Difference between revisions of "WebDev 2009.12.09-Agenda and Minutes"
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== 1. Administrative Update (Todd, 10 minutes) == | == 1. Administrative Update (Todd, 10 minutes) == | ||
− | == 2. | + | * Scheduling for next weeks -- regular call 12/16; 12/23; 01/06; -- off 12/30 |
+ | * Development deadline -- 12/16 | ||
+ | |||
+ | == 2. Discuss WS209 update status (Norie; 10 minutes) == | ||
+ | |||
+ | * GFF and acedb steps mostly complete | ||
+ | * Anticipate being complete Friday | ||
+ | * Changes from Michael | ||
+ | * Todd will install MySQL 5.1 to match databases from Michael | ||
+ | * Cleaned up display for the updated disease search | ||
== 3. GBrowse2 Progress (Abby & Xiaoqi; 10 minutes) == | == 3. GBrowse2 Progress (Abby & Xiaoqi; 10 minutes) == | ||
+ | |||
+ | AC: | ||
+ | * links provided below | ||
+ | * some gene models feature doesn't link properly to details page | ||
+ | * library conflict occasionally dogs work | ||
+ | * gbrowse_details need some debugging for some tier III features | ||
+ | * standardization of displays well underway | ||
+ | * footer issue | ||
+ | * toggle header | ||
+ | |||
+ | XS: | ||
+ | * imbedded images, necessary functionalities that enable them to work will be released soon: LS | ||
+ | * inclusion of protein motif? | ||
+ | |||
Tier I: | Tier I: | ||
Line 37: | Line 60: | ||
http://dev.wormbase.org/db/gb2/gbrowse/m_incognita/ | http://dev.wormbase.org/db/gb2/gbrowse/m_incognita/ | ||
+ | |||
+ | |||
+ | |||
+ | * Nbrowse -- what to do given new db requirements. TH: Grant read-only access to the world for nbrowse db; will contact Mark. | ||
== 4. Define SAB Goals (All; 10 minutes) == | == 4. Define SAB Goals (All; 10 minutes) == | ||
+ | |||
+ | * GBrowse II Rollout | ||
+ | * [[Species_available_through_WormBase_%28overview%29|Tier II/Tier III handling]] | ||
+ | ** some file downloads not working | ||
+ | ** check genome browser linkings | ||
+ | ** matrix needs populating by SAB meeting time -- careful assessment of genome handling | ||
+ | ** we need direct links to Gbrowsers | ||
+ | ** AC still working with config files | ||
+ | ** Gbrowse updated in CPAN | ||
+ | |||
+ | * Site 2.0 demo | ||
== 5. WormBase 2.0 installation issues (All; 10 minutes) == | == 5. WormBase 2.0 installation issues (All; 10 minutes) == | ||
+ | |||
+ | * Questions? | ||
+ | * AC got test 1 to work, 2nd part not working (starting the test server) -- check hard coded path in config file | ||
+ | * TH: Report issues on the tracker | ||
+ | * 5.10.1 required; 5.10.0 has weird bug which is difficult to unravel -- TH to post test script vs. 5.10.0 | ||
== 6. Open Table == | == 6. Open Table == |
Latest revision as of 17:47, 9 December 2009
Contents
Agenda
1. Administrative Update (Todd, 10 minutes)
- Scheduling for next weeks -- regular call 12/16; 12/23; 01/06; -- off 12/30
- Development deadline -- 12/16
2. Discuss WS209 update status (Norie; 10 minutes)
- GFF and acedb steps mostly complete
- Anticipate being complete Friday
- Changes from Michael
- Todd will install MySQL 5.1 to match databases from Michael
- Cleaned up display for the updated disease search
3. GBrowse2 Progress (Abby & Xiaoqi; 10 minutes)
AC:
- links provided below
- some gene models feature doesn't link properly to details page
- library conflict occasionally dogs work
- gbrowse_details need some debugging for some tier III features
- standardization of displays well underway
- footer issue
- toggle header
XS:
- imbedded images, necessary functionalities that enable them to work will be released soon: LS
- inclusion of protein motif?
Tier I:
http://dev.wormbase.org/db/gb2/gbrowse/c_elegans/
http://dev.wormbase.org/db/gb2/gbrowse/c_elegans_gmap/ <-- Does not work in dev or live
http://dev.wormbase.org/db/gb2/gbrowse/c_elegans_pmap/
Tier II:
http://dev.wormbase.org/db/gb2/gbrowse/c_brenneri/
http://dev.wormbase.org/db/gb2/gbrowse/c_briggsae/
http://dev.wormbase.org/db/gb2/gbrowse/c_japonica/
http://dev.wormbase.org/db/gb2/gbrowse/c_remanei/
http://dev.wormbase.org/db/gb2/gbrowse/p_pacificus/
Tier III:
http://dev.wormbase.org/db/gb2/gbrowse/b_malayi/
http://dev.wormbase.org/db/gb2/gbrowse/h_contortus/
http://dev.wormbase.org/db/gb2/gbrowse/m_hapla/
http://dev.wormbase.org/db/gb2/gbrowse/m_incognita/
- Nbrowse -- what to do given new db requirements. TH: Grant read-only access to the world for nbrowse db; will contact Mark.
4. Define SAB Goals (All; 10 minutes)
- GBrowse II Rollout
- Tier II/Tier III handling
- some file downloads not working
- check genome browser linkings
- matrix needs populating by SAB meeting time -- careful assessment of genome handling
- we need direct links to Gbrowsers
- AC still working with config files
- Gbrowse updated in CPAN
- Site 2.0 demo
5. WormBase 2.0 installation issues (All; 10 minutes)
- Questions?
- AC got test 1 to work, 2nd part not working (starting the test server) -- check hard coded path in config file
- TH: Report issues on the tracker
- 5.10.1 required; 5.10.0 has weird bug which is difficult to unravel -- TH to post test script vs. 5.10.0