Difference between revisions of "April 2012 GMOD Meeting"

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{{UnderConstruction|More details on this meeting will become available as the date gets closer.}}
 
  
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The 2012 GMOD meeting will be held April 5-6, in Washington, DC, immediately following [http://pir.georgetown.edu/biocuration2012/ Biocuration 2012].  If you are unfamiliar with GMOD Meetings, see the writeup of the [[September 2010 GMOD Meeting]] to get an idea.
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The 2012 [[Meetings|GMOD meeting]] was held April 5-6, in Washington, DC, immediately following [http://pir.georgetown.edu/biocuration2012/ Biocuration 2012].
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== Registration ==
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Registration will open in February.
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== Keynote Speaker ==
 
== Keynote Speaker ==
  
 
<div class="emphasisbox">
 
<div class="emphasisbox">
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{{ImageRight|DeannaChurch.jpg|Deanna M. Church|150|http://about.me/dmchurch}}
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[[File:DeannaChurch.jpg|right|95px|link=http://about.me/dmchurch|Deanna M. Church]]
 
<div style="font-size: 150%; padding-bottom: 0.3em">Deanna M. Church</div>
 
<div style="font-size: 150%; padding-bottom: 0.3em">Deanna M. Church</div>
  
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Research Institute at Mount Sinai Hospital in Toronto.
 
Research Institute at Mount Sinai Hospital in Toronto.
 
</div>
 
</div>
 +
Links to slides on SlideShare:
 +
<p>Part 1: http://www.slideshare.net/deanna.church/church-gmod2012-pt1</p>
 +
<p>Part 2: http://www.slideshare.net/deanna.church/church-gmod2012-pt2</p>
 
</div>
 
</div>
  
 
== Location ==
 
== Location ==
  
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The meeting will be held in the [http://maps.google.com/maps?q=Reiss+Science+Bldg,+Georgetown+University,+Washington,+District+of+Columbia+20007&hl=en&oe=utf-8&client=firefox-a&geocode=Ff-1UQId2_Nn-w&hnear=Reiss+Science+Bldg,+Washington,+District+of+Columbia,+20007&t=h&z=17 Reiss Science Building] at Georgetown University.
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The meeting will be held in the [http://maps.google.com/maps?q=Reiss+Science+Bldg,+Georgetown+University,+Washington,+District+of+Columbia+20007&hl=en&oe=utf-8&client=firefox-a&geocode=Ff-1UQId2_Nn-w&hnear=Reiss+Science+Bldg,+Washington,+District+of+Columbia,+20007&t=h&z=17 Reiss Science Building], room 103 (the lecture hall on the first floor) at Georgetown University.
 +
 
 +
== Agenda ==
 +
 
 +
Note: I am actively working on this agenda; everything about it may change (likely even) until this note goes away.
 +
 
