Difference between revisions of "Jun 2016 GMOD Meeting"

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<center>Fancy logo here. </center>
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| rowspan="1" | [[Image:GMOD2016ColorsBigLetters_300px.png|300px|center]]
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| style="font-size: 170%; line-height: 120%" |<b>2016 GMOD Meeting</b><br /><br />June 30 - July 1, 2016<br />[http://iu.edu/ Indiana University]<br />Bloomington, Indiana, United States <br /><br /><div style="font-size: 80%; line-height: 80%"><br /><br />[https://twitter.com/search?q=%23GMOD2016 #GMOD2016] &nbsp;&nbsp; [https://twitter.com/gmodproject @gmodproject]</div>
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|}
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</center>
  
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GMOD will be holding a community meeting on June 30th and July 1st in Bloomington, IN, immediately after the [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference (GCC2016)].
 
  
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'''[https://gmod-sandiego-2014.eventbrite.com/ Please register online at Eventbrite by June 20th 2016].'''
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GMOD will be holding a community meeting on June 30th and July 1st in Bloomington, IN, immediately after the [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference (GCC2016)].  [[Meetings|GMOD Meetings]] are a mix of [[GMOD Membership#Users|user]] and [[GMOD Membership#Developers|developer]] presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing.
 +
 
 +
 
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Please register online at Eventbrite by June 20th 2016.''' Early bird registration ends May 21.
  
 
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.
 
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.
Line 9: Line 16:
 
If you have any suggestions or requests for the meeting, please contact the [mailto:help@gmod.org GMOD help desk].
 
If you have any suggestions or requests for the meeting, please contact the [mailto:help@gmod.org GMOD help desk].
  
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==Keynote Speaker==
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== About GMOD ==
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'''GMOD''' is the Generic Model Organism Database project, a collection of interoperable open-source [[GMOD Components|software components]] for annotating, visualizing, managing and analyzing biological data.  GMOD is also an active community of software developers and biologists addressing common challenges with their data.
 +
 
 +
The GMOD suite includes widely used tools such as [[GBrowse]] and [[JBrowse]] (and [[WebGBrowse]]) for genome browsing, [[Apollo]], [[Canto]] and [[MAKER]] for genome annotation, [[GBrowse_syn]] and [[CMap]] for comparative genomics visualization, [[Chado]], [[BioMart]] and [[InterMine]] for data integration, management, and querying, and [[Galaxy]] and [[Ergatis]] (and [[ISGA]]) for data analysis.
 +
 
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<!-- ==Keynote Speaker==
  
 
<div class="emphasisbox">
 
<div class="emphasisbox">
 
To be announced
 
To be announced
 
</div>
 
</div>
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-->
  
 
==Registration==
 
==Registration==
  
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Please [https://gmod2016.eventbrite.com/ register online at EventBrite].  Early bird registration ends May 30th.
+
Please register online at EventBrite.  Early bird registration ends May 30th.
  
 
The registration fee includes lunch on June 30th.
 
