Difference between revisions of "PAG 2012"

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[[File:Paglogo.gif|right|link=http://www.intl-pag.org/|PAG 2012 Conference]]
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GMOD had a strong presence at the [http://www.intl-pag.org/ Plant and Animal Genome Conference (PAG XX)].  '''There was again an all-day dedicated [[#About GMOD Components|GMOD Workshop]] at PAG.'''  The workshop was in addition to the hands-on GBrowse tutorial that was also offered.  As in past years (see [[PAG 2011|2011]], [[PAG 2010|2010]], [[PAG 2009|2009]]), there were also many workshops, computer demos, and posters, either about GMOD and [[GMOD Components]], or using GMOD components.
! {{#icon: Paglogo.gif|PAG 2012 Conference||http://www.intl-pag.org/}}
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| GMOD will have a strong presence at the [http://www.intl-pag.org/ Plant and Animal Genome Conference (PAG XX)].  '''There will again be an all-day dedicated [[#About GMOD Components|GMOD Workshop]] at PAG.'''  The workshop is in addition to the hands-on GBrowse tutorial that is offered every year.  As in past years (see [[PAG 2011|2011]], [[PAG 2010|2010]], [[PAG 2009|2009]]), there will also be many workshops, computer demos, and posters, either about GMOD and [[GMOD Components]], or using GMOD components. This page will list known GMOD-related content once the program becomes available.
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|}
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{{UnderConstruction|}}
 
  
 
== About GMOD Components ==
 
== About GMOD Components ==
  
This list will become more populated as the program finalizes.
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Talks that prominently feature GMOD components.
  
 
{| class="wikitable"
 
{| class="wikitable"
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|-
 
|-
 
! rowspan="1" | Saturday<br />Jan 14
 
! rowspan="1" | Saturday<br />Jan 14
|
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! Workshop
|
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! 10:20-12:30
|
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| '''[http://pag.confex.com/pag/xx/webprogram/Paper3059.html DNA Subway]''', Jason Williams, Uwe Hilgert, [[User:Mckays|Sheldon McKay]]
|
+
| [[Apollo]], [[GBrowse]]
 
|-
 
|-
! rowspan="1" | Sunday<br />Jan 15
+
! rowspan="2" | Sunday<br />Jan 15
 
! rowspan="1" | Computer & Training Workshop
 
! rowspan="1" | Computer & Training Workshop
! 1:30-3:40
+
! rowspan="1" | 1:30-3:40
| '''The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own [[GBrowse]]''', [[User:Scott|Scott Cain]]
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| '''The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own [[GBrowse]]''', [[User:Scott|Scott Cain]].    Get the [ftp://ftp.gmod.org/pub/gmod/Meetings/2012/PAG/gmod_pag_2012.tar.bz2 VMware image via ftp]
 
| [[GBrowse]]
 
| [[GBrowse]]
 +
|-
 +
! [http://pag.confex.com/pag/xx/webprogram/Session1139.html Cloud Computing Workshop]
 +
! 1:40-2:10
 +
| '''[http://pag.confex.com/pag/xx/webprogram/Paper4623.html The Galaxy Platform: running analyses in the cloud]''', Dannon Baker
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| [[Galaxy]]
 
|-
 
|-
 
! rowspan="1" | Monday<br />Jan 16
 
! rowspan="1" | Monday<br />Jan 16
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! Computer & Training Workshop
 
! Computer & Training Workshop
 
! 3:50-6:00
 
! 3:50-6:00
| '''[http://www.intl-pag.org/19/19-gramene.html Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses]''', Ken Youens-Clark
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| '''[http://pag.confex.com/pag/xx/webprogram/Session1121.html Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses]''', Ken Youens-Clark, Taner Sen
| [[CMap]]
+
| [[CMap]], [[Pathway Tools]]
 