 +
=== Thursday April 5===
 +
 
 +
{| class="wikitable"
 +
! Time
 +
! Topic
 +
! Presenter(s)
 +
! Presentation
 +
|-
 +
| 9:15
 +
| Introductions
 +
| [[User:Scott|Scott Cain]]
 +
|
 +
|-
 +
| 9:45
 +
| The State of GMOD
 +
| [[User:Scott|Scott Cain]]
 +
| [[Media:State_of_GMOD_2012.pdf|PDF]]
 +
|-
 +
| 10:15
 +
| Coffee break
 +
|
 +
|
 +
|-
 +
| 10:30
 +
| [http://www.reactome.org Reactome]
 +
| [[User:Robin.haw|Robin Haw]]
 +
| [[Media:2012_Reactome_GMOD.pdf|Slides]]
 +
|-
 +
| 11:00
 +
| Keynote: Navigating genomics resources at NCBI
 +
| Deanna Church
 +
|
 +
|-
 +
| 12:00
 +
| Lunch
 +
|
 +
|
 +
|-
 +
| 1:15
 +
| GLEAN and [[MAKER]]
 +
| Aaron Mackey
 +
| [[Media:Aarom_mackey.pptx|PPTX]]
 +
|-
 +
| 1:45
 +
| Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal
 +
| [[User:Richard Hayes|Richard Hayes]]
 +
|
 +
|-
 +
| 2:15
 +
| InterMOD
 +
| Ben Hitz
 +
| [[Media:Bhitz_InterMOD_2012.pdf|PDF]]
 +
|-
 +
| 2:45
 +
| Coffee break
 +
|
 +
|
 +
|-
 +
| 3:30
 +
| [[JBrowse]]
 +
| [[User:RBuels|Robert Buels]]
 +
| [[Media:RBuels_JBrowse_apr2012.pdf|PDF]]
 +
|-
 +
|
 +
| [[WebApollo]]
 +
| [[User:Elee|Ed Lee]]
 +
|
 +
|-
 +
|
 +
| Tengcha (A generic middle-ware for retrieving data from Chado databases)
 +
| [[User:justaddcoffee|Justin Reese]]
 +
| [[Media:JustinReese_April2012.pptx|PPTX]]
 +
|-
 +
| 5:00
 +
| Dinner (on your own)
 +
|
 +
|
 +
|-
 +
| 7:00
 +
| [[#Galaxy Workshop|Galaxy CloudMan Workshop]]
 +
| [[User:Clements|Dave Clements]]
 +
| [[Media:April2012GalaxyCloudManWorkshop.pdf|slides]], [http://galaxyproject.org/wiki/Admin/Cloud/Getting%20Started Hands-on]
 +
|-
 +
|}
 +
 
 +
===Friday April 6===
 +
 
 +
{| class="wikitable"
 +
! Time
 +
! Topic
 +
! Presenter(s)
 +
! Links
 +
|-
 +
| 9:15
 +
| [[Galaxy]] Update
 +
| [[User:Clements|Dave Clements]]
 +
| [[Media:April2012GalaxyUpdate.pdf|slides]], [http://usegalaxy.org/ Web site]
 +
|-
 +
| 9:45
 +
| [[Tripal]]
 +
| [[User:Laceyanne_sanderson|Lacey Sanderson]]
 +
| [[Media:LaceySanderson_Tripal_GMOD2012.ppt|PPT]]
 +
|-
 +
| 10:15
 +
| [http://www.abrowse.org/ ABrowse]
 +
| Kong Lei
 +
| [[Media:KongLei_abrowse.pptx|PPTX]]
 +
|-
 +
| 10:45
 +
| Coffee break
 +
|
 +
|
 +
|-
 +
| 11:00
 +
| [http://epigenomegateway.wustl.edu/ Epigenome Browser]
 +
| Xin Zhou
 +
| [[Media:XinZhou.pdf|PDF]]
 +
|-
 +
| 11:30
 +
| [http://cas-bioinfo.cas.unt.edu/mgsv/ Genome synteny viewer for customized data - extending GSV to multiple genome pairs]
 +
| [http://cas-bioinfo.cas.unt.edu/group/research.html Qunfeng Dong]
 +
| [[Media:QunfengDong_April2012.pdf|PDF]]
 +
|-
 +
| 12:00
 +
| Lunch
 +
|
 +
|
 +
|-
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| 1:00
 +
| GMOD's Future: Meetings and Focus, a discussion
 +
| [[User:Scott|Scott Cain]]
 +
|
 +
|-
 +
| colspan=4 bgcolor=#eee |
 +
|-
 +
| rowspan=9 | 1:15
 +
| colspan=3 | Lightning talks, including an MGI update, an introduction to the interaction Chado module, and PolyBrowse
 +
|-
 +
| MGI Update
 +
| Joel Richardson
 +
| [[media:April2012_MGIUpdate.pptx|PPTX]]
 +
|-
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| [[Chado]] Interaction Module
 +
| Andy Schroeder
 +
| [[media:April2012_ChadoInteractionModule.pdf|PDF]]
 +
|-
 +
| Using Images from Journals @ [http://xenbase.org Xenbase]
 +
| Jeff Bowes
 +
|
 +
|-
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| [http://nonb.abcc.ncifcrf.gov/Help/help_feature.php PolyBrowse]
 +
| Regina Cer
 +
| [[media:April2012_PolyBrowse.pdf|PDF]]
 +
|-
 +
| [http://biodbnet.abcc.ncifcrf.gov/ bioDBnet] & Flexible Database Integrator
 +
| Uma Mudunuri
 +
| [[media:April2012_FlexibleDatabaseIntegrator.pdf|PDF]]
 +
|-
 +
| [http://opossumbase.org/ OpossumBase]
 +
| [[User:Childers|Chris Childers]]
 +
|
 +
|-
 +
| Google Summer of Code
 +
| Robin Haw
 +
|
 +
|-
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| Community Building, Outreach and Support
 +
| [[User:Clements|Dave Clements]]<br />(+ Robin Haw)
 +
| [[media:April2012_CommunityBuilding.pdf|PDF]]
 +
|}
  
