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.



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.