May 2005 GMOD Meeting

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Generic Model Organism Database Construction Set

Meeting 6

May 16-17, 2005 SRI, Menlo Park, CA



9:00am Introductions
Scott Cain, GMOD coordinator
9:15 Project updates (short!)
  • cmap-050516.pdf CMAP
  • gbrowse-050516.ppt GBrowse
  • sgd-050516.ppt SGD
10:00 Break
10:15 cain-050516.ppt My trip to France (setting up ParameciumDB)
Scott Cain
10:45 kenny-050516.ppt Textpresso update
Eimear Kenney
11:15 karp-050516.ppt Pathway Tools
Peter Karp
12:00 Lunch
1:15 just-050516.ppt Porting CHADO and GMOD Tools to Oracle and Integration with dictyBase
Eric Just
2:00 mungall-050516.ppt chado design, XSL, XML, XORT
Pinglei Zhou and Chris Mungall
2:45 Break
3:00 kasprzyk-050516.ppt BioMart and chado
Arek Kasprzyk
3:45 oconnor-050516.ppt Turnkey
Brian O'Connor
4:30 Wrap up for the day--items to discuss over dinner
Scott Cain

Tuesday, May 17

9:00 zhang-050517.ppt Comparative genome annotation of D. pseudoobscura and its

implementation in chado

Peili Zhang
9:45 sybil for comparative genomics
Samuel Angiuoli
10:30 Break
10:45 apollo.ppt Apollo Update
Nomi Harris and Mark Gibson
10:45 smutniak-050516.ppt Transposon Insertions and Transposon Constructs editor
Frank Smutniak
12:00 Lunch
1:15 harris-050517.ppt Bio::GMOD and standard URLs
Todd Harris
2:15 faga_050517.pdf Interaction Browsers (a presentation prepared at the meeting because the topic came up)
Ben Faga
2:30 Break
3:00 das.ppt Das2
Lincoln Stein
3:45 day-050517.ppt Package Management for Bioinformatics Libraries, Applications and Data
Allen Day
4:30 what_next.ppt Wrap up; next meeting, etc (with notes in the presentation from items discussed)
Lincoln Stein and Scott Cain

GMOD Architecture Working Group


The Architecture Working Group will make recommendations to the GMOD consortium on any cross-project policies which can lead to a more cohesive software project. The group will take into consideration:

  • Interoperability with other GMOD components
  • Performance
  • Platform independence

GMOD will announce the recommendations and provide a repository for the recommendations on the website. Future developers will be pointed to these recommendations.


The group will discuss which recommendations are needed and decide on an issue on which to make a recommendation. One or two recommendations at a time will be chosen to work on. The timeline will obviously be very different for each recommendation – some will be short with near consensus early on and will just be a matter of formalizing. Others will be more contentious and require more work to gain consensus on.

Timeline of a recommendation

Two to three weeks: Discussion of the current problem, specify exactly what the proposals should address. Any use cases are developed at this time. At the end of this time a request for proposals will go out.

Two weeks: Time for members of the working group to generate one or more proposed solutions to a problem. These solutions are formally written and submitted to the group.

Three weeks: Discuss and iterate on one or more proposals, come to a consensus. At the end of this time, one person will be delegated to 'close' the proposal by formalizing any suggested modifications to the recommendation. After one last review the proposal is formally submitted to GMOD.


Communication will take place primarily over email on the group list. One conference call per month can be expected and we will work out a time among the group that will be our standard time for a conference call. We will try to limit conference calls to one hour per month per active recommendation.