Difference between revisions of "Jan 2014 GMOD Meeting"

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[[File:2014-gmod-san-diego.png|right|alt=January 2014 GMOD Community Meeting logo|300px]]
 
[[File:2014-gmod-san-diego.png|right|alt=January 2014 GMOD Community Meeting logo|300px]]
  
GMOD will be holding a community meeting on January 16th and 17th 2014 in San Diego, CA, immediately after [http://www.intlpag.org/ PAG XXII].
+
GMOD held a community meeting in San Diego in January 2014. Materials from the meeting are currently being gathered and will all be assembled here. If you attended the meeting and have slides or a poster to share, please add it to the wiki or email it to [mailto:help@gmod.org the GMOD helpdesk] and we will post it for you.
  
'''[https://gmod-sandiego-2014.eventbrite.com/ Please register online at Eventbrite by January 14th 2014].'''
 
 
For those who would like to present a talk or poster, the meeting registration form includes a section for submitting the presentation title and abstract. If you presented a GMOD-related poster at PAG, we welcome you to present it at the GMOD Community Meeting.
 
 
If you have any suggestions or requests for the meeting, please contact the [mailto:help@gmod.org GMOD help desk].
 
  
 
==Keynote Speaker==
 
==Keynote Speaker==
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<div style="font-size: 120%">
 
<div style="font-size: 120%">
Tentative title: "A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes"
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"A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes"
  
 
Andrew Su is an Associate Professor in the Department of Molecular and Experimental Medicine at the Scripps Research Institute. His research focuses on applying the tools of bioinformatics, statistics, crowdsourcing, and computer science to biomedical discovery.  Prior to joining Scripps in July 2011, he was the Associate Director of Bioinformatics at the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, CA. He also serves as an Executive Editor of the journal Gene and on the Scientific Advisory Board of the Gene Ontology Consortium.
 
Andrew Su is an Associate Professor in the Department of Molecular and Experimental Medicine at the Scripps Research Institute. His research focuses on applying the tools of bioinformatics, statistics, crowdsourcing, and computer science to biomedical discovery.  Prior to joining Scripps in July 2011, he was the Associate Director of Bioinformatics at the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, CA. He also serves as an Executive Editor of the journal Gene and on the Scientific Advisory Board of the Gene Ontology Consortium.
 
</div>
 
</div>
 
</div>
 
</div>
 
==Finding the meeting room==
 
 
To get to the meeting room, go through the lobby and into the diner.  Turn left at the end of the bar, follow the hall until the end.
 
 
==Registration==
 
 
Please [https://gmod-sandiego-2014.eventbrite.com/ register online at EventBrite].
 
 
The registration fee includes lunch on both days.
 
  
 
==Agenda==
 
==Agenda==
 
This is a tentative agenda, some times may shift around still.
 
  
 
===Thursday, January 16===
 
===Thursday, January 16===
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| The State of GMOD
 
| The State of GMOD
 
| [[User:Scott|Scott Cain]]
 
| [[User:Scott|Scott Cain]]
| [[Media:State_of_GMOD_2014.pdf|Slides]]
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| [[Media:State_of_GMOD_2014.pdf|Slides]], [http://youtu.be/8DXWzgag8R4 YouTube]
 
|-
 
|-
 
| 10:15
 
| 10:15
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| High throughput comparative genomics using a Chado backend
 
| High throughput comparative genomics using a Chado backend
 
| [[User:Mara Kim|Mara Kim]]
 
| [[User:Mara Kim|Mara Kim]]
| [[Media:MaraKim_GMOD2014.pdf|Slides]]
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| [[Media:MaraKim_GMOD2014.pdf|Slides]], [http://youtu.be/Soam8O3g1jg YouTube]
 
|-
 
|-
 
| 11:00
 
| 11:00
 
| '''Keynote:''' A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes
 
| '''Keynote:''' A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes
 
| Andrew Su
 
| Andrew Su
|[[Media:AndrewSu_GMOD2014.pptx|Slides]]
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|[[Media:AndrewSu_GMOD2014.pptx|Slides]],[https://www.youtube.com/watch?v=RVijs5ry05E YouTube] and [https://www.youtube.com/watch?v=dGHXo-iNsyU some of the discussion following]
 
