WormBase-Caltech Weekly Calls

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August 3, 2017

WB grant

  • Progress (maintenance stuff) can be written as of last grant cycle
  • Current projects and report the steady state

CRISPR alleles

  • Some authors not reporting CRISPR alleles with standard nomenclature
  • Some in Paul's lab creating same knockin with same name (should be distinct). Mary Ann to update nomenclature guidelines.
  • Some (e.g. Bruce Bowerman) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene
    • RNAi mapping pipeline not setup to handle this
    • Could maybe use endogenous sequence near insertion site (not ideal, for off-target effects)
    • Maybe best, once new ?Phenotype_experiment model is in place, to just refer to perturbed gene

Ontology Browser

  • Has been less stable lately; Raymond has needed to restart machine
  • Being served from Dell server (in Braun building)

August 10, 2017

WormBase grant

  • Neuronal wiring with Scott Emmons? Maybe not for this round
  • Transcription regulatory networks? Is a priority
  • Paul will assemble existing parts and send around for review

Entity markup

  • InSilico entity linking project requires curator link checking - for missing links as well as for faulty links - bad links are already an issue when ambiguities exist and this will grow as an issue when we start marking up multiple mod entities in the same paper
  • There is a brief summary table outlining the link URLs and predicted quality - this is a useful feature of the current system set up by Arun, we are creating the same type of feature in the new inteface
  • Could Cecilia check links?
  • New interface will come out in a few months; if anyone starts now, they'll have to relearn when the new interface comes out
  • Eventually markup should be job of authors during the process of writing. Need an authoring tool - this can be made - there needs to be more discussion between wormbase, and insilico if this is going to be part of the insilico phase II or not

Sequence features

  • Should we have a standard human readable names for sequence features?
  • Should we consolidate several features associated with the same gene when displaying in network views?
  • Is there an automated way to give them public names?
  • Maybe name automatically, but then allow manual overwriting
  • Use gene name when experimentally demonstrated connection
  • Needs to be automated, rule-based
  • Could name based on neighboring gene(s)

Person lineage graph

  • Progress made in development, direct lineage running off of Datomic. All of it will need to be completed before it can go into production.

Docker container system

  • Potentially very useful for WB web services

Consider content for NAR paper

  • Send ideas to Raymond


  • Input for the WB grant?
  • Could discuss microreviews

Concise descriptions

  • Automated descriptions good for genes with little info
  • Human-written descriptions good for genes with lots of info; don't change too frequently
  • Some have suggested including protein domain info