WormBase-Caltech Weekly Calls

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November 5, 2015

IEA GO Annotations informating descriptions for non-elegans

  • Some non-elegans genes have confident-sounding descriptions, about localization for example; likely not manual
  • Will make sure automated descriptions handle IEA's appropriately

Wen using Textpresso machine to build SPELL

  • Athena was taking 48 hours to build SPELL (4GB max memory allotted)
  • Textpresso machine took 24 hours (8GB memory allotted)
  • Maybe we can use Textpresso machine for future builds
  • SPELL java program running on Athena (alloted 4GB out of 6GB)
  • Can monitor Athena memory usage; check for any memory leaks

Community Curation Tracker CGI

SObA Graphs for phenotype

  • Juancarlos will transfer code tomorrow, if there are no change requests before then
  • Existing feature requests will be added to future releases of SObA


  • Daniela spoke with Daniel about having web pages in WormBook style to house micropublications

Status of WormBase User Survey?

Sending author updates

  • Would be nice to have a mechanism to update authors on what has been curated for their paper
  • Could give paper data summaries as well as recent updates to curation for a paper

Objectifying/Itemizing annotations from Postgres

  • What if we objectified itemized Postgres entries for easier display of all annotations per paper, for example?
  • May require addition of a text field tag to the ?Paper class, for example, that would capture each annotation item for a paper
  • This would be in lieu of actually objectifying all annotations