|-
 
|-
 
| 12:00
 
| 12:00
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| 2:30
 
| 2:30
 
| Crowdsourcing genomics with Ash dieback
 
| Crowdsourcing genomics with Ash dieback
| Dan MacLean and Martin Page
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| [http://www.tsl.ac.uk/profile/dan-maclean.asp Dan MacLean] and [http://www.tsl.ac.uk/profile/martin-page.asp Martin Page]
| [[Media:Dan_MacLean_2014.pdf|Slides]]
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| [https://github.com/danmaclean/talks/tree/master/GMOD_san_diego_jan_2014 Slides and resources], [http://youtu.be/wjne4d32bbU YouTube]
 
|-
 
|-
 
| 3:00
 
| 3:00
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|-
 
|-
 
| 3:45
 
| 3:45
| Drunken Noodle (Really Ken?)
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| Drunken Noodle (really, Ken?)
 
| Ken Youens-Clark
 
| Ken Youens-Clark
| [[Media:Ken_Youens_Clark_2014.pdf|Slides]]
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| [[Media:2014-KYClark-CMap.pdf|Slides]]
 
|-
 
|-
 
| 4:15
 
| 4:15
 
| Creating and Maintaining Sustainable Scientific Resources
 
| Creating and Maintaining Sustainable Scientific Resources
 
| Bob Muller
 
| Bob Muller
| [[Media:Bob_Muller_2014.pdf|Slides]]
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| [[Media:Bob_Muller_2014.pdf|Slides]], [http://youtu.be/KsBZxiGsOps YouTube]
 
|-
 
|-
 
| 4:45
 
| 4:45
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| [[User:Scott|Scott Cain]]
 
| [[User:Scott|Scott Cain]]
 
|
 
|
|-
 
| 5:00
 
| colspan=3 |Dinner (on your own)
 
|-
 
 
|}
 
|}
  
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|-
 
|-
 
| 09:15
 
| 09:15
| Unit testing for chado databases
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| Unit testing for Chado databases
 
| Siddhartha Basu
 
| Siddhartha Basu
| [http://testgenomes.dictybase.org/test-chado.slide Slides]
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| [http://testgenomes.dictybase.org/test-chado.slide Slides], [http://youtu.be/9F6rskt3JRM YouTube]
 
|-
 
|-
 
| 09:45
 
| 09:45
 
| [[Tripal]]
 
| [[Tripal]]
 
| Lacey Sanderson
 
| Lacey Sanderson
| [[Media:LaceySanderson_Tripal_GMOD2014.ppt|Slides]]
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| [[Media:Tripal-GMOD-2014.pptx|Slides]] [http://www.youtube.com/watch?v=qSwb3cGtzJg YouTube]
 
|-
 
|-
 
| 10:15
 
| 10:15
 
| The FlyBase health module
 
| The FlyBase health module
 
| Andy Schroeder
 
| Andy Schroeder
| [[Media:2014_Andy_Schroeder.pdf|Slides]]
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| [[Media:2014_Chado_health_module.pdf|Slides]], [http://youtu.be/ahA4EYgY-G0 YouTube]
 
|-
 
|-
 
| 10:45
 
| 10:45
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| [[Canto]] community curation tool (screencast)
 
| [[Canto]] community curation tool (screencast)
 
| [[User:Girlwithglasses|Amelia Ireland]] for Val Wood, PomBase
 
| [[User:Girlwithglasses|Amelia Ireland]] for Val Wood, PomBase
| [[http://youtu.be/ Video]]
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| [http://www.youtube.com/watch?v=-cj_PdJi68A Video at YouTube]
 
|-
 
|-
 
| 12:00
 
| 12:00
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|-
 
|-
 
| 1:15
 
| 1:15
| MAKER
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| [[MAKER]]
 
| Daniel Ence  
 
| Daniel Ence  
 
| [[Media:Daniel_Ence_2014.pptx|Slides]]
 
| [[Media:Daniel_Ence_2014.pptx|Slides]]
 
|-
 
|-
 
| 1:45
 
| 1:45
| colspan=3 | Lightning talks, including CViT (Chromosome Visualization Tool)
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| Google Summer of Code
 +
| Amelia Ireland
 +
| [[GSoC|GSoC and the Genome Informatics group]]
 
