GMOD
Jan 2014 GMOD Meeting
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.
Contents
Keynote Speaker
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 | <a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/a/a8/State_of_GMOD_2014.pdf” |
class=”internal” title=”State of GMOD 2014.pdf”>Slides</a>, 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 unavailable |
| 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