Difference between revisions of "WBConfCall 2013.06.20-Agenda and Minutes"

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=====Thursday 20:00-21:30=====
=====Thursday 20:00-21:30=====
Wen Chen, Daniela, Todd, Abby, JD, Kevin
Wen Chen, Daniela, Todd, Abby, JD, Kevin, Gary
=====Thursday 21:30-23:00=====
=====Thursday 21:30-23:00=====
Wen Chen, Todd, Abby, JD, Kevin
Wen Chen, Todd, Abby, JD, Kevin, Gary
=====Friday 20:00-21:30=====
=====Friday 20:00-21:30=====
Todd, Abby, JD, Kevin
Todd, Abby, JD, Kevin, Gary
=====Friday 21:30-23:00=====
=====Friday 21:30-23:00=====
Todd, Abby, JD, Kevin
Todd, Abby, JD, Kevin,Gary
=====Saturday 15:00-16:45=====
=====Saturday 15:00-16:45=====
Todd, Kimberly, Abby, JD, Daniela, Kevin
Todd, Kimberly, Abby, JD, Daniela, Kevin, Gary
=====Saturday 16:45-18:30=====
=====Saturday 16:45-18:30=====
Todd, Abby, JD, Kevin
Todd, Abby, JD, Kevin, Gary
=== WS239 Models and upload schedule ===
=== WS239 Models and upload schedule ===

Revision as of 13:12, 21 June 2013

Agenda and Minutes

NOTE: Next sitewide meeting 11-July-2013 (04-July US National Holiday)

Help Desk Issues

  • Unresolved help desk issues
    • #1438 Track errors on RNA seq GBrowse view
    • #1091 OP50 sequence data deposition
      • Future: Don't think this will happen for WS239, but we do need to agree how to do this.
      • mh6: we surely can host the Excel file for WS239. I was also checking with the bacteria collection people if they want to add the SNPs to the parent strain on their site.
      • Should this be an agenda item for this meeting? @karen
    • #673 Upload Custom Tracks (.bed) The conversation seemed to have suggested someone would get back to Christian; however, I could not find a follow up message.
      • Pending:
    • #716 download fasta sequences of all C. elegans genes in operons I posted a response, but it did not address the issue that trying to download all the sequences of all genes in the operon at once results in a blank page. Would someone please check this out and get back to the user?
      • DONE: currently not possible to do this in bulk, but I will get back to the user and provide the data. @paul-davis
    • #942 User: CDS summary page feature request Has this been resolved for WS238? or should it be moved to another milestone? Can we consider this one 'helped' to remove it from the unhelped issues?
      • DONE: The original query was resolved the later additions are pending future schema modifications.....yes it can be moved to helped.
    • #1101 The gene name "sym-5" does not redi... Still waiting on the updated ortholog names filter... any updates on when this will come through?
      • DONE - WS239: fixed as it's a data issue.
    • #507 search for loci in a given region This particular message was first posted nine months ago, addressed for a while, then lost. In the meantime other people have been asking for the quick interval search option as well. While we do have interval search options available through the genetic map and GBrowse, I think the issue is the results page. In the old site, the page returned an easy to browse list of genes in table format with other summary information. Users would like this kind of tool again. http://legacy.wormbase.org/db/searches/interval Am I missing where this functionality exists on the new site? or can we get back to Michael Glotzer with an estimated time for developing such a tool?
      • Pending: I think the ticket covers what you are asking here, the tool wasn't ported and at present isn't planned although @acabunoc is assigned with a WS239 milestone so she might be able to comment??
    • #1375 Use of "login" when meaning "log in" User had corrected grammar and typos and requests we change login to log in when we are expecting users to do something. It was suggested that someone would be getting back to the user in specific response to this request. Would someone please get back to the user
      • DONE: @kyook, looking at the ticket I think you can respond to them as 2 of the 3 issues have been resolved by @gw3 (I don't have Dona********** (dhes**************) email address).
    • #1403 which UCSC wig formats gbrowse can take Would someone please respond to Kohta?
      • Pending: @tharris, do you know for the specific version of GBrowse we have??


  • Strategy for posters. There a 3 poster sessions, but our posters have all been scheduled for the first two (with a 2/4 split).
    • Presumably we still intend to display posters in our booth?
    • Proposal: we use the booth to display as many posters as we can that are not currently "on". Currently "on" posters are displayed in their proper/expected place.