 
== Suggested Agenda Items ==
 
== Suggested Agenda Items ==
Line 58: Line 229:
 
* GLEAN and [[MAKER]] --Aaron Mackey
 
* GLEAN and [[MAKER]] --Aaron Mackey
 
* [[Galaxy]] Update -- [[User:Clements|Dave Clements]]
 
* [[Galaxy]] Update -- [[User:Clements|Dave Clements]]
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* Future [[Meetings|GMOD Meetings]]? 1) Stay the course or shift in focus 2) colocate with Biocuration, PAG, ... -- suggested by [[User:Clements|Dave Clements]]
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* Future [[Meetings|GMOD Meetings]]? -- suggested by [[User:Clements|Dave Clements]]
 +
*# Stay the course or shift in emphasis?
 +
*# Consistently co-locate with [[:Category:Conferences|another meeting]]: Biocuration, [[PAG 2012|PAG]], [[ISMB 2010|ISMB]], Genome Informatics, ...?
 
* GMOD in the Cloud -- suggested by [[User:Clements|Dave Clements]]
 
* GMOD in the Cloud -- suggested by [[User:Clements|Dave Clements]]
 +
* [http://www.abrowse.org/ ABrowse] a new genome browser -- Kong Lei
 +
* [http://reactome.org/ Reactome] -- Robin Haw
 +
* InterMOD update -- Ben Hitz
 +
* Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal -- [[User:Richard Hayes|Richard Hayes]] <!-- commented out by Scott; I agree, good topic (time permitting, this recent work involves GBrowse and should be broadly applicable) -->
 +
* BioStudio genome editor -- Sarah Richardson
 +
* [http://epigenomegateway.wustl.edu/ Epigenome Browser] -- Xin Zhou
 +
* Genome synteny viewer for customized data - extending GSV to multiple genome pairs -- Qunfeng Dong
 +
* JBrowse/WebApollo update - Rob Buels/Ed Lee
 +
* Tripal Update (New Release this Summer!) --Lacey Sanderson
 +
* GMOD and Google Summer of Code -- Robin Haw
  
 
== [[Galaxy]] Workshop ==
 
== [[Galaxy]] Workshop ==
−
{{ImageRight|GalaxyLogoBigger.png|Galaxy Workshop|200|Galaxy}}
 
  
−
A [[Galaxy]] workshop will be held the evening of April 5, after the first day of the meeting.  Details to follow.
+
<center>
 +
{|
 +
| rowspan="2" | [[File:GalaxyLogoBigger.png|280px|Galaxy Workshop]]
 +
| rowspan="2" | &nbsp;&nbsp;&nbsp;
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! style="text-align: left; font-size: 140%" | Galaxy CloudMan Workshop
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|-
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| style="font-size: 120%" | 7-9pm, April 5, 2012<br />Reiss Science Building, Georgetown University
 +
|}
 +
</center>
 +
 
