Difference between revisions of "WBConfCall 2018.12.06-Agenda and Minutes"

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* Interactions working group
 
* Interactions working group
 
** Want to (eventually) turn large scale mutant expression data into regulatory interactions; Wen: can already do this with expression cluster data and SPELL data
 
** Want to (eventually) turn large scale mutant expression data into regulatory interactions; Wen: can already do this with expression cluster data and SPELL data
 +
** Could generate a "regulatory" build (for WB, Alliance, etc.)
 
** Also want to turn, for example, ChIP-Seq data into protein-DNA interactions (users often want a list of target genes for a transcription factor)
 
** Also want to turn, for example, ChIP-Seq data into protein-DNA interactions (users often want a list of target genes for a transcription factor)
 
** Newer data standards may be more amenable to such an automated pipeline
 
** Newer data standards may be more amenable to such an automated pipeline

Revision as of 17:17, 6 December 2018

Agenda

Help Desk unresolved issues

Help Desk email list

  • Cecilia needs to be added to help@wormbase.org email list

2019 International C. elegans Meeting

January 8 --- Workshop Applications due
February 6 -- Abstract Submission Site opens
February 14 - Meeting Registration Site opens
March 28 ---- Abstract Submission Deadline
March 28 ---- Travel Award Application Deadline
April 30 ---- Early Registration Deadline
May 15 ------ Housing Reservation Deadline


Minutes

Help Desk

  • GitHub ticket 6747 - Wen will respond
  • GitHub ticket 6775 - Raymond will respond
  • Todd needs to add Cecilia's caltech email address to the mailing list

Workshop

  • Ranjana will take lead
  • Want to cover tools, SimpleMine, WormMine, BioMart
  • Superficial coverage and/or specific use cases? Let users ask specific questions?
  • Can run help desk at poster sessions? Bring projector or monitor and laptop? Quite noisy
    • Probably no separate rooms, could we setup a section in the seats? May be difficult to get power, traffic
    • Setup a screen on the score board? ;p
  • Run two workshops? One for overview, another for feedback? Last time, we did same content twice

New microarray

  • Wen will contact Hinxton

Alliance all hands meeting

  • Fate of current and future working groups
    • Literature and text mining
    • Kimberly and Michael can talk to RGD folks about text mining etc.
    • Grant goes in in January - would be good to have 1 page plan for each topic (including text mining)
    • Triage discussion should include MGD/MGI
  • Expression working group
    • Starting to talk about RNA-Seq data
    • Group mentioned starting with only wild type RNA-Seq data
    • Wen surprised that mutant RNA-seq would not be included; Wen will join expression working group call to discuss
    • Is the plan to just include external RNA-Seq data sources? What effort are the individual MODs currently putting in to curate RNA-Seq data?
  • Interactions working group
    • Want to (eventually) turn large scale mutant expression data into regulatory interactions; Wen: can already do this with expression cluster data and SPELL data
    • Could generate a "regulatory" build (for WB, Alliance, etc.)
    • Also want to turn, for example, ChIP-Seq data into protein-DNA interactions (users often want a list of target genes for a transcription factor)
    • Newer data standards may be more amenable to such an automated pipeline

JBrowse

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