Difference between revisions of "WebDev 2013.10.25-Agenda and Minutes"

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* JD: all code committed and available to Joachim
 
* JD: all code committed and available to Joachim
−
** committed progress on orthology work
+
** committed progress on orthology work - in upgrade-loader branch
  
 +
* WIki is being fleshed out
 +
** Joachim: still a bit superficial. A lot of experimentation going on.
 +
** JD: originally wrote it more generally - now adding specific commands/machines/etc
 +
** Joachim: take documentation and run it yourself, fill in parts missing as you build the mine yourself again
 +
 +
* JD: creating graphic of all git branches and description of what they're used for
 +
 +
* Joachim: doing the actual build, once finished should be able to move it to production
 +
** need to test if he can actually deploy the mine himself
 +
** JD: added path to archived versions on wiki
 +
** hoping for mine next week
  
 
== 3. InterMine status (JD; 10 minutes) ==
 
== 3. InterMine status (JD; 10 minutes) ==
 
* WS239 mine has been released, but I have discovered duplicate records caused by the addition of new species.  The configuration has been updated, but a new build must be compiled.  Until then, the mine will be rolled back to WS238.
 
* WS239 mine has been released, but I have discovered duplicate records caused by the addition of new species.  The configuration has been updated, but a new build must be compiled.  Until then, the mine will be rolled back to WS238.
 
* The process of automating second-degree ( record -> middleman record -> annotation ) is 50-75% done.  Branch "upgrade-loader" contains work and can be found on git.
 
* The process of automating second-degree ( record -> middleman record -> annotation ) is 50-75% done.  Branch "upgrade-loader" contains work and can be found on git.
 +
 +
* JD: will rebuild today.
 +
** should be finished by monday
 +
 +
* Todd: priority today - flesh out docs, help Joachim
  
 
== 4. Discuss WS239 issues (all; 10 minutes) ==
 
== 4. Discuss WS239 issues (all; 10 minutes) ==
 
* location hotfix ready
 
* location hotfix ready
 +
* variation hotfix
 +
 +
* JD: finished all other assigned issues, except cell lineage.
 +
** Cytoscape not the best tool.
 +
** Will implement using existing lineage tool
 +
** http://wormweb.org/celllineage#c=ABprpaaap&z=1
 +
** on hold now
  
 
== 5. Define WS240 plans (all; 15 minutes) ==
 
== 5. Define WS240 plans (all; 15 minutes) ==
 +
TH Wish list:
 +
* Move forward with knowledgebase idea
 +
** biostars?
 +
** phylogenetics people contacting biostars
 +
*** requested branding, better lookup
 +
** we need a simplification of our process
 +
* GFF3 - WS240
 +
** support for files - KH fixed most issues from WS239
 +
* Cloud - writing scripts
 +
** fixes needed on app side
 +
*** will create issues for these
 +
* Backend
 +
* Joachim: Intermine & visualization & gbrowse
 +
** start WS240 Intermine build
  
 
== 6. Open Table (all; 5 minutes) ==
 
== 6. Open Table (all; 5 minutes) ==

Revision as of 15:49, 25 October 2013

Agenda

1. Administrative Update (Todd; 5 minutes)

2. InterMine handover status (JD, Joachim;15 minutes)

http://wiki.wormbase.org/index.php/Administration:Installing_WormMine

3. InterMine status (JD; 10 minutes)

  • WS239 mine has been released, but I have discovered duplicate records caused by the addition of new species. The configuration has been updated, but a new build must be compiled. Until then, the mine will be rolled back to WS238.
  • The process of automating second-degree ( record -> middleman record -> annotation ) is 50-75% done. Branch "upgrade-loader" contains work and can be found on git.

4. Discuss WS239 issues (all; 10 minutes)

  • location hotfix ready

5. Define WS240 plans (all; 15 minutes)

6. Open Table (all; 5 minutes)

Minutes

1. Administrative Update (Todd; 5 minutes)

  • 240 build underway

2. InterMine handover status (JD, Joachim;15 minutes)

  • slowly, still haven't built everything
  • bugs and other issues fixed along the way
  • currently hanging for Joachim
    • JD unsure of problem - never seen this
  • JD: all code committed and available to Joachim
    • committed progress on orthology work - in upgrade-loader branch
  • WIki is being fleshed out
    • Joachim: still a bit superficial. A lot of experimentation going on.
    • JD: originally wrote it more generally - now adding specific commands/machines/etc
    • Joachim: take documentation and run it yourself, fill in parts missing as you build the mine yourself again
  • JD: creating graphic of all git branches and description of what they're used for
  • Joachim: doing the actual build, once finished should be able to move it to production
    • need to test if he can actually deploy the mine himself
    • JD: added path to archived versions on wiki
    • hoping for mine next week

3. InterMine status (JD; 10 minutes)

  • WS239 mine has been released, but I have discovered duplicate records caused by the addition of new species. The configuration has been updated, but a new build must be compiled. Until then, the mine will be rolled back to WS238.
  • The process of automating second-degree ( record -> middleman record -> annotation ) is 50-75% done. Branch "upgrade-loader" contains work and can be found on git.
  • JD: will rebuild today.
    • should be finished by monday
  • Todd: priority today - flesh out docs, help Joachim

4. Discuss WS239 issues (all; 10 minutes)

  • location hotfix ready
  • variation hotfix

5. Define WS240 plans (all; 15 minutes)

TH Wish list:

  • Move forward with knowledgebase idea
    • biostars?
    • phylogenetics people contacting biostars
      • requested branding, better lookup
    • we need a simplification of our process
  • GFF3 - WS240
    • support for files - KH fixed most issues from WS239
  • Cloud - writing scripts
    • fixes needed on app side
      • will create issues for these
  • Backend
  • Joachim: Intermine & visualization & gbrowse
    • start WS240 Intermine build

6. Open Table (all; 5 minutes)

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