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. Discus WS209 update status (Norie; 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) ==
 
== 3. GBrowse2 Progress (Abby & Xiaoqi; 10 minutes) ==
http://dev.wormbase.org/db/gb2/gbrowse/b_malayi/
 
  
http://dev.wormbase.org/db/gb2/gbrowse/c_brenneri/
+
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/
  
http://dev.wormbase.org/db/gb2/gbrowse/c_elegans_gmap/
+
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/
 
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_japonica/
  
 
http://dev.wormbase.org/db/gb2/gbrowse/c_remanei/
 
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/h_contortus/
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http://dev.wormbase.org/db/gb2/gbrowse/m_incognita/
 
http://dev.wormbase.org/db/gb2/gbrowse/m_incognita/
  
http://dev.wormbase.org/db/gb2/gbrowse/p_pacificus/
+
 
 +
 
 +
* 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

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

6. Open Table