The registration fee includes lunch on June 30th.
 +
 +
==Draft Agenda==
 +
 +
===Walnut room, Thursday, June 30===
 +
 +
 +
{| class="wikitable"
 +
! Time
 +
! Topic
 +
! Presenter(s)
 +
! Presentation
 +
|-
 +
|08:50
 +
|Pre-meeting continental breakfast
 +
|
 +
|
 +
|-
 +
|09:15
 +
|  Introductions
 +
|
 +
|
 +
|-
 +
|09:40
 +
| The State of GMOD
 +
|[[User:Scott|Scott Cain]]
 +
| [[Media:GMOD2016_GMOD.pdf|Intro]],  [[Media:GMOD2016_InterMine.pdf|InterMine]],  [https://www.dropbox.com/s/7i39svwlegfr4rq/MAKER_GMOD_2016.pdf?dl=0  MAKER]
 +
|-
 +
|10:10
 +
| Introduction to uMOD
 +
|[[User:Scott|Scott Cain]]
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| [[Media:GMOD2016_uMOD.pdf|Slides]]
 +
|-
 +
|10:35
 +
| Coffee
 +
|
 +
|
 +
|-
 +
|10:50
 +
| GMOD in Action: The Legume Federation Project
 +
| Ethalinda Cannon
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| [[Media:LegFed_GMOD2016.pdf|Slides]]
 +
|-
 +
|11:20
 +
| [[JBrowse]] Update
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| Eric Yao
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| [https://drive.google.com/a/berkeley.edu/file/d/0BzJAAJpIcu9hVFloS2R6ZUxhcUE/view?usp=sharing Slides]
 +
|-
 +
|11:50
 +
|Lunch
 +
|
 +
|
 +
|-
 +
|1:00 
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| [[Apollo]]: Collaborative Manual Annotation in the GMOD Workflow
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| [https://github.com/nathandunn Nathan Dunn]
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|[http://f1000research.com/slides/5-1389 Slides]
 +
|-
 +
|1:30 
 +
| [[Tripal]] Update
 +
| Lacey-Anne Sanderson
 +
|
 +
|-
 +
|2:30 
 +
|Coffee
 +
|
 +
|
 +
|-
 +
|2:45
 +
|[[Galaxy]] Update
 +
|[[User:Clements|Dave Clements]], [https://github.com/bgruening Bjöern Grüning]
 +
| [[:File:GMOD2016_Galaxy.pdf|Slides]]
 +
|-
 +
|3:15 
 +
|EvidentialGene project at http://eugenes.org/EvidentialGene/
 +
|  Don Gilbert
 +
| [http://arthropods.eugenes.org/EvidentialGene/about/evigenegmod1606iu.pdf Slides]
 +
|-
 +
|3:45
 +
| FlyBase Update and Chado discussion
 +
|[[User:Jogoodma|Josh Goodman]]
 +
|
 +
|}
 +
 +
===Friday, July 1===
 +
 +
{| class="wikitable"
 +
! Time
 +
! Topic
 +
! Presenter(s)
 +
! Presentation
 +
|-
 +
|08:50
 +
|Pre-meeting continental breakfast
 +
|
 +
|
 +
|-
 +
|09:15
 +
|Tripal Expression module and search
 +
|Meg Staton
 +
|[[:File:GMOD_Staton.pdf|Slides]]
 +
|-
 +
|09:45
 +
| Lightning talks, including Asela Dassanayake, Eric Rasche and Thoba Lose
 +
|
 +
|[[Media:GMOD_Asela.pdf|Asela/LanzaTech]]
 +
|-
 +
|11:30
 +
|Lunch (on your own)
 +
|
 +
|
 +
|-
 +
|1:00
 +
| Tripal workshop
 +
|
 +
|
 +
|}
  
 
==Agenda items==
 
==Agenda items==
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More to be added as we confirm more speakers.  If you are interested in giving a talk please contact the [mailto:help@gmod.org GMOD help desk].
 
More to be added as we confirm more speakers.  If you are interested in giving a talk please contact the [mailto:help@gmod.org GMOD help desk].
  
−
 
+
* GMOD project updates, including [[Tripal]], [[Galaxy]], [[JBrowse]], [[Chado]], [[MAKER]].
−
* GMOD project updates, including [[Tripal]], [[Galaxy]], [[JBrowse]], [[Chado]], [[MAKER]] and [[WebApollo]].
+
* Introduction to umod ([[User:Scott|Scott Cain]])
 +
* "Apollo:  Collaborative Manual Annotation in the GMOD Workflow" (Nathan Dunn)
 +
* Tripal update (Lacey Sanderson)
 +
* Tripal Expression module and search (Ming Chen)
 +
* EvidentialGene project at  http://eugenes.org/EvidentialGene/ ([[User:Dongilbert|Don Gilbert]])
 +
* DictyBase on using and extending GMOD tools (Chado, JBrowse) and new infrastructure(docker and possibly kubernetes) (Siddhartha Basu)
 +
* GMOD in Action: The Legume Federation Project (Ethalinda Cannon)
 +
*[[Tripal]] Workshop (Friday afternoon)
  
 
==Logistics==
 
==Logistics==
  
−
If you require lodging, we have partnered with the [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference],  please go here: [https://indianauniv.ungerboeck.com/prod/SignIn.aspx?ReturnUrl=%2fprod%2femc00%2fregister.aspx%3fOrgCode%3d10%26EvtID%3d6925%26AppCode%3dREG&OrgCode=10&EvtID=6925&DictSeq=27&Lang=*&AppCode=REG&CultureInfo=en-US GCC16 registration page] .
+
If you require lodging, we have partnered with the [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference].
 +
 
 +
You DO NOT have to register for the GCC2016 conference to utilize housing. Just check HOUSING ONLY when registering.
 +
 
 +
=== Shared Rides ===
 +
 
 +
Please put your travel times [https://docs.google.com/spreadsheets/d/1sBD74e9DTldNshPgZzRNQspts1f9pASjMww105-m-5s/edit#gid=0 here].
 +
 
