WBConfCall 2021.10.07-Agenda and Minutes

Agenda and Minutes

Helpdesk

ftp site questions

• Wormbase - Data Citation Index [Web of Science]
  • Do we still have files that are agnostic wrt release name but always either current or current development?
• Hello, I am trying to download all th...
  • Do we have https downloads links available from the WormBase home page yet?
  • Should all WormBase downloads be available from the same site?
• Related to Add links to the https-driven downloads site

updating laboratory information

• Hello, How can we change the lab repr...

user accounts at WB and the Alliance

• HI Wormbase, I just started an accoun...

e-PCR and gmap tools throwing errors

• e-PCR throwing error
• Server Error: 500 at tools/gmap/run Error M...
  • Three additional tickets describing the same issue: #8382 , #8381 and #8375

tree display

• {"readyState": 4,"requestURL": "/tools/tree/run?in...

WB Genetics manuscript

Thank you so much to everyone for your contributions to content and edits! [Paul D]

Build WS283

Build WS283 has started in Hinxton

New and interesting things: Several model changes, eg to variants

Additional C. briggsae operons Large batch of new strains and variants from KO consortium, CGC and NBRP

AOB

WormBase's All Species page (https://wormbase.org/species/all#0123--10-02) updated with new genomes from WB ParaSite release 16

Todd and Magz set the 4 release dates for 2022.

Many thanks for being patient with the EBI FTP migration, which was very unfortunately timed.

Minutes

Help Desk

Web of Science Data Citation Index

• Having some FTP issues
• Also, was accessing a WS276 file; doesn't seem to be a current equivalent:
  • ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/species/c_elegans/PRJNA13758/annotation/c_elegans.PRJNA13758.WS276.reuters_citation_index.xml.gz
• Todd: These should be automatically updated; file name may have diverged and broken the link

FTP issues; migration to HTTPS download site

• Paul D added link from "Downloads" to User Guide with relevant links
• When WS282 is released, the live link will be added (today or tomorrow)

Changing lab representative

• Who curates this? Cecilia curates lab information, but not sure if she curates this
• Tim S sends monthly updates; may be a data update lag
• Paul D will check on update to data

Community Forum issues

• User unable to make some comments; Todd will look into it and get back to user
• Unable to post links

ePCR, GMap, and Tree Display issues

• Adam looked into Tree Display issue; may be able to provide similar info from Datomic
• Adam would prefer we deprecate/retire Tree Display and remove one more dependency on ACEDB
• Todd: these are periodic, recurring issues about depending on ACEDB
  • Could possibly setup multiple redundancies providing ACEDB, but may not be worth it
• How important are these tools to WB and users?
• Curators really like the Tree Display
  • Are there current alternatives to Tree Display?
  • Adam can demo using REST endpoint for Datomic
  • Thomas Down had created a Datomic tree viewer; not sure what the state of that tool is