July 2008 GMOD Meeting
 |
GMOD Community Meeting July 16-17, 2008 (prior to ISMB) University of Toronto |
__NOTITLE__
The next GMOD community meeting has been scheduled for July 16-17, 2008 at the University of Toronto, immediately before ISMB 2008 (also in Toronto), and just a few days after the 2008 GMOD Summer School.
Watch this space for more information as the meeting gets nearer. If you have any questions or requests about the July 2008 meeting, please contact the GMOD Help Desk at help@gmod.org. See the November 2007 GMOD Meeting page for an idea of what happens at GMOD meetings.
Contents
Registration
July 2008 GMOD Meeting Registration
Housing at the meeting
We have arranged for a block of hotel rooms at the Courtyard Marriott Downtown Toronto, though many people who are attending ISMB and BOSC may just extend their stays at their hotels. To get the discounted rate of $139, call 800-847-5075 and ask for either the “GMOD Meeting” or code “CMG”. This block is only available until June 17th, after which rooms will be based upon availability only.
Agenda
The meeting will be held in the MaRS conference room, at 101 College Street.(Google Maps) or MaRS directions. We will be in room CR-2AB, which is on the first floor. There should be signs pointing out the location.
July 16
| Time | Topic | Who | Presentation |
|---|---|---|---|
| 9:00 | Introductions | Scott Cain | PDF PPT |
| 9:30 | The State of GMOD | Scott Cain | PDF PPT |
| 10:10 | break | ||
| 10:40 | MediaWiki/TableEdit Roundtripping | Jim Hu | PDF PPT |
| 11:00 | More MediaWiki enhancements | Sheldon McKay | PDF PPT |
| SGN Community Annotation | Lukas Mueller | PDF PPT | |
| WikiMods & Chado API | Brad Arshinoff | PDF PPT | |
| 11:30 | Lunch | ||
| 1:30 | GMOD Help Desk | Dave Clements | PDF PPT |
| 2:15 | Rearchitecting Apollo and the need for a database independent Biological API layer | Ed Lee | PDF PPT |
| 2:50 | break | ||
| 3:20 | InterMine and Chado | Richard Smith | PDF PPT |
| 3:50 | Show and Tell | "What I did with my Summer" | |
| CMap | Ben Faga | PDF PPT |
July 17
| Time | Topic | Who | Presentation |
|---|---|---|---|
| 9:00 | New things for GBrowse 1.69 and 2.0 | Sheldon McKay, Lincoln Stein | PDF PPT |
| 9:30 | New things for GBrowse 3.0 | Ian Holmes | PDF PPT |
| 10:00 | break | ||
| 10:30 | The need for a computable common gene page (Don Gilbert's proposal) | Scott Cain, Lincoln Stein | PDF PPT |
| 11:30 | Lunch | ||
| 1:30 | More Show and Tell or a mini hackathon or go see Toronto | ||
Attendees
- David Arcoleo - BesSpace
- Brad Arshinoff - XanthusBase
- Jeff Bowes - Xenbase
- Robert Buels - Sol Genomics Network (SGN)
- Scott Cain - GMOD
- Dave Clements - NESCent, GMOD
- Sean Davey - BirdBase, U of Arizona
- Victor de Jager University of Nijmegen, The Netherlands & Centre for Molecular and Biomolecular Informatics
- Mary E Dolan Mouse Genome Informatics, The Jackson Laboratory
- Ben Faga - CSHL
- Saravanamuttu Gnaneshan Centre for Infections, Health Protection Agency
- Yunchen Gong - University of Toronto
- Josh Goodman - FlyBase
- Todd Harris - WormBase
- Chris Hemmerich - Center for Genomics and Bioinformatics, Indiana U.
- Ian Holmes - UC Berkeley
- Jim Hu - EcoliWiki, Texas A&M
- Thomas Keane - Wellcome Trust Sanger Institute
- Ed Lee - BBOP and Apollo
- Suzi Lewis - BBOP
- Margie Manker - The Centre for Applied Genomics, Toronto
- Sheldon McKay - modENCODE, WormBase
- Lukas Mueller Sol Genomics Network (SGN)
- Brian O'Connor - UCLA
- Joshua Orvis - Institute for Genome Sciences, University of Maryland
- Barry Sanders, BeeSpace
- Stéphanie Sidibe Bocs - CIRAD
- Richard Smith - InterMine (and InterMine)
- Kevin Snyder - Xenbase; University Of Calgary
- Jason Stajich - UC Berkeley
- Haiyan Zhang - FlyBase
- Junjun Zhang - The Hospital for Sick Children, Toronto
Agenda Proposals
If you have something you want to be on the agenda at this meeting please add it below.
- The AJAX-GBrowse project, as demo'd at http://genome.biowiki.org/ - Ian Holmes
- InterMine and Chado Richard Smith (Scott 14:04, 6 June 2008 (EDT))
- Advances in the Common Gene Page effort (see also here an old page at blog.gmod.org: http://blog.gmod.org/common_gene_pages , as well as Don Gilbert's page on the topic on his server: http://eugenes.org/gmod/gene-report-examples/ ) (Scott 14:04, 6 June 2008 (EDT))
- TableEdit round trip/integration progress and plans --JimHu 18:35, 6 June 2008 (EDT)
- Java Chado data model API with higher level, user friendly "Biological" layer Ed
- GBrowse 1.69 show and tell Sheldon McKay
- MediaWiki enhancements Sheldon McKay
- GMOD Help Desk - Dave Clements
- priorities for 2008-2009
- Evaluation - Has the Help Desk been helpful? - Dave and Don Gilbert
- Grant review service
- Funding GMOD
- GMOD and the Google Summer of Code in 2009?
- The Chado Natural Diversity module
- Galaxy Integration. Galaxy already integrates with BioMart, and the current (May 2008) development version of Galaxy integrates with the current (May 2008, 1.69 Beta, e.g. "stable") development version of GBrowse. Once this goes to production in both Galaxy and GBrowse, should Galaxy work on integrating with other GMOD components such as Chado or InterMine?