 +
 
 +
<center>
 +
<div class="emphasisbox">
 +
<div style="font-size: 115%">"It's tempting to see bioinformatics as a collection of potential problems. Being at a GMOD meeting helps us see bioinformatics as a collection of potential solutions."</div>
 +
<div style="padding-top: 0.5em">Isabelle Phan, [http://www.seattlebiomed.org SBRI], and past GMOD meeting participant</div>
 +
</div>
 +
</center>
  
−
You DO NOT have to register for the GCC16 conference to utilize housing.  Just check HOUSING ONLY when registering.
+
<center>(Thanks to [[User:Clements|Dave Clements]] for the nice logo)</center>
  
 
[[Category:Meetings]]
 
[[Category:Meetings]]
 
[[Category:GMOD Community]]
 
[[Category:GMOD Community]]

Latest revision as of 03:23, 23 August 2016

GMOD2016ColorsBigLetters 300px.png
 2016 GMOD Meeting

June 30 - July 1, 2016
Indiana University
Bloomington, Indiana, United States


GMOD will be holding a community meeting on June 30th and July 1st in Bloomington, IN, immediately after the 2016 Galaxy Community Conference (GCC2016). GMOD Meetings are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing.


Please register online at Eventbrite by June 20th 2016. Early bird registration ends May 21.

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 have any suggestions or requests for the meeting, please contact the GMOD help desk.

About GMOD

GMOD is the Generic Model Organism Database project, a collection of interoperable open-source software components for annotating, visualizing, managing and analyzing biological data. GMOD is also an active community of software developers and biologists addressing common challenges with their data.

The GMOD suite includes widely used tools such as GBrowse and JBrowse (and WebGBrowse) for genome browsing, Apollo, Canto and MAKER for genome annotation, GBrowse_syn and CMap for comparative genomics visualization, Chado, BioMart and InterMine for data integration, management, and querying, and Galaxy and Ergatis (and ISGA) for data analysis.


Registration

Please register online at EventBrite. Early bird registration ends May 30th.

The registration fee includes lunch on June 30th.

Draft Agenda

Walnut room, Thursday, June 30

Time Topic Presenter(s) Presentation
08:50 Pre-meeting continental breakfast
09:15 Introductions
09:40 The State of GMOD Scott Cain Intro, InterMine, MAKER
10:10 Introduction to uMOD Scott Cain Slides
10:35 Coffee
10:50 GMOD in Action: The Legume Federation Project Ethalinda Cannon Slides
11:20 JBrowse Update Eric Yao Slides
11:50 Lunch
1:00 Apollo: Collaborative Manual Annotation in the GMOD Workflow Nathan Dunn Slides
1:30 Tripal Update Lacey-Anne Sanderson
2:30 Coffee
2:45 Galaxy Update Dave Clements, Bjöern Grüning Slides
3:15 EvidentialGene project at http://eugenes.org/EvidentialGene/ Don Gilbert Slides
3:45 FlyBase Update and Chado discussion Josh Goodman

Friday, July 1

Time Topic Presenter(s) Presentation
08:50 Pre-meeting continental breakfast
09:15 Tripal Expression module and search Meg Staton Slides
09:45 Lightning talks, including Asela Dassanayake, Eric Rasche and Thoba Lose Asela/LanzaTech
11:30 Lunch (on your own)
1:00 Tripal workshop

Agenda items

More to be added as we confirm more speakers. If you are interested in giving a talk please contact the GMOD help desk.

  • GMOD project updates, including Tripal, Galaxy, JBrowse, Chado, MAKER.
  • Introduction to umod (Scott Cain)
  • "Apollo: Collaborative Manual Annotation in the GMOD Workflow" (Nathan Dunn)
  • Tripal update (Lacey Sanderson)
  • Tripal Expression module and search (Ming Chen)
  • EvidentialGene project at http://eugenes.org/EvidentialGene/ (Don Gilbert)
  • DictyBase on using and extending GMOD tools (Chado, JBrowse) and new infrastructure(docker and possibly kubernetes) (Siddhartha Basu)
  • GMOD in Action: The Legume Federation Project (Ethalinda Cannon)
  • Tripal Workshop (Friday afternoon)

Logistics

If you require lodging, we have partnered with the 2016 Galaxy Community Conference.

You DO NOT have to register for the GCC2016 conference to utilize housing. Just check HOUSING ONLY when registering.

Shared Rides

Please put your travel times here.


"It's tempting to see bioinformatics as a collection of potential problems. Being at a GMOD meeting helps us see bioinformatics as a collection of potential solutions."
Isabelle Phan, SBRI, and past GMOD meeting participant
(Thanks to Dave Clements for the nice logo)
Retrieved from "http://gmod.org/mediawiki/index.php?title=Jun_2016_GMOD_Meeting&oldid=27269"