WBConfCall 2018.12.06-Agenda and Minutes

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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
  • Scott would like a chunk of time to cover JBrowse content
  • Maybe Chris and Scott can run a WormMine/JBrowse workshop and Ranjana can run another workshop for (other) WB content and tools

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 track significant thresholds

  • User wrote in asking about how to distinguish significant peaks in ChIP-Seq tracks
  • For most (all?) of these tracks, there is information associated including score mean and score standard deviation
  • However, we have a standard default view of minimum score of 0 and maximum score of 100, across the board, even though the mean and standard deviations can vary greatly
  • Scott and Chris discussed, have a preliminary proposal to calculate minimum score displayed and maximum score displayed on a track-by-track basis, probably setting minimum to mean + ~2 standard deviations and maximum to mean + ~4 standard deviations
  • Raymond interested in this issue as well; Scott, Chris, and Raymond will discuss and come up with an automated approach
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