WormBase-Caltech Weekly Calls

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Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

GoToMeeting link: https://www.gotomeet.me/wormbase1

2019 Meetings

January 3, 2019

WS270 Citace upload

  • Next Tuesday, Jan 8th, 10am Pacific

Gene descriptions

  • Valerio generated new files to ignore/filter-out problematic genes
  • Still need to validate new pipeline
  • Barring any major issues, will submit new files for WS270 (can load old files if needed)
  • Maybe should define a test set (random sample) to test each release? Already have a test set

Protege Tutorial

January 11th, 2019

WB workshop at IWM 2019

Here's a draft, need to finalize as Jan 15th is the deadline

Possible Title 1: Data in WormBase and how to query it
Possible Title 2: WormBase 2019 - Data, Tools and Community Curation
This workshop will be an interactive session with users in order to discuss the types of data in WormBase and how to query them using the right tools.  We will discuss recent changes to WormBase community annotation forms and how to use them to contribute data to WormBase.  We will also present updates to ParaSite, a portal to parasitic worm genomic data, and how to find cross-species data at the Alliance of Genome Research.

1:00 pm  
Keep your widgets open: a wealth of gene-related data on the gene page
(This will be a quick walk-through of the gene page for orienting Users before we jump into the tools; can point to data related to Gene function, expression and disease models) - Ranjana Kishore
1:10 pm   
Use the right tool for the right data:
Get simple lists using SimpleMine - Wen Chen
Tissue enrichment analysis tools - Kimberly Van Auken
Tools for RNA seq data - Wen Chen
Get batch gene data using the WormBase Ontology Browser - Raymond Lee
Get the big picture: visualize annotations using the SOBA tool -Raymond Lee
1.50 pm  WormBase ParaSite: Exploring lots of genomes - Kevin Howe

2.00 pm  Find cross-species data at the Alliance of Genome Research - Chris Grove

2.10 pm  Be a Community Curator: submit your data to WormBase - Daniela Raciti

2.10-2.30pm. Open forum for questions

Finalize Protege tutorial time

  • Best final options:
    • Wed, Jan 16th, 1pm Pacific/4pm Eastern
    • Thurs, Jan 17th, 11am Pacific/2pm Eastern
    • Thurs, Jan 17th, 1pm Pacific/4pm Eastern
  • Propose we go with Wed, Jan 16th, 1pm Pacific/4pm Eastern