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 | + | 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. |
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==Keynote Speaker== | ==Keynote Speaker== | ||
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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. | ||
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==Agenda== | ==Agenda== | ||
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===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]] | + | | [[Media:State_of_GMOD_2014.pdf|Slides]], [http://youtu.be/8DXWzgag8R4 YouTube] |
|- | |- | ||
| 10:15 | | 10:15 | ||
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| 10:30 | | 10:30 | ||
| High throughput comparative genomics using a Chado backend | | High throughput comparative genomics using a Chado backend | ||
− | | Mara Kim | + | | [[User:Mara Kim|Mara Kim]] |
− | | [[Media:MaraKim_GMOD2014.pdf|Slides]] | + | | [[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]] | + | |[[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 | + | | [http://www.tsl.ac.uk/profile/dan-maclean.asp Dan MacLean] and [http://www.tsl.ac.uk/profile/martin-page.asp Martin Page] |
− | | [ | + | | [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 ( | + | | Drunken Noodle (really, Ken?) |
| Ken Youens-Clark | | Ken Youens-Clark | ||
− | | [[Media: | + | | [[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]] | + | | [[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]] | ||
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|} | |} | ||
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|- | |- | ||
| 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://youtu.be/9F6rskt3JRM YouTube] |
|- | |- | ||
| 09:45 | | 09:45 | ||
| [[Tripal]] | | [[Tripal]] | ||
| Lacey Sanderson | | Lacey Sanderson | ||
− | | [[Media: | + | | [[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: | + | | [[Media:2014_Chado_health_module.pdf|Slides]], [http://youtu.be/ahA4EYgY-G0 YouTube] |
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| 10:45 | | 10:45 | ||
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| 11:00 | | 11:00 | ||
− | | | + | | Coffee Genome Hub |
| Stéphanie Bocs | | Stéphanie Bocs | ||
| [[Media:Stephanie_Bocs_2014.pdf|Slides]] | | [[Media:Stephanie_Bocs_2014.pdf|Slides]] | ||
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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://www.youtube.com/watch?v=-cj_PdJi68A Video at YouTube] |
|- | |- | ||
| 12:00 | | 12:00 | ||
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|- | |- | ||
| 1:15 | | 1:15 | ||
− | | MAKER | + | | [[MAKER]] |
| Daniel Ence | | Daniel Ence | ||
− | | [[Media:Daniel_Ence_2014. | + | | [[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 | ||
+ | | 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]] | ||
|} | |} | ||
− | == | + | ===Posters=== |
− | + | [[Media:Gitc-giab-poster.pdf|GMOD in the Cloud and GMOD in a Box: Instant Virtual Servers for Genomics Data]] | |
− | [ | + | [[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
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, 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 |
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