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Generic Model Organism Database Construction Set | Generic Model Organism Database Construction Set | ||
| − | + | ==Meeting 6== | |
May 16-17, 2005 | May 16-17, 2005 | ||
SRI, Menlo Park, CA | SRI, Menlo Park, CA | ||
| − | + | ==Presentations== | |
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| − | 9:00 Comparative genome annotation of D. pseudoobscura and its implementation in chado | + | * [[Media:Apollo.ppt|Apollo.ppt]] |
| − | Peili Zhang | + | * [[Media:Cain-050516.ppt|Cain-050516.ppt]] - GMOD business and setting up [[ParameciumDB]] |
| − | 9:45 sybil for comparative genomics | + | * [[Media:Cmap-050516.pdf|Cmap-050516.pdf]] |
| − | Samuel Angiuoli | + | * [[Media:Das.ppt|Das.ppt]] |
| − | 10:30 Break | + | * [[Media:Day-050517.ppt|Day-050517.ppt]] |
| − | 10:45 Apollo Update | + | * [[Media:Faga_050517.pdf|Faga_050517.pdf]] |
| − | Nomi Harris and Mark Gibson | + | * [[Media:Gbrowse-050516.ppt|Gbrowse-050516.ppt]] |
| − | 10:45 Transposon Insertions and Transposon Constructs editor | + | * [[Media:Just-050516.ppt|Just-050516.ppt]] |
| − | Frank Smutniak | + | * [[Media:Kasprzyk-050516.ppt|Kasprzyk-050516.ppt]] - [[BioMart]] and [[Chado]] |
| − | 12:00 Lunch | + | * [[Media:Karp-050516.ppt|Karp-050516.ppt]] |
| − | 1:15 Bio::GMOD and standard URLs | + | * [[Media:Mungall-050516.ppt|Mungall-050516.ppt]] |
| − | Todd Harris | + | * [[Media:Oconnor-050516.ppt|Oconnor-050516.ppt]] |
| − | 2:15 Interaction Browsers (a presentation prepared at the meeting because the topic came up) | + | * [[Media:Sgd-050516.ppt|Sgd-050516.ppt]] |
| − | Ben Faga | + | * [[Media:Smutniak-050516.ppt|Smutniak-050516.ppt]] |
| − | 2:30 Break | + | * [[Media:What_next.ppt|What_next.ppt]] |
| − | 3:00 Das2 | + | * [[Media:Zhang-050517.ppt|Zhang-050517.ppt]] |
| − | Lincoln Stein | + | |
| − | 3:45 Package Management for Bioinformatics Libraries, Applications and Data | + | ==Agenda== |
| − | Allen Day | + | |
| − | 4:30 Wrap up; next meeting, etc (with notes in the presentation from items discussed) | + | <table cellpadding="6" width="75%"> |
| − | Lincoln Stein and Scott Cain | + | <tr> |
| + | <td valign="top" width="15%">9:00am</td> | ||
| + | <td width="85%">Introductions<br> | ||
| + | Scott Cain, GMOD coordinator</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">9:15</td> | ||
| + | <td width="85%">Project updates (short!)<br> | ||
| + | <ul> | ||
| + | <li>cmap-050516.pdf CMAP | ||
| + | <li>gbrowse-050516.ppt GBrowse | ||
| + | <li>sgd-050516.ppt SGD | ||
| + | </ul> | ||
| + | </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">10:00</td> | ||
| + | <td width="85%">Break<br> | ||
| + | </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">10:15</td> | ||
| + | <td width="85%">cain-050516.ppt My trip to France (setting up ParameciumDB)<br> | ||
| + | Scott Cain</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">10:45</td> | ||
| + | <td width="85%">kenny-050516.ppt Textpresso update<br> | ||
| + | Eimear Kenney</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">11:15</td> | ||
| + | <td width="85%">karp-050516.ppt Pathway Tools<br> | ||
| + | Peter Karp</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td valign="top" width="15%">12:00</td> | ||
| + | <td width="85%">Lunch<br> | ||
| + | </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">1:15</td> | ||
| + | <td width="85%">just-050516.ppt Porting CHADO and GMOD Tools to Oracle and Integration with dictyBase<br> | ||
| + | Eric Just</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">2:00</td> | ||
| + | <td width="85%">mungall-050516.ppt chado design, XSL, XML, XORT<br>Pinglei Zhou and Chris Mungall | ||
| + | </td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td valign="top" width="15%">2:45</td> | ||
| + | <td width="85%">Break<br> | ||
| + | </td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td valign="top" width="15%">3:00</td> | ||
