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May 2005 GMOD Meeting
Generic Model Organism Database Construction Set
May 16-17, 2005 SRI, Menlo Park, CA
- Cain-050516.ppt - GMOD business and setting up ParameciumDB
- Kasprzyk-050516.ppt - BioMart and Chado
Scott Cain, GMOD coordinator
|9:15||Project updates (short!)
|10:15||cain-050516.ppt My trip to France (setting up ParameciumDB)
|10:45||kenny-050516.ppt Textpresso update
|11:15||karp-050516.ppt Pathway Tools
|1:15||just-050516.ppt Porting CHADO and GMOD Tools to Oracle and Integration with dictyBase
|2:00||mungall-050516.ppt chado design, XSL, XML, XORT
Pinglei Zhou and Chris Mungall
|3:00||kasprzyk-050516.ppt BioMart and chado
|4:30||Wrap up for the day--items to discuss over dinner
Tuesday, May 17
|9:00||zhang-050517.ppt Comparative genome annotation of D. pseudoobscura and its
implementation in chado
|9:45||sybil for comparative genomics
|10:45||apollo.ppt Apollo Update
Nomi Harris and Mark Gibson
|10:45||smutniak-050516.ppt Transposon Insertions and Transposon Constructs editor
|1:15||harris-050517.ppt Bio::GMOD and standard URLs
|2:15||faga_050517.pdf Interaction Browsers (a presentation prepared at the meeting because the topic came up)
|3:45||day-050517.ppt Package Management for Bioinformatics Libraries, Applications and Data
|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
- 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.