WBConfCall 2023.04.20-Agenda and Minutes

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Agenda and Minutes

New 18 C. elegans wild isolate genomes from Cristian Riccio

  • Sarah sent an email with details on 28th of March to Paul, Todd and Scott.

Cristian generated 18 high quality C. elegans genomes assembled from PacBio data from wild isolates which came from Erik Andersen’s lab, and were collected from across the world. The isolates were cultured a few times to increase the homozygosity and are now frozen in Eric Miska’s lab in Cambridge. Cristian lifted over the annotations from N2, ~98% mapped, and he has been exploring structural variants (50bp - 10kb, NGMLR & Sniffles) with a subset experimentally validated, and noted some missing genes due to this i.e. natural knock-outs. Cristian has deposited the reads into ENA, and the assemblies and VCFs (SVs against N2) into Zenodo. He can share Assemblies, mapped annotations, VCFs and bams with us as necessary.

Potential options moving forward: - We could add these 18 new genomes in as tier 3 species - gene trees / synteny would probably be the most useful views, keeping in mind that the annotation is only lifted over. Timelines on this with current resourcing are not great... - We showed Cristian the SV view shared by Scott and he was interested in this for his data mapped to N2 - but commented that he only has SVs up to 10kb, and no translocations. Would this data work? Is this view based on mapped reads / bams? Can the VCF of SVs be visualised too?

I explained that we would need to discuss whether bringing in all of these genomes was the right way forward and what the timelines would be, but if not we can explore whether WormBase ParaSite or Ensembl Metazoa could take them i.e. if we only want to display the SVs as tracks on N2 rather than bringing them in as new species for WB.

What do you think?

  • Still awaiting response - do we want these as tier 3 or as SVs wrt N2?
  • Should these be rendered in JBrowse 2?
  • Todd: What would happen to this data going forward into the Alliance? If this data won't be supported at the Alliance, it may not be the long term solution the authors are looking for.
  • Paul S: in the future (not this year, necessarily) we will figure out how we want to handle this data; can ask the WB SAB in May
    • What is an immediate stop gap measure to implement and send to Cristian? Just make data available and work on additional implementation later
    • Minimal implementation?
      • What does it take to build JBrowse tracks? Scott: FASTA files, VCFs; nice-to-haves: BAM files, descriptions (data meta data), gene models if available
      • Make files available for download: whatever they provide (FASTA, etc.)
    • Scott Cain can get back in touch with Cristian and keep Sarah and Stavros in the loop

Help Desk

  • Please double-check any tickets assigned to you and close, if you can
    • My script is using downloads.wormbase.org - Todd replied; will leave open for now in case there's more follow up
    • Hello, could you please reference.... - I'm leaving this open as a reminder to follow-up with Ranjana and Valerio about references for automated descriptions
    • {"readyState": 4,"requestURL": "/rest/widget/variation/WBVar00543472/molecular_details","status": 500,"statusText": "Internal Server Error"} - there are three similar tickets for this issue. Paolo replied on one, but I'm leaving them open in case there's still work to do.
    • The search directory on the top right.... - request to help with search behavior. Todd, Scott, and Paolo have commented.

Links to Alliance


IWM Meeting

  • Planning for the WB workshop; anything to discuss?

AWS credentials

  • 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
      • Also
        • export WB_DB_URI="datomic:ddb://us-east-1/WSNames/wormbase"
      • And .jar was originally at
        • aws s3 cp s3://wormbase/names/exporter/wb-names-export.jar 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.
  • AWS credentials leaked
    • AWS has become very strict; locked our account
    • Todd H has fully shut down nefarious resources across the globe; still had to petition AWS
    • Bottom line: We will use a more restrictive set of credentials for a WB AWS superuser; everyone else has access but with more restricted permissions
    • If anyone has permission problems accessing AWS, let Todd know
    • Todd retired some outdated credentials (10+ years old); it is good practice to regularly change credentials
    • Google accounts also affected; strongly encourage using 2-factor authentication

Tazendra migration

  • Caltech curation/Postgres server is migrating to AWS
  • Everything is being dockerized and moved to AWS
    • Valerio: we are using names from a domain I setup with 'textpresso-central'; would be good to setup names under the wormbase.org domain
    • Valerio will specify to Todd where they should point
  • Will eventually need to make changes once the switch is official

WormBase ParaSite 18 has been released

Our Release 18 is out since last week - https://wbparasite.wordpress.com/2023/04/13/wormbase-parasite-release-18-our-biggest-update-yet/.

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