|-
 
|-
 
! rowspan="1" | Wednesday<br />Jan 18
 
! rowspan="1" | Wednesday<br />Jan 18
! Workshop
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! rowspan="1" | [http://pag.confex.com/pag/xx/webprogram/Session1123.html GMOD Tutorial]
! 10:20-5:00
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| colspan="5" style="padding: 1em" bgcolor="#ddffdd" | <span style="font-size:140%;">'''10:20-5:00''', [[User:Scott|Scott Cain]] Pacific Salon 3</span>
| colspan="4" style="font-size:140%; padding: 1em" bgcolor="#ddffdd" | '''GMOD Workshop''', [[User:Scott|Scott Cain]] Pacific Salon 3
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{| class="wikitable"
 +
! 10:20-10:30
 +
| '''Introduction'''
 +
| [[User:Scott|Scott Cain]]
 +
|-
 +
! 10:30-11:30
 +
| '''[[Galaxy]]''' ([[Media:PAG2012GalaxyIntroTalk.pdf|PDF]])
 +
| [[User:Clements|Dave Clements]]
 +
|-
 +
! 11:30-12:30
 +
| '''[[MAKER]]'''
 +
| [[User:Bmoore|Barry Moore]]
 +
|-
 +
! 1:30-2:30
 +
| '''[[JBrowse]]''' ([[Media:Rbuels_jbrowse_pag2012.pdf|PDF]])
 +
| [[User:RobertBuels|Robert Buels]]
 +
|-
 +
! 2:30-3:30
 +
| '''[[GBrowse_syn|Using the Generic Synteny Browser (GBrowse_syn)]]'''
 +
| [[User:Mckays|Sheldon McKay]]
 +
|-
 +
! 3:45-4:45
 +
| '''[[Tripal|Tripal: A Construction Toolkit for Online Genomic Databases]]'''
 +
| [[User:Sficklin|Stephen Ficklin]]
 +
|-
 +
|}
 
|}
 
|}
  
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! rowspan="1" | Tuesday<br />Jan 17
 
! rowspan="1" | Tuesday<br />Jan 17
 
| rowspan="1" | Workshop
 
| rowspan="1" | Workshop
| 3:50-7:00
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|
| '''DNA Subway''', Uwe Hilgert
+
|
|  
+
|
 
|-
 
|-
 
! rowspan="1" | Wednesday<br />Jan 18
 
! rowspan="1" | Wednesday<br />Jan 18
 
| Computer Demos
 
| Computer Demos
| 10:20-12:30
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| 11:35-11:50
|
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| [http://pag.confex.com/pag/xx/webprogram/Paper3329.html MAPHiTS: an efficient workflow for SNP detection], Marc Bras ([[Media:PAG2012MAPHiTSTalk.pdf|PDF]], [http://urgi.versailles.inra.fr/download/w_other/MAPHiTS-PAG_DemoFinal.m4v Video (no sound)])
|
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| [[Galaxy]]
 
|}
 
|}
  
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! Components
 
! Components
 
|-
 
|-
! rowspan="1" valign="top" | EVEN Numbered Poster Session<br />Monday<br />Jan 16
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! rowspan="2" valign="top" | EVEN Numbered Poster Session<br />Monday<br />Jan 16
! rowspan="1" valign="top" | 10:00-11:30
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! rowspan="2" valign="top" | 10:00-11:30
|
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| [http://pag.confex.com/pag/xx/webprogram/Paper2810.html P698: Developing Tools for Genomic Analysis in a Wide Bulb Onion (''Allium cepa L.'') Cross], John McCallum
|
+
| [[Galaxy]]
 +
|-
 +
| [http://pag.confex.com/pag/xx/webprogram/Paper3290.html P936: DDBJ Sequence Read Archive and a cloud-computing based annotation tool for new-generation sequencing data], Hideki Nagasaki
 +
| [[Galaxy]]
 
|-
 
|-
 
! colspan="4" |
 
! colspan="4" |
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! rowspan="1" valign="top" | ODD Numbered Poster Session<br>Monday<br />Jan 16
 
! rowspan="1" valign="top" | ODD Numbered Poster Session<br>Monday<br />Jan 16
 
! rowspan="1" valign="top" | 3:00-4:30
 
! rowspan="1" valign="top" | 3:00-4:30
|  
+
| [http://pag.confex.com/pag/xx/webprogram/Paper2789.html P987: GMOD in the Cloud], [[User:Scott|Scott Cain]] ([[Media:PAG2012GMODInTheCloud.pdf|PDF]])
|
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| [[Chado]], [[Ergatis]], [[Galaxy]], [[GBrowse]], [[JBrowse]], [[Tripal]]
 
|-
 
|-
 
|}
 
|}
 
 
<!--
 
{{ImageRight|Jan2009MtgLogoNoText.png|GMOD Roadshow||}}
 
 
== Roadshow ==
 
 
As shown above, GMOD will have a large number of representatives at PAG XIX.  Three of them, [[User:DanB|Dan Blankenberg]] of the [[Galaxy]] project, [[User:MitchSkinner|Mitch Skinner]], lead [[JBrowse]] developer, and [[User:Scott|Scott Cain]], GMOD Project Coordinator, are available to visit organizations in the San Diego area during the conference.
 
