November 2007 GMOD Meeting

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The meeting will take place November 5, 1:30PM to November 7, 12:00PM at Cold Spring Harbor Laboratory following the Genome Informatics meeting.

Possible topics

  • community annotation - FlyBase seconds this topic
  • Chado standard on ortholog/paralog/synteny storage.
  • The state of GFF tools in BioPerl. Some of the auditing and examples are on a Bioperl wiki page.
  • GMOD releases and packaging
    • How hard would it be to heap together specific releases of popular GMOD components into a named/numbered release that has gone through some level of compatibility testing?
    • How much pain does a lack of such a release currently cause users?
    • how much might the community annotation server help with this?


The registration page is available at Please note that there is a $25 registration fee for the meeting to cover meals and other costs associated with the meeting.

Getting to Cold Spring Harbor Laboratory

Please see the page at for more information:


Some indeterminate spot: New features in GBrowse - Lincoln Stein

November 5

1:00 Shuttle from Grace Auditorium to Woodbury

1:30 Introductions

2:30 Coffee

5:30 Shuttle from Woodbury to Grace Auditorium

November 6

8:50 Shuttle from Grace Auditorium to Woodbury

9:15 Community Annotation

  • Linda Sperling - ParameciumDB
  • Lukas Muller - SGN
  • Michael Caudy - FlyBase Drupal

10:30 Coffee

12:00 Lunch

1:00 Standards and applications for storing comparative genome data

  • Haiming Wang - GBrowse: SynView and the Generic database adaptor
  • Victor Strelets - FlyBase Orthoview (GBrowse)
  • Sheldon McKay - gbrowse_syn

2:30 Coffee

5:30 Shuttle from Woodbury to Grace Auditorium

November 7

8:50 Shuttle from Grace Auditorium to Woodbury

9:15 BioPerl

  • GFF3 tools
  • SeqFeatures/FeatureIO
  • Sequence Ontology

10:30 Coffee

12:00 Shuttle from Woodbury to Grace Auditorium

Discussion Topics

  • Community Annotation
    • DAS
  • Comparative Genomics
    • Synteny viewers
    • Chado data storage
  • BioPerl and GFF(2/3)\
    • GFF Questions
  • Postgres Tuning / M.V.
    • Performance Stratagies
  • Apollo-Chado Connection
    • Perfomance
    • Too many JDBC Adaptors
  • Chado
    • ID Generation
    • Moving away from Postgres
  • Genome Analysis
    • Galaxy
  • What Should GMOD Focus On (What's Missing)
    • Analysis
    • MicroArrays
    • What is the GMOD Community and how best can we serve them?
    • Missing Chado pieces (phylogenetics)
    • Is there a need for individual MODs?
  • What should GMOD help desk do?
  • What should be the outcome of this meeting?
    • UIs: Picture Intensive



The meeting will be held off campus at the CSHL Woodbury building. If you miss the 'GMOD shuttle' for the meeting, the lab runs shuttles occasionally to Woodbury. Here is the schedule for it.


Last minute notes

I sent this in an email to registered attendees on Nov. 2:

I would like to point out a few items related to last minute preparations for the GMOD meeting:

1. The meeting itself will be taking place at the Woodbury Auditorium, which is off the CSHL campus. There will be a shuttle that will take people between Grace Auditorium and Woodbury. The shuttle Monday afternoon will leave Grace at 1:00.

2. The agenda for Monday is quite wide open on purpose. In past GMOD meetings, the opening portion of the meeting has generally be devoted to introductions and progress reports. Please be prepared to give at least a few sentences on why you are here, and if you like, you can prepare some slides (think 10-15 minutes) on what your group has been doing that relates to GMOD.

3. The meeting wiki page at

will continue to be a good source of information about the meeting, including an attendee list, and starting on Monday, a section for coordinating rides to the airport for Wednesday. Please feel free to add additional notes about the meeting there.

Airport Rides

Air Port - Desired Airport Arrival Time - Name

  • LGA
    • 2:15pm (3:15 flight)- Ben
    • 5:00pm Flight - Dave Clements
    • 4:30pm (6:00 flight) - Jay
  • JFK
    • 2:15PM? (3:30 flight) - Suzanne
    • 2:30PM (4:00 flight) - JasonS