|-
 
|-
 +
| 2:00
 +
| Lightning talks
 +
| colspan=2 |
 +
*CViT: Chromosome Visualization Tool - [[Media:Cvit GMOD2014.pptx|Slides]] - [http://youtu.be/Ye2WVFwvmz0 YouTube]
 +
*Updates from the Cancer Genome Project - [[Media:2014 CGP updates.pdf|Slides]]
 +
*Evolutionary Synthesis of Human Pregnancy - [[Media:2014-McGary.pdf|Slides]]
 
|}
 
|}
  
==Logistics==
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===Posters===
  
The meeting will take place at the [http://www.bw7seas.com/ Best Western Seven Seas] (a short distance from the Town and Country where the [http://www.intlpag.org/ Plant and Animal Genomes meeting] is held).  A block of rooms is being held for attendees of the GMOD meeting at a very good room rate.  To make reservations in this block, you '''must call''' (not reserve online) (800) 328-1618 and ask for the GMOD rate.
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[[Media:Gitc-giab-poster.pdf|GMOD in the Cloud and GMOD in a Box: Instant Virtual Servers for Genomics Data]]
  
[http://doodle.com/csctga8kgxfkmuas Doodle for airport shuttles]
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[[Media:2014 CGP Poster.pdf|Challenges in providing a genome browser for large-scale projects]]
  
 
[[Category:Meetings]]
 
[[Category:Meetings]]
 
[[Category:GMOD Community]]
 
[[Category:GMOD Community]]

Latest revision as of 07:49, 8 May 2014

January 2014 GMOD Community Meeting logo

GMOD held a community meeting in San Diego in January 2014. Materials from the meeting are currently being gathered and will all be assembled here. If you attended the meeting and have slides or a poster to share, please add it to the wiki or email it to the GMOD helpdesk and we will post it for you.


Keynote Speaker

Andrew Su
Andrew Su

"A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes"

Andrew Su is an Associate Professor in the Department of Molecular and Experimental Medicine at the Scripps Research Institute. His research focuses on applying the tools of bioinformatics, statistics, crowdsourcing, and computer science to biomedical discovery. Prior to joining Scripps in July 2011, he was the Associate Director of Bioinformatics at the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, CA. He also serves as an Executive Editor of the journal Gene and on the Scientific Advisory Board of the Gene Ontology Consortium.

Agenda

Thursday, January 16

Time Topic Presenter(s) Presentation
09:15 Introductions Scott Cain
09:30 The State of GMOD Scott Cain Slides, YouTube
10:15 Coffee break
10:30 High throughput comparative genomics using a Chado backend Mara Kim Slides, YouTube
11:00 Keynote: A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes Andrew Su Slides,YouTube and some of the discussion following
12:00 Lunch and poster session
1:15 JBrowse and WebApollo Robert Buels Slides
2:00 Migrating from GBrowse to JBrowse Richard Hayes Slides
2:30 Crowdsourcing genomics with Ash dieback Dan MacLean and Martin Page Slides and resources, YouTube
3:00 Coffee break
3:15 Galaxy Project Update Dave Clements Slides
3:45 Drunken Noodle (really, Ken?) Ken Youens-Clark Slides
4:15 Creating and Maintaining Sustainable Scientific Resources Bob Muller Slides, YouTube
4:45 Wrap up Scott Cain

Friday, January 17

Time Topic Presenter(s) Links
09:15 Unit testing for Chado databases Siddhartha Basu Slides, YouTube
09:45 Tripal Lacey Sanderson Slides YouTube
10:15 The FlyBase health module Andy Schroeder Slides, YouTube
10:45 Coffee break
11:00 Coffee Genome Hub Stéphanie Bocs Slides
11:30 Canto community curation tool (screencast) Amelia Ireland for Val Wood, PomBase Video at YouTube
12:00 Lunch
1:15 MAKER Daniel Ence Slides
1:45 Google Summer of Code Amelia Ireland GSoC and the Genome Informatics group
2:00 Lightning talks
  • CViT: Chromosome Visualization Tool - Slides - YouTube
  • Updates from the Cancer Genome Project - Slides
  • Evolutionary Synthesis of Human Pregnancy - Slides

Posters

GMOD in the Cloud and GMOD in a Box: Instant Virtual Servers for Genomics Data

Challenges in providing a genome browser for large-scale projects