Difference between revisions of "January 2009 GMOD Meeting"

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|[http://genome.biowiki.org JBrowse] (aka GBrowse 3.0)
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|[[Media:Jan2009JBrowse.ppt|ODP]], [[Media:Jan2009JBrowse.pdf|PDF]]
|[[Media:Jan2009JBrowse.odp|ODP]], [[Media:Jan2009JBrowse.pdf|PDF]]
|12:00 PM
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Revision as of 22:40, 16 January 2009

January 2009 GMOD Meeting
January 15-16, 2009

Following PAG 2009
San Diego, California, USA
{{#icon: SanDiegoConvention.gif|San Diego Convention and Visitors Bureau http://www.sandiego.org/nav/Visitors}}


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.


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
svn repository for BIR-TAB: svn://public-svn.modencode.org/modencode
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 BeeSpace Barry Sanders, Dave Arcoleo PPT, PDF
10:30 AM Break
11:00 AM WebGBrowse GBrowse configuration management Ram Podicheti PPT, PDF
11:30 AM JBrowse (aka GBrowse 3.0) Mitch Skinner ODP, PDF
12:00 PM Lunch one hour 30 minutes
1:30 PM Ecoliwiki and Table Editor Daniel Renfro PPT, PDF
2:00 PM Generic Gene Page XML Scott Cain PPT, PDF
2:30 PM GMODWeb and package management Brian O'Connor PPT, PDF
3:00 PM Other topics/Show and tell


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.)

Thanks to the generous support of Doreen Ware and USDA-ARS, registration for this meeting was free.

Agenda Proposals

If you have something you want to be on the agenda at this meeting please add it below.

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
Ian Holmes UC Berkeley
Robin Houston Pathogen Informatics, Sanger Institute
Jim Hu Texas A&M University/EcoliWiki and GONUTS
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 (SBRI)
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


If you attended the meeting, please fill out a one page questionnaire about the meeting. This will help GMOD have better meetings in the future.