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<div style="float: right; margin-left: 1em; padding-left: 1em; width: 220px; border: 1px solid">
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[[File:AmazonWebServicesLogo.png|200px|link=http://aws.amazon.com/|Amazon Web Services]]<br />
 +
This workshop is generously supported by an [http://aws.amazon.com/education/ AWS in Education] grant award
 +
</div>
 +
A [http://wiki.g2.bx.psu.edu/Admin/Cloud Galaxy CloudMan] workshop will be held the evening of April 5, after the first day of the meeting.  In this hands-on workshop, participants will use [http://wiki.g2.bx.psu.edu/Admin/Cloud Galaxy CloudMan] to setup a fully populated and scalable instance of the [[Galaxy]] data integration and analysis framework.  The workshop will use [http://aws.amazon.com/ Amazon Web Services]' [http://aws.amazon.com/ec2/ Elastic Compute Cloud (EC2)] and [http://aws.amazon.com/ebs/ Elastic Block Storage (EBS)] platforms.
 +
 
 +
Participants need to bring their own laptops (or partner with someone who brings one).
 +
 
 +
Please [[#Registration|register]] for the workshop when you register for the meeting.  The workshop is free, but space is limited and [[#Registration|registration]] is required.
 +
 
 +
Please contact [[User:Clements|Dave Clements]] if you have any questions.
 +
 
 +
== Registration ==
 +
 
 +
Registration is closed.
 +
 
 +
== Logistics ==
 +
 
 +
=== About the meeting space===
 +
 
 +
Apparently, the lecture hall where the meeting will be held is typically kept quite cold (60 degF) so wearing a jacket or sweater is a very good idea.
 +
 
 +
=== Hotels ===
 +
 
 +
We haven't reserved a block of rooms anywhere.  Rather, I suggest you look at the [http://pir.georgetown.edu/biocuration2012/hotels.html Biocurator meeting's hotel page] for places to stay.
 +
 
 +
=== Getting There ===
 +
 
 +
* [http://www.library.georgetown.edu/visiting/transportation Public Transportation to Georgetown]
 +
 
 +
== Feedback ==
 +
 
 +
<div style="font-size: 120%; text-align: center; margin: 1em; padding: 1em; border: 1px solid gray">Please '''[https://docs.google.com/spreadsheet/viewform?formkey=dFFTdmExc0Z1YlhhNS1IV085YWFYUFE6MQ provide feedback]''' on your experience at this meeting.</div>
 +
 
 +
Feedback will be summarized and posted here once we have it.
  
 
== Previous Meeting ==
 
== Previous Meeting ==

Latest revision as of 18:52, 8 October 2012

April2012MeetingLogo.png April 2012 GMOD Meeting

Immediately following Biocuration 2012
April 5-6, Washington, DC, United States


The 2012 GMOD meeting was held April 5-6, in Washington, DC, immediately following Biocuration 2012.

Keynote Speaker

Deanna M. Church
Deanna M. Church

Tentative title: "Navigating genomics resources at NCBI"

Deanna Church, Ph.D., is a staff scientist at NCBI, where she oversees several projects concerning managing and displaying genomic data, including dbVar, a database of genomic structural variation, the NCBI Map Viewer, the Clone database, and the NCBI Remap service. Dr. Church is also a member of the Genome Reference Consortium (GRC) an international consortium charged with improving the human, mouse, and zebrafish assemblies, and was an author on the two seminal manuscripts describing the human and mouse genome sequences. She has experience in molecular biology, genetics, genomics, bioinformatics, and is currently focusing on making genomic data more useful through large-scale annotation and comparative genomics. She graduated from the University of Virginia with a BA in Liberal Arts in 1990, and received her doctoral degree in the Biological Sciences at the University of California, Irvine in 1997. She performed postdoctoral work with Dr. Janet Rossant at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto.

Links to slides on SlideShare:

Part 1: http://www.slideshare.net/deanna.church/church-gmod2012-pt1

Part 2: http://www.slideshare.net/deanna.church/church-gmod2012-pt2

Location

The meeting will be held in the Reiss Science Building, room 103 (the lecture hall on the first floor) at Georgetown University.

Agenda

Note: I am actively working on this agenda; everything about it may change (likely even) until this note goes away.