 
If you would like to arrange a visit with '''Dan, Mitch''', and/or '''Scott''' to discuss '''[[Galaxy]], [[JBrowse]]''', or any other '''[[GMOD Components]]''', please contact [mailto:dan@bx.psu.edu Dan], [mailto:mitch_skinner@berkeley.edu Mitch] and [mailto:scott@scottcain.net Scott] directly.
 
 
== Flier ==
 
 
A [[:Image:GMODatPAG2011.pdf|flier highlighting some of the GMOD-related content at PAG XIX is available]].  Hard copies of this flier will be available at the conference.  If you will be presenting at PAG, please feel free to print out several copies and make them available at your talk or poster.
 
-->
 
  
 
== See Also ==
 
== See Also ==

Latest revision as of 18:18, 2 October 2012

PAG 2012 Conference

GMOD had a strong presence at the Plant and Animal Genome Conference (PAG XX). There was again an all-day dedicated GMOD Workshop at PAG. The workshop was in addition to the hands-on GBrowse tutorial that was also offered. As in past years (see 2011, 2010, 2009), there were also many workshops, computer demos, and posters, either about GMOD and GMOD Components, or using GMOD components.


About GMOD Components

Talks that prominently feature GMOD components.

Day Track Time Title & Presenter Components
Saturday
Jan 14
Workshop 10:20-12:30 DNA Subway, Jason Williams, Uwe Hilgert, Sheldon McKay Apollo, GBrowse
Sunday
Jan 15
Computer & Training Workshop 1:30-3:40 The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse, Scott Cain. Get the VMware image via ftp GBrowse
Cloud Computing Workshop 1:40-2:10 The Galaxy Platform: running analyses in the cloud, Dannon Baker Galaxy
Monday
Jan 16
Tuesday
Jan 17
Computer & Training Workshop 3:50-6:00 Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses, Ken Youens-Clark, Taner Sen CMap, Pathway Tools
Wednesday
Jan 18
GMOD Tutorial 10:20-5:00, Scott Cain Pacific Salon 3
10:20-10:30 Introduction Scott Cain
10:30-11:30 Galaxy (PDF) Dave Clements
11:30-12:30 MAKER Barry Moore
1:30-2:30 JBrowse (PDF) Robert Buels
2:30-3:30 Using the Generic Synteny Browser (GBrowse_syn) Sheldon McKay
3:45-4:45 Tripal: A Construction Toolkit for Online Genomic Databases Stephen Ficklin

Projects Using GMOD Components

Day Track Time Title & Presenter Components
Saturday
Jan 14
Computer Demos 1:30-3:40
Sunday
Jan 15
Computer Demos 3:50-6:00
Monday
Jan 16
Computer Demos 12:50-3:00
Tuesday
Jan 17
Workshop
Wednesday
Jan 18
Computer Demos 11:35-11:50 MAPHiTS: an efficient workflow for SNP detection, Marc Bras (PDF, Video (no sound)) Galaxy

Posters

Track Time Title & Author Components
EVEN Numbered Poster Session
Monday
Jan 16
10:00-11:30 P698: Developing Tools for Genomic Analysis in a Wide Bulb Onion (Allium cepa L.) Cross, John McCallum Galaxy
P936: DDBJ Sequence Read Archive and a cloud-computing based annotation tool for new-generation sequencing data, Hideki Nagasaki Galaxy
Track Time Title & Author Components
ODD Numbered Poster Session
Monday
Jan 16
3:00-4:30 P987: GMOD in the Cloud, Scott Cain (PDF) Chado, Ergatis, Galaxy, GBrowse, JBrowse, Tripal

See Also