participants were required to bring their own laptops, already 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.
+
The first session started with a basic VMware image built specifically for the course.  We then built upon that image in each succeeding session.  (We also had intermediate VMware images available if things did not go well, but these were not needed.)
  
 
=== VMware on Windows and Linux ===
 
=== VMware on Windows and Linux ===
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=== VMware on Mac OS X ===
 
=== VMware on Mac OS X ===
 +
 +
Participants could also bring newer Macs with Intel processors.  (The Intel processor is a requirement for all the packages discussed below.)
  
 
{|
 
{|
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|}
 
|}
  
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; Mac OS 10.5 (Leopard) and Boot Camp
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; VMware Fusion
 
{|
 
{|
−
| <span class="plainlinks"> [http://www.apple.com/macosx/features/bootcamp.html http://gmod.org/wiki/images/0/09/AppleBootCampLogo.jpg]</span>
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| <span class="plainlinks"> [http://www.vmware.com/products/fusion/ http://gmod.org/wiki/images/0/02/VMWareFusionsLogo.jpg]</span>
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| 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 Linux.  From there you can install the VMware player for your OS.*
+
| [http://www.vmware.com/products/fusion/ VMware Fusion] ($79.99) allows you to run VMware images, Windows and Linux under Mac OS.  This was the most popular choice of the class's Mac users, perhaps because '''a fully functional, 30 day free trial version of VMware Fusion was available for download.'''
 
|}
 
|}
  
−
; VMware Fusion
+
; Mac OS 10.5 (Leopard) and Boot Camp
 
{|
 
{|
−
| <span class="plainlinks"> [http://www.vmware.com/products/fusion/ http://gmod.org/wiki/images/0/02/VMWareFusionsLogo.jpg]</span>
+
| <span class="plainlinks"> [http://www.apple.com/macosx/features/bootcamp.html http://gmod.org/wiki/images/0/09/AppleBootCampLogo.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.  '''A fully functional, 30 day trial version, of VMware Fusion is available for download.'''
+
| The [http://www.apple.com/macosx/ Leopard release of Mac OS (10.5)] 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 Linux.  From there you can install the VMware player for your OS.*
 
|}
 
|}
  
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{|
 
{|
 
| <span class="plainlinks"> [http://www.parallels.com/en/products/desktop/ http://gmod.org/wiki/images/5/51/ParallelsDesktopLogo.gif]</span>
 
| <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.  '''A fully functional, 15 day trial version of Parallels Desktop for Mac is available for download.'''
+
| 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.  Unlike Fusion, you can't run VMware images directly under Parallels.  You can in theory install VMware player on Linux running under Parallels, but no one in the class tried this approach, despite their being '''a fully functional, 15 day free trial version of Parallels Desktop for Mac available for download.'''
 
|}
 
|}
  
 
{|
 
{|
 
| valign="top" | '''*'''
 
| 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.''
+
| ''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.''
 
|}
 
|}
  
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= Cost =
+
= Cost and REgistration =
  
−
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.
+
There was no tuition cost for the GMOD Summer School.  Participants were responsible for their own travel, lodging and meal expenses.   
  
−
= Registration =
+
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).
−
 
+
−
'''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 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 the [http://www.millenniumhotels.com/millenniumdurham/index.html Millennium Hotel Durham].  The Millennium provides a free shuttle to and from NESCent.  We have negotiated a special room rate of $114 per night, including tax.  '''To get that rate [https://reservations.synxis.com/LBE/rez.aspx?Hotel=11543&Chain=5303&lang=1&group=7243&arrive=07/10/2008&depart=07/13/2008&adult=1&child=0 click here]''', or you call the Millennium directly at 1 800 633 5379. Finally you can book through the general [http://www.millenniumhotels.com/durham hotel website].  '''Our group code is 7243.'''
+
NESCent is adjacent to [http://www.ninthst.com/ Durham's 9<sup>th</sup> Street District] where participants ate most of their meals.
−
 
+
−
The Millennium offers a shuttle between the airport and the hotel for $35 each way.  If you are taking the Millennium shuttle, the hotel recommends calling them (919 383 8575) as soon as you are on the ground so they can dispatch the shuttle immediately.  You can also call them from a courtesy phone in the baggage area.  [http://www.charlenesaferide.com/index.html Charlene's Safe Ride] is another option, offering rides to the Millennium for around $30.  Taxi fare is around $42.
+
−
 
+
−
We are currently also negotiating room rates and shuttles with other lower cost, but also less convenient, housing options.
+
−
 
+
−
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], including breakfast options. 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 =
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<br />A flier with the schedule on it also available for [[Media:GMODSummerSchoolFlier2008.pdf|download]].
 
<br />A flier with the schedule on it also available for [[Media:GMODSummerSchoolFlier2008.pdf|download]].
 
|}
 
|}
−
 
−
Please post these at your organization.
 
  
 
= Acknowledgements =
 
= 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]]
 
[[Image:SummerSchoolSmall.png|center]]

Revision as of 00:00, 30 July 2008

SummerSchoolSmall.png
 2008 GMOD Summer School

July 11-13, 2008
National Evolutionary Synthesis
  Center (NESCent)
Durham, North Carolina, USA

__NOTITLE__

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.

Date 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?

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.

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

VmwareLogoSmall.jpg Participants were required to bring their own laptops, already capable of running a VMware system image.

The first session started with a basic VMware image built specifically for the course. We then built upon that image in each succeeding session. (We also had intermediate VMware images available if things did not go well, but these were not needed.)

VMware on Windows and Linux

WindowsLogoSmall.jpg LinuxLogoSmall.jpg 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 could also bring newer Macs with Intel processors. (The Intel processor is a requirement for all the packages discussed below.)

AppleSmall.gif 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 ($79.99) allows you to run VMware images, Windows and Linux under Mac OS. This was the most popular choice of the class's Mac users, perhaps because a fully functional, 30 day free trial version of VMware Fusion was available for download.
Mac OS 10.5 (Leopard) and Boot Camp
AppleBootCampLogo.jpg 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.*
Parallels Desktop for Mac
ParallelsDesktopLogo.gif Another option is Parallels Desktop for Mac ($79.99). Like Fusion, Parallels allows you to run Windows and Linux under Mac OS. Unlike Fusion, you can't run VMware images directly under Parallels. You can in theory install VMware player on Linux running under Parallels, but no one in the class tried this approach, despite their being a fully functional, 15 day free trial version of Parallels Desktop for Mac available for download.
* 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.

SummerSchoolPoster2008Thumb.png


A poster (US Letter size) announcing the 2008 GMOD Summer School is available for download.

SummerSchoolFlier2008.png


A flier with the schedule on it also available for download.

Acknowledgements

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

SummerSchoolSmall.png
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