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?

Registration

The registration page is available at http://blog.gmod.org/register.html. 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 cshl.edu for more information: http://meetings.cshl.edu/travel.html.

Agenda

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 ? Scott

10:15 Community Annotation

  • Linda Sperling - ParameciumDB
  • Lukas Muller - SGN

10:30 Coffee

  • Michael Caudy - FlyBase Drupal

12:00 Lunch

1:00 Standards and applications for storing comparative genome data

  • Steve Fisher - GBrowse: SynView and the Generic database adaptor
  • Victor Strelets - FlyBase Orthoview (GBrowse)

2:30 Coffee

  • Sheldon McKay - gbrowse_syn


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, Apollo, genome-Wiki
  • Comparative Genomics
  • BioPerl and GFF(2/3)
    • GFF Questions
  • Postgres Tuning / Materialized Views
    • Performance Stratagies
  • Apollo-Chado Connection
  • Chado
    • ID Generation
    • Moving away from Postgres
    • Missing Chado pieces (phylogenetics)
  • What Should GMOD Focus On (What's Missing)
    • Genome Analysis (Galaxy, Ergatis, ...)
    • MicroArrays
    • What is the GMOD Community and how best can we serve them?
    • Is there a need for individual MODs?
  • What should GMOD help desk do?
    • UIs: Picture Intensive
  • What should be the outcome of this meeting?

Presentations

Location

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.

Attendees

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
    • 6:30pm (7:30 flight) - Scott
  • JFK
    • 2:15PM? (3:30 flight) - Suzanne
    • 2:30PM (4:00 flight) - JasonS (I'm considering taking the train)

Tuesday Ride (not Weds)

  • LGA, 2:45p pickup at Woodbury Genome Center, Syosset limo - Don Gilbert
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