WBConfCall 2023.07.06-Agenda and Minutes

Regrets

Stavros - clashing school meeting announced this morning. I may not be able to attend or will join late...

HelpDesk

Outstanding issues:

• New widget/section on how to cite WormBase
• Issue with ASNS-1 (started at Hixton, then bounced to CalTech)
  • Kimberly said she'd take a look
• Landing page for papers that have not been uploaded yet

Chris pointed out that there was a proliferation of very strange labels for issues that are almost certainly not intended and they should be deleted to get rid of the cruft.

• strange issue labels

Next Help Desk Officer -Karen, July 10th-24th.

New staff member - WormBase ParaSite

Steph Brown joined the WBPS team last week. She's based in Matt Berriman's group in Glasgow. Welcome to the team Steph!

WB AWS EC2 instance for WBPS Web Apollo is down

This is the server hosting WBPS's Apollo instances for our user communities on this URL: http://apollo-test.wormbase.org:8080/apollo/annotator/index Slack discussion: https://wormbase.slack.com/archives/C6GJ97BL2/p1688463613605809 WB WebApollo set-up documentation: https://www.ebi.ac.uk/seqdb/confluence/display/WORMBASE/WormBase+Apollo+Instances

• It was pointed out that the WBPS Web Apollo server has been down for about a week which is affecting users, making this a critical outage.

Brief JBrowse update

Lots of docs added to the blog: https://blog.wormbase.org/tags/jbrowse2/

On staging:

• Added links to the Alliance for all N2 genes
  • In JBrowse 1, a click on a gene now pops up a dialog offering to got to either AGR or WB
  • in JBrowse 2, a click on a gene brings up the details frame that has links to AGR, WB and JBrowse 1
• Added the CRISPR tracks from JB1 to JB2
• Example JBrowse 2 view: https://staging.d2jjb0xowet5mr.amplifyapp.com/?session=share-sGGM_%2FEuD%2F&password=1E6tU

Scott can roll these changes out to production with a minimum of fuss.

A few suggested items:

• • Add a link in the Help menu of WB's JBrowse 2 to the docs on the blog
  • Tick the "News" box on the block to get them to show up on the main page (for a while)
  • The user guide (https://wormbase.org/about/userguide/for_users#2310--10) should be updated for JBrowse (and to remove mention of GBrowse)

Worm23 - comments, plans, conclusions

eg. see https://github.com/WormBase/website/issues/9268

• • Definitely need to add "how to cite" ALL of the dropdowns (why is it only under the Downloads menu?)
  • Also, adding tool specific cites (eg, for Textpresso) would be a good idea where appropriate

• issues around non-elegans species