Difference between revisions of "WormBase-Caltech Weekly Calls"

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** We will link to the CeNGEN homepage wherever appropriate
 
** We will link to the CeNGEN homepage wherever appropriate
 
* All else will depend on Eduardo's tools for single cell expression data
 
* All else will depend on Eduardo's tools for single cell expression data
 +
* Display solutions can be used for Alliance single-cell data in general
 +
* May want to consider future use cases, e.g. mutant-vs-WT expression, chemical/drug-induced expression, etc.
  
 
=== Chen building access ===
 
=== Chen building access ===

Revision as of 19:43, 11 March 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings


2021 Meetings

January

February


March 4, 2021

Webinar Monday

  • Juancarlos can send a reminder email; he just needs the text for the body of the email message
  • Can we send the webinar reminder to WB staff? Cannot use staff@wormbase.org to register
  • Raymond will try to remember to forward to staff

Neural Network (NN) evaluation

  • Kimberly (and other curators) looking through NN results
  • Had previously prevented LOW scoring SVMs(?) from being sent to authors
  • We need an agreed upon protocol for evaluation
  • To avoid bias, we should randomly sample papers; usually will find negatives; how do we represent high, medium and low-scoring papers in the set without making curators review >> 100 papers?
  • Michael will come up with protocol and send around list of papers for each data type (in Google Doc)
  • Perhaps evaluation should happen on non-curated, newer papers


March 11, 2021

Spreadsheet for Data not in ACEDB

CeNGEN To Dos

  • Daniela, Wen, Valerio, Eduardo, Raymond met with CeNGEN
  • Want to add JBrowse track for promoters(?)
  • Three things:
    • CeNGEN will provide histograms that we can put on each gene page, similar to modENCODE plots (do they provide static images or data that we process and display as histograms?)
    • Their tool can assess "enriched" genes by cell type (enriched vs. neurons or vs. all cell types; not just housekeeping genes); these can be sent to WB -> SObA and enrichment analysis
    • We will link to the CeNGEN homepage wherever appropriate
  • All else will depend on Eduardo's tools for single cell expression data
  • Display solutions can be used for Alliance single-cell data in general
  • May want to consider future use cases, e.g. mutant-vs-WT expression, chemical/drug-induced expression, etc.

Chen building access

  • You'll need an ID with RFID?
  • help.caltech.edu -> request type Card Office
  • It will be ready and wait for you at the Reddoor cafe.