WBConfCall 2021.07.01-Agenda and Minutes

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Help Desk

Open tickets:

Ticket: https://github.com/WormBase/website/issues/8296

Issue: Genetic Map tool down with the following error: Caught exception in WormBase::Web::Controller::Tools->tools "Could not connect to database acedb _WS280, host: 7e85f19c6634"

User wants to: This WBG article says, "Map data have been deposited in ACeDB." I would like to know the flanking markers used to map ccIs4251 and the observed recombination events that gave rise to the reported map position.


Caltech

Hinxton

Preparation for WS282

Build species: C.elegans

Hinxton build master: Stavros

New data/model?

Antibody model updated

Single Cell Tools

1. Discussion on the reception of the app during the poster session

  • Well received and generated lots of discussion. Users were generally surprised by how easy it is to do differential expression
  • Demonstrated use of swarm plot and histograms for identifying cell type markers. Suggestion that users might like to sort histograms by expression level (currently alphabetical)- to be discussed further in CalTech call.

2. Suggestions on curating validated marker genes at WormBase and interaction with the wormcells-viz app

  • Daniela could shift priorities to curate marker genes.
  • WB IDs are needed for cell types, and these need to be mapped to anatomy terms [Not sure I got this right: please correct!]
  • Input from Hinxton needed on how CeNGen data can be displayed as sequence features.
  • Users need to be able to extract sequence that they can use to drive reporters. The reporter class has a text field that can be used for this. Paul/Daniela/Raymond will discuss the details.

IWM 2021

  • Worth reviewing the questions received in the workshop to help choose future webinars. The Q+A doc has been posted on the blog already.
  • New datasets:
 * ModERN - Chris happy to contribute to bringing in this dataset, is there a point person at Hinxton?
  • Related: have run out of identifiers for Sequence Features, need to expand the namespace. Need to revisit what ought to be accessioned (consider performance where there are millions of objects in a class). Subclasses are an option. Consider in the context of LinkML.