WBConfCall 2023.04.06-Agenda and Minutes

Agenda and Minutes

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IWM Meeting

• Planning for the WB workshop
• Need some separate meetings for this?
• TH: who’s attending? Do we have travel funds available?

New items

• WB needs Genes from nameserver, which is on AWS, so need creds or AMI ?
  • TH
    • I will give a post-mortem of the recent credential leak at the next conference call.
    • The preferred and recommended way to do this would be via an assumed role, not dedicated AWS CLI credentials.
    • I think you mean instance? AMIs are images of instances. IMHO a stand-alone instance is overkill, and already have instances available to run a cron.
  • Juancarlos
    • That's great. I don't know much about AWS. If you're able to set up a cronjob to daily
      • java -cp wb-names-export.jar clojure.main -m wormbase.names.export gene genes.csv
    • And put the output genes.csv somewhere web accessible, I think that's all Caltech would need.
    • I don't know much more about it, other than Matt Russell told me to run that (we went back and forth a bunch of times before it worked).
    • Here's a copy of the .jar file
      • https://tazendra.caltech.edu/~azurebrd/var/work/todd/wb-names-export.jar
  • Thanks, JC! We can make that work from one of our persistent instances. I will look when I return from vacation.

IWM

• Mary Ann Mahoney would ask for more details when the time is right. It's accepted we have the workshop. Ranjana has 4 talks listed. 90 minutes total. 60 mins of talks, 30 mins of open Q&A. Ranjana would like to go to the meeting. May is early registration deadline. https://docs.google.com/document/d/1ZYjSX2UGcvLY2lRY5qGuVYO1Q7euHlXZ6kHJ0W0AEVA/edit?usp=sharing
• Paul S will look into funds, Todd should talk to Paul S. If people want to go, go, Paul will figure out funds later. Everyone use sick leave and vacation time so we have money, that accounts for +/- 2 people's salary. Paul's lab will send just a couple of people.
• Raymond : use Ranjana's document to organize talks, review topics, and other things.
• Ranjana :
  • Talk 1: Starting with one and arriving at many: Using WormBase and the Alliance of Genome Resources for gene data. (10 mins + 5 mins for questions)** Talk 2: What tool do I use? Matching tools to data searching (10 mins + 5 mins for questions)
  • Talk 3: JBrowse and recent updates to genome browsing (10 mins + 5 mins for questions)
  • Talk 4: Be ACKnowledged and help us curate your paper! (10 mins + 5 mins for questions)
  • 30 mins Q and A session after Talk 4:: All questions related to WormBase or the Alliance will be answered.
• Chris could do first talk, Ranjana would like to highlight disease under gene umbrella.
• Todd could do the tools talk, otherwise Raymond could.
• Scott not sure if he's going, to talk about JBrowse, but could record a talk in advance and be on zoom.
• Daniela / Kimberly will probably be there for ACKnowledge, Valerio won't be there.
• Paul : Can we talk about sequence ? How is WormBase handling other assemblies.
• Stavros would like to be there, but Sarah Dyer has the last word.
• Paul will try to organize an SAB to handle some comments. Alliance should be able to handle orthologies in the next phase, but could be delayed a year or so, but not forever. Want more people contributing to worm, collecting info is great to get more people what they need.
• Raymond : put that in talk 4 ?
• Paul : Listen to people in booth.
• Ranjana : Use Q&A section.
• Wen : ParaSite workshop invited us.
• Karen : Acknowledge people who curated with prizes or callout ?
• Valerio : ACK has list of top contributors, meant for public acknowledgement, Kimberly / Daniela should say something, new logo, probably swag.
• Raymond : mugs and shot glasses were popular, could be special swag.
• Karen : worm oscar trophies, a worm holding a worm.
• Raymond : list people who are going / not going on document.
• Chris : Meeting organizers requested 30 min Q&A.
• Ranjana : There have been questions before and various WormBase staff around.
• Raymond : Could remove questions on 4 talks to have extra time for 5th talk.
• Ranjana : Could ask to reserve questions for Q&A
• Chris : Would be good to get questions right away so people don't wait an hour.
• Paul : Could ask people to come to the booth, and then get feedback. Encourage people to come to booth for prizes.

Grant

• Paul : Summary statement for WormBase grant. Love everything. 2 criticisms. Alliance is good, but what if it fails. Weren't as innovative as previous years. Because we're not proposing tools. Score is 14 which is amazing. We can be innovative.
• Karen : They've complained before about tool making.
• Paul : Study section has bioinformaticians instead of elegans researchers, not the same as NIH. Don't have to worry for 5 years. Go back and say our job is to innovate. We should aggresively figure out how to get more resources for MOD, in and out of country. Innovation for that is good. Do cool stuff. It's gotta be fun. Rejuvenate, re-enjoy.
• Wen : Design game for community curation, exchange points for something.

Links to Alliance

• Chris spreadsheet for All Hands face 2 face for places to link WormBase to the Alliance, even before trying to embed Alliance widgets. Chris can coordinate with web team. Will add link here later. Will make sure OICR is aware

WS289 model change

• Ranjana has a small model change to get asserted human genes in at the point of curation. Mark and Stavros have looked it over. Stavros has said there's time to get that in. Stavros will try to do it next week or on the 17th after holiday. Wen thought upload would be the 11th, if build won't start until 27th, could postpone upload until 18th. Stavros needs a couple of days pre-build, will start on 17th. Ranjana could push model change build to next release, need model change. Mark can do model change on Tuesday 11th. Caltech needs it by upload on the 11th. Mark will do model change tonight. Ranjana and Juancarlos will change dumpers. Raymond : rebuild CitaceMinus with new models and notify people. Wen : prefer procedure to have model changes 2 weeks before. Mark : Magdalena knew procedure, but left, so EBI needs to know. Stavros : Asked for model changes a couple of weeks ago. Ranjana : Came up after face 2 face, let's hold off.