January 2009 GMOD Meeting
January 2009 GMOD Meeting January 15-16, 2009 Following PAG 2009 San Diego, California, USA |
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The next GMOD Community Meeting is scheduled for January 15-16, 2009, in San Diego, immediately following Plant and Animal Genome (PAG 2009). The meeting will be held at the Best Western Seven Seas, which is adjacent to the Town and Country Resort, where PAG is being held.
If you are curious about what happens at a GMOD meeting, see the July 2008 GMOD Meeting page for notes from the previous meeting. GMOD meetings are open to anyone. If you are a GMOD user and/or developer, or just want to learn more about GMOD then you are encouraged to attend.
More information on the meeting will be posted here as it becomes available. Please contact the GMOD Help Desk if you have any questions about the meeting.
Contents
Agenda
To upload your presentation to the GMOD web site, click on the PPT or PDF link in the schedule. The upload may warn you. Ignore those warnings.
If you don't have a wiki login, either create one, or e-mail your presentation to Dave Clements.
We'll remove unused links a week after the meeting.
Thursday, January 15
Time | Topic | Presenter(s) | Presentation Links |
---|---|---|---|
10:00 AM | Registration | ||
10:30 AM | Introductions | Scott Cain | |
11:00 AM | The State of GMOD | Scott Cain | PPT, PDF |
11:30 AM | A variety of GMOD Help Desk stuff | Dave Clements | PPT, PDF |
12:00 PM | Lunch | one hour 30 minutes | |
1:30 PM | Drupal and MarineGenomics.org | Stephen Ficklin | PPT, PDF |
2:00 PM | Artemis and Chado at GeneDB | Robin Houston | PPT, PDF |
2:30 PM | modENCODE: extending Chado, BIR-TAB, & GBrowse for automating data validation & display | Nicole Washington | PPT, PDF |
3:00 PM | Break | ||
3:30 PM | A RESTful interface for MODs? | Josh Goodman | PPT, PDF |
4:00 PM | Metadata Input and Submission Tool and GIS linked metagenomic database | Iddo Friedberg and Christopher Condit | PPT, PDF |
4:30 PM | Data Representation in Chado: Best Practices | Joshua Orvis and/or Scott Cain | PPT, PDF |
5:00 PM | Dinner (on your own) |
Friday, January 16
Time | Topic | Presenter(s) | Presentation Links |
---|---|---|---|
9:00 AM | Chado and GUS at SBRI | Dhileep Sivam and Isabelle Phan | PPT, PDF |
9:30 AM | BioMart | Arek Kasprzyk | PPT, PDF |
10:00 AM | GMODWeb and package management | Brian O'Connor | PPT, PDF |
10:30 AM | Break | ||
11:00 AM | BeeSpace | Barry Sanders, Dave Arcoleo | PPT, PDF |
11:30 AM | WebBrowse GBrowse configuration management | Ram Podicheti | PPT, PDF |
12:00 PM | Lunch | one hour 30 minutes | |
1:30 PM | JBrowse (aka GBrowse 3.0) | Mitch Skinner | PPT, PDF |
2:00 PM | Ecoliwiki and Table Editor | Daniel Renfro | PPT, PDF |
2:30 PM | Generic Gene Page XML | Scott Cain | PPT, PDF |
3:00 PM | Other topics/Show and tell |
Registration
Registration is now closed.
If you wanted to attend but have not yet registered:
- we at least plan to have all of the presentations online after the meeting. (Yes, I know: it's not the same as being there.)
- You can sign up for the waiting list and we'll let you know as openings occur.
Thanks to the generous support of Doreen Ware and USDA-ARS, registration for this meeting is free.
Agenda Proposals
If you have something you want to be on the agenda at this meeting please add it below.
- Natural Diversity Module in Chado -- Clements 14:23, 13 November 2008 (UTC)
- Using the 2008 GMOD Community Survey for guidance -- Clements 21:46, 20 November 2008 (UTC)
- Common data representation (best practices) --Jorvis 23:29, 20 November 2008 (UTC)
- Including high throughput sequencing data --Scott 18:07, 8 December 2008 (UTC)
- 2009 GMOD Summer School, in Durham North Carolina, and possibly in Oxford, UK. Clements 19:50, 24 November 2008 (UTC)
- Beespace Navigator 4.0 and the Gene Summarizer automatic gene curation engine. -- Barry Sanders, 03 December 2008
- Common Gene Page XML format. Status update and discussion of future directions. --Jogoodma 18:38, 11 December 2008 (UTC)
Meeting Participants
Name | Affiliation(s) |
---|---|
Dave Arcoleo | BeeSpace |
Saravanaraj Ayyampalayam | University of Georgia |
Hugo Berube | National Research Council Canada |
Robert Buels | SGN |
Ramesh Buyyarapu | Alabama A&M University |
Scott Cain | GMOD, Ontario Institute for Cancer Research (OICR) |
Jing Chen | UCSD |
Chris Childers | Georgetown University |
Kevin Clancy | Life Technologies |
Dave Clements | NESCent / GMOD |
Christopher Condit | University of California San Diego |
Heather Estrella | Pfizer |
Kathleen Falls | FlyBase |
Stephen Ficklin | Clemson University Genomics Institute / MarineGenomics.org, Fagaceae.org |
Brian Fox | UCSD |
Iddo Friedberg | University of California San Diego |
Carol Germain | Pfizer |
Josh Goodman | FlyBase |
Dong He | CalTech, SpBase |
Christopher Hemmerich | Indiana University - Center for Genomics and Bioinformatics |
Robin Houston | Pathogen Informatics, Sanger Institute |
Ying Huang | University of California, San Diego |
Arek Kasprzyk | OICR/BioMart |
Andrei Kouranov | Protein Data Bank |
Daniel Lang | University of Freiburg, cosmoss.org |
Pierre Larmande | Joint Research Unit Plant Development and Genetic Improvement |
Ping Ling | Pfizer |
Dorrie Main | Genome Database for Rosaceae |
Weidong Mao | Virginia State Unviersity |
Sheldon McKay | Cold Spring Harbor Laboratory iPlant/GMOD |
Rex Nelson | SoyBase |
Brian O'Connor | UCLA |
Joshua Orvis | Institute for Genome Sciences |
Georgios Pappas, Jr | EMBRAPA/Brazil |
Isabelle Phan | SBRI |
Ram Podicheti | Center for Genomics and Bioinformatics |
Gowthaman Ramasamy | Seattle Biomedical Research Institue (SBRI), Seattle,WA |
Robert Reed | U.C. Irvine |
Justin Reese | Georgetown University, BeeBase and Bovine Genome Database |
Daniel Renfro | EcoliWiki |
Peter Rose | UCSD - Protein Data Bank |
Barry Sanders | BeeSpace |
Andy Schroeder | FlyBase |
Dhileep Sivam | University of Washington & Seattle Biomedical Research Institute |
Mitch Skinner | UC Berkeley, JBrowse project |
Russell Smithies | AgResearch |
Weijia Su | Tyler Applied Systems, Inc. |
Shulei Sun | UCSD |
Randall Svancara | Genome Database for Rosaceae |
Adrian Tivey | Pathogen Informatics, Sanger Institute |
Nicole Washington | LBNL, modENCODE, GBrowse, Phenote |
John Westbrook | PSIKB / PDB |
Geoff Winsor | Pseudomonas Genome Database (Simon Fraser University) |
Zi Yang | Pfizer |
Andreas Zimmer | University of Freiburg/cosmoss.org |