Thursday April 5

Time Topic Presenter(s) Presentation
9:15 Introductions Scott Cain
9:45 The State of GMOD Scott Cain PDF
10:15 Coffee break
10:30 Reactome Robin Haw Slides
11:00 Keynote: Navigating genomics resources at NCBI Deanna Church
12:00 Lunch
1:15 GLEAN and MAKER Aaron Mackey PPTX
1:45 Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal Richard Hayes
2:15 InterMOD Ben Hitz PDF
2:45 Coffee break
3:30 JBrowse Robert Buels PDF
WebApollo Ed Lee
Tengcha (A generic middle-ware for retrieving data from Chado databases) Justin Reese PPTX
5:00 Dinner (on your own)
7:00 Galaxy CloudMan Workshop Dave Clements slides, Hands-on

Friday April 6

Time Topic Presenter(s) Links
9:15 Galaxy Update Dave Clements slides, Web site
9:45 Tripal Lacey Sanderson PPT
10:15 ABrowse Kong Lei PPTX
10:45 Coffee break
11:00 Epigenome Browser Xin Zhou PDF
11:30 Genome synteny viewer for customized data - extending GSV to multiple genome pairs Qunfeng Dong PDF
12:00 Lunch
1:00 GMOD's Future: Meetings and Focus, a discussion Scott Cain
1:15 Lightning talks, including an MGI update, an introduction to the interaction Chado module, and PolyBrowse
MGI Update Joel Richardson PPTX
Chado Interaction Module Andy Schroeder PDF
Using Images from Journals @ Xenbase Jeff Bowes
PolyBrowse Regina Cer PDF
bioDBnet & Flexible Database Integrator Uma Mudunuri PDF
OpossumBase Chris Childers
Google Summer of Code Robin Haw
Community Building, Outreach and Support Dave Clements
(+ Robin Haw) 		PDF

Suggested Agenda Items

  • GMOD/Chado/GBrowse update --Scott Cain
  • GLEAN and MAKER --Aaron Mackey
  • Galaxy Update -- Dave Clements
  • Future GMOD Meetings? -- suggested by Dave Clements
    1. Stay the course or shift in emphasis?
    2. Consistently co-locate with another meeting: Biocuration, PAG, ISMB, Genome Informatics, ...?
  • GMOD in the Cloud -- suggested by Dave Clements
  • ABrowse a new genome browser -- Kong Lei
  • Reactome -- Robin Haw
  • InterMOD update -- Ben Hitz
  • Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal -- Richard Hayes
  • BioStudio genome editor -- Sarah Richardson
  • Epigenome Browser -- Xin Zhou
  • Genome synteny viewer for customized data - extending GSV to multiple genome pairs -- Qunfeng Dong
  • JBrowse/WebApollo update - Rob Buels/Ed Lee
  • Tripal Update (New Release this Summer!) --Lacey Sanderson
  • GMOD and Google Summer of Code -- Robin Haw

Galaxy Workshop

Galaxy Workshop     Galaxy CloudMan Workshop
7-9pm, April 5, 2012
Reiss Science Building, Georgetown University


Amazon Web Services
This workshop is generously supported by an AWS in Education grant award

A Galaxy CloudMan workshop will be held the evening of April 5, after the first day of the meeting. In this hands-on workshop, participants will use Galaxy CloudMan to setup a fully populated and scalable instance of the Galaxy data integration and analysis framework. The workshop will use Amazon Web Services' Elastic Compute Cloud (EC2) and Elastic Block Storage (EBS) platforms.

Participants need to bring their own laptops (or partner with someone who brings one).

Please register for the workshop when you register for the meeting. The workshop is free, but space is limited and registration is required.

Please contact Dave Clements if you have any questions.

Registration

Registration is closed.

Logistics

About the meeting space

Apparently, the lecture hall where the meeting will be held is typically kept quite cold (60 degF) so wearing a jacket or sweater is a very good idea.

Hotels

We haven't reserved a block of rooms anywhere. Rather, I suggest you look at the Biocurator meeting's hotel page for places to stay.

Getting There

Feedback

Please provide feedback on your experience at this meeting.

Feedback will be summarized and posted here once we have it.

Previous Meeting

Retrieved from "http://gmod.org/mediawiki/index.php?title=April_2012_GMOD_Meeting&oldid=21959"