  • A4 hand-out summarising WormBase events?

Abby prepared a cheat sheet, she will make room for the WormBase events (prepared by Todd?)

  • Sign up for table duty (see below)

Looks Great! Thank you for signing up everyone!

  • Location and time of post-meeting meeting?

12:30-14:00 (12:30-2:00pm) We will pick a place near the registration office. Travelers will need to check out in the morning and bring their bags to the registration office

*Wen will make and print out WormBase specific nametags. (KY has one from last time)

WormBase IWM event schedule

  • Wed Jun 26
    • 19:40-19:45 (7:40-7:45pm) Plenary 1 - Kevin - Royce Hall
  • Thu Jun 27
    • 13:30 – 14:30 (1:30-2:30) WB Tutorial: Data Mining - Todd, JD - West Coast Meeting Room
    • 13:30 – 14:30 (1:30-2:30) WB Tutorial: Genomes, Comparative Genomics...Kevin - Bradley International Ballroom
    • 20:00 – 23:00 (8:00-11:00) WB Table - Pauley Pavilion
    • 21:30 – 23:00 (9:30-11:00) Odd "A" Posters (Mary Ann and Karen) - Pauley Pavilion
  • Fri Jun 28
    • 20:00 – 23:00 (8:00-11:00) WB Table - Pauley Pavilion
    • 20:00 – 21:30 (8:00-9:30) Even "B" Posters (Michael P. and Ranjana) - Pauley Pavilion
    • 21:30 – 23:00 (9:30-11:00) Odd "B" Posters (Xiaodong and James) - Pauley Pavilion
  • Sat Jun 29
    • 13:30 – 15:00 (1:30-3:00) WB Tutorial: Phenotypes, Interactions... Chris and Karen - Bradley International Ballroom
    • 13:30 – 15:00 (1:30-3:00) WB Tutorial: Data Mining - Todd, JD - West Coast meeting room
    • 15:00 – 18:30 (3:00-6:30) WB Table - Pauley Pavilion
  • Sun Jun 30
    • TBD (11-12?) Post-IWM WB meeting - TBA

Sign up for table duty

Thursday 20:00-21:30

Wen Chen, Daniela, Todd, Abby, JD, Kevin, Gary

Thursday 21:30-23:00

Wen Chen, Todd, Abby, JD, Kevin, Gary

Friday 20:00-21:30

Todd, Abby, JD, Kevin, Gary

Friday 21:30-23:00

Todd, Abby, JD, Kevin,Gary

Saturday 15:00-16:45

Todd, Kimberly, Abby, JD, Daniela, Kevin, Gary

Saturday 16:45-18:30

Todd, Abby, JD, Kevin, Gary

WS239 Models and upload schedule

  • When to CVS Tag 11th July
  • Only proposal going into WS239



	 Synonym Broad ?Text
		 Exact ?Text
		 Narrow ?Text
		 Related ?Text
	 Status UNIQUE Valid


		       Pseudogene ?Pseudogene XREF GO_term // [030801 krb]
  • Upload 19th July 2013

  • WS239 building 22nd July - 9th August (+/-)


See notes in line above.

  • WormMine discussion
    • header/footer in place
    • most milestones reached, and things are on track for the release, remaining issues include
      • model additions: expanding transcripts (done Mon), variation, expression (done Mon)
    • Domain name will be available that will go to JD's production server
    • We will be releasing a working Beta version

Need to put a disclaimer on the site that it is beta

    • For the beta release, JD wants templates, and to arrange them as they are on Flymine, that is they are listed at the bottom of the page under tag names.
    • use "-->" to make arrows
    • curators are experiencing many problems with having public tagged lists and templates stable on the site.
    • After a webapp reload, all public lists and templates are removed from the front site, curators have to log in and refresh their own instance for the lists and templates to be restored to the main page.
    • if a curator is not logged in, they cannot see their lists as public (Chris posted this on the issue tracker)
    • can't see template tags publicly, but apparently can filter using them
    • Daniela says the add tag function is frozen - posted on issue tracker
    • JD talking to intermine developers about the tag issues and will try to get it fixed.
  • Michael P arranged Genenames server dumps for Caltech. Caltech needs to take a look and comment on its usefulness.
  • IWM arrival times:
    • Hinxton and JD arriving on 25th
    • Abby and Todd arriving 26th
    • Caltech will head over after noon on 26th.