Difference between revisions of "Jan 2014 GMOD Meeting"
(→Friday, January 17) |
m (Updating, adding links, etc.) |
||
Line 1: | Line 1: | ||
[[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 | + | 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. |
− | |||
− | |||
− | |||
− | |||
− | |||
==Keynote Speaker== | ==Keynote Speaker== | ||
Line 16: | Line 11: | ||
<div style="font-size: 120%"> | <div style="font-size: 120%"> | ||
− | + | "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> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
==Agenda== | ==Agenda== | ||
− | |||
− | |||
===Thursday, January 16=== | ===Thursday, January 16=== | ||
Line 83: | Line 66: | ||
| Crowdsourcing genomics with Ash dieback | | Crowdsourcing genomics with Ash dieback | ||
| Dan MacLean and Martin Page | | Dan MacLean and Martin Page | ||
− | | [ | + | | [https://github.com/danmaclean/talks/tree/master/GMOD_san_diego_jan_2014 Slides and resources] |
|- | |- | ||
| 3:00 | | 3:00 | ||
Line 94: | Line 77: | ||
|- | |- | ||
| 3:45 | | 3:45 | ||
− | | Drunken Noodle ( | + | | Drunken Noodle (really, Ken?) |
| Ken Youens-Clark | | Ken Youens-Clark | ||
| [[Media:Ken_Youens_Clark_2014.pdf|Slides]] | | [[Media:Ken_Youens_Clark_2014.pdf|Slides]] | ||
Line 107: | Line 90: | ||
| [[User:Scott|Scott Cain]] | | [[User:Scott|Scott Cain]] | ||
| | | | ||
− | |||
− | |||
− | |||
− | |||
|} | |} | ||
Line 122: | Line 101: | ||
|- | |- | ||
| 09:15 | | 09:15 | ||
− | | Unit testing for | + | | Unit testing for Chado databases |
| Siddhartha Basu | | Siddhartha Basu | ||
| [http://testgenomes.dictybase.org/test-chado.slide Slides] | | [http://testgenomes.dictybase.org/test-chado.slide Slides] | ||
Line 147: | Line 126: | ||
| [[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 | ||
− | | | + | | Video to be uploaded soon |
|- | |- | ||
| 12:00 | | 12:00 | ||
Line 153: | Line 132: | ||
|- | |- | ||
| 1:15 | | 1:15 | ||
− | | MAKER | + | | [[MAKER]] |
| Daniel Ence | | Daniel Ence | ||
| [[Media:Daniel_Ence_2014.pptx|Slides]] | | [[Media:Daniel_Ence_2014.pptx|Slides]] | ||
|- | |- | ||
| 1:45 | | 1:45 | ||
− | | | + | | Google Summer of Code |
− | | [[ | + | | Amelia Ireland |
+ | | [[GSoC|GSoC and the Genome Informatics group]] | ||
|- | |- | ||
+ | | 2:00 | ||
+ | | colspan=2 | Lightning talks, including CViT (Chromosome Visualization Tool) | ||
+ | | | ||
+ | *CViT: Chromosome Visualization Tool [[Media:Cvit GMOD2014.pptx|Slides]] | ||
+ | *Updates from the Cancer Genome Project [[Media:2014 CGP updates.pdf|Slides]] | ||
+ | |||
|} | |} | ||
− | |||
− | + | ===Posters=== | |
− | [ | + | [[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]] |
Revision as of 21:55, 21 January 2014
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
"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 |
10:15 | Coffee break | ||
10:30 | High throughput comparative genomics using a Chado backend | Mara Kim | Slides |
11:00 | Keynote: A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced Genomes | Andrew Su | Slides |
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 |
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 |
4:45 | Wrap up | Scott Cain |
Friday, January 17
Time | Topic | Presenter(s) | Links |
---|---|---|---|
09:15 | Unit testing for Chado databases | Siddhartha Basu | Slides |
09:45 | Tripal | Lacey Sanderson | Slides |
10:15 | The FlyBase health module | Andy Schroeder | Slides |
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 to be uploaded soon |
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, including CViT (Chromosome Visualization Tool) |
Posters
Challenges in providing a genome browser for large-scale projects