| + | <td width="85%">kasprzyk-050516.ppt BioMart and chado<br> | ||
| + | Arek Kasprzyk</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">3:45</td> | ||
| + | <td width="85%">oconnor-050516.ppt Turnkey<br> | ||
| + | Brian O'Connor</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">4:30</td> | ||
| + | <td width="85%">Wrap up for the day--items to discuss over dinner <br> | ||
| + | Scott Cain</td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | |||
| + | <h4>Tuesday, May 17</h4> | ||
| + | |||
| + | <table cellpadding="6" width="75%"> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">9:00</td> | ||
| + | <td width="85%">zhang-050517.ppt Comparative genome annotation of D. pseudoobscura and its | ||
| + | implementation in chado <br> | ||
| + | Peili Zhang</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">9:45</td> | ||
| + | <td width="85%">sybil for comparative genomics<br> | ||
| + | Samuel Angiuoli</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">10:30</td> | ||
| + | <td width="85%">Break<br> | ||
| + | </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">10:45</td> | ||
| + | <td width="85%">apollo.ppt Apollo Update<br> | ||
| + | Nomi Harris and Mark Gibson</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">10:45</td> | ||
| + | <td width="85%">smutniak-050516.ppt Transposon Insertions and Transposon Constructs editor<br> | ||
| + | Frank Smutniak</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">12:00</td> | ||
| + | <td width="85%">Lunch<br> | ||
| + | </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">1:15</td> | ||
| + | <td width="85%">harris-050517.ppt Bio::GMOD and standard URLs<br> | ||
| + | Todd Harris</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">2:15</td> | ||
| + | <td width="85%">faga_050517.pdf Interaction Browsers (a presentation prepared at the meeting because the topic came up)<br> | ||
| + | Ben Faga</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">2:30</td> | ||
| + | <td width="85%">Break<br> | ||
| + | </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">3:00</td> | ||
| + | <td width="85%">das.ppt Das2<br> | ||
| + | Lincoln Stein</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">3:45</td> | ||
| + | <td width="85%">day-050517.ppt Package Management for Bioinformatics Libraries, Applications and Data <br> | ||
| + | Allen Day</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td valign="top" width="15%">4:30</td> | ||
| + | <td width="85%">what_next.ppt Wrap up; next meeting, etc (with notes in the presentation from items discussed) <br> | ||
| + | Lincoln Stein and Scott Cain</td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | |||
| + | ==GMOD Architecture Working Group== | ||
| + | |||
| + | ===Goal=== | ||
| + | |||
| + | 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. | ||
| + | |||
| + | ===Workflow=== | ||
| + | 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=== | ||
| + | |||
| + | 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. | ||
[[Category:Meetings]] | [[Category:Meetings]] | ||
Latest revision as of 17:07, 14 March 2008
Generic Model Organism Database Construction Set
Contents
Meeting 6
May 16-17, 2005 SRI, Menlo Park, CA
Presentations
- Apollo.ppt
- Cain-050516.ppt - GMOD business and setting up ParameciumDB
- Cmap-050516.pdf
- Das.ppt
- Day-050517.ppt
- Faga_050517.pdf
- Gbrowse-050516.ppt
- Just-050516.ppt
- Kasprzyk-050516.ppt - BioMart and Chado
- Karp-050516.ppt
- Mungall-050516.ppt
- Oconnor-050516.ppt
- Sgd-050516.ppt
- Smutniak-050516.ppt
- What_next.ppt
- Zhang-050517.ppt
Agenda
| 9:00am | Introductions Scott Cain, GMOD coordinator |
| 9:15 | Project updates (short!)
|
| 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 |
| 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
Goal
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.
Workflow
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
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.
