Difference between revisions of "WormBase-Caltech Weekly Calls"

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* Has text mining
 
* Has text mining
 
* Cross-species comparisons available
 
* Cross-species comparisons available
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== April 16, 2015 ==
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=== Topic 1 ===
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=== Topic 2 ===

Revision as of 15:33, 16 April 2015

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings


2015 Meetings

January

February

March


April 2015

April 2, 2015

Adding Species information to nightly geneace dumps

WormBase Ontology Browser WS248 online on Dev

  • Caveat: the rest of the WormBase data on the Dev site is WS247 (one release behind)
    • Would explain some discrepancies

Micropublication form

  • Daniela waiting for feedback from Paul's lab
  • Will send to Alison Frand and Elissa Hallem at UCLA to get input

Mary Ann's IWM abstract for community annotation

  • People can send comment over next day or two
  • Will make revisions and send around next week


April 9, 2015

Tazendra

  • Had some glitches with secondary hard drive this week, not sure what the problem is
  • /home2 directory is not intended as a primary storage; curators need to back data up
  • Paper PDFs stored on /home2 as the primary storage location
  • Papers are backed up on Athena (Wen's computer)
  • TIF files are stored on CDs
  • Main Tazendra hard drive backed up (RAIDed/mirrored), backed up nightly up to ~1 month (or 0.5 month), monthly for a year, but no older versions

Citace data upload

  • April 28th, 10am

Community Annotation Forms

  • Mary Ann's IWM (poster) abstract includes community annotation forms
  • Community annotation form list:
    • Micropublication
    • Gene Expression form (made 15 years ago); mostly not used; micropublication form could be co-opted
    • Gene description form (primarily for the community to edit the automated concise descriptions)
    • "Submit Data" list on WormBase (http://www.wormbase.org/about/userguide/submit_data#0--10)
  • Would be good to have a community annotation portal/landing page
  • Mary Ann will send around a summary of discussions about community annotation, along with prioritization of forms for curators and Juancarlos
  • Relevant curators should consider reviewing existing forms for updates

modSeek

  • http://seek.princeton.edu/modSeek/
  • Princeton 6th year grad student developed it (leaving within 6 months)
  • "Seek" developed for human on microarray and RNAseq data
  • 5 model organisms in "modSeek": yeast, worm, fly, mouse, zebrafish
  • Pulls in data from Gene Expression Omnibus (GEO)
  • Analysis computed from raw data
  • Data from SPELL should be reasonably transferred to modSeek
  • We need to determine if WormBase data can be updated per release
  • Has text mining
  • Cross-species comparisons available


April 16, 2015

Topic 1

Topic 2