WormBase-Caltech Weekly Calls May 2013

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May 2, 2013


  • Google Doc for collecting questions, comments and data here
  • Example queries/questions
    • How to get GO terms for a list of genes?
    • Check FlyMine as a positive control (for functionality and templates)

International Worm Meeting

  • Souvenirs: espresso cups!
  • Posters
    • We will generate templates for posters and send around
    • We can't/won't get the extra space we hoped to get, as of right now
    • Will have to put posters in their designated locations, unless something changes


  • Do we need new computers? Could order by June
  • Spica getting old
  • Elbrus? Tenaya?
  • New server?
  • Postgres backup? Currently on external hard drives. Amazon backup? Network hard drives?
  • On tazendra, users can store files on /home2
  • Mac users have local backup (Time Machine); critical content should be backed up elsewhere also, perhaps

May 9, 2013

Handling Dead Genes

  • Dumping process changes outlined here
  • Will get sorted out before the WS239 upload
  • Chris will begin with Juancarlos

IWM Preparations

  • Workshops
    • WormMine
      • Needs testing
      • Regular conference call 9:30am PDT every Thursday (when no 8:30 international conference call)
      • Also conference call after every international conference call
        • Documentation
          • JD started a Wiki Page for documentation
          • Testing documentation on Wiki here
  • Posters
    • Need a template
    • Text and figures can be assembled in meantime
  • Souvernirs
    • Espresso cups
    • Need a logo: worm shape with "WormBase" above/below it

WormBase Outreach YouTube Channel

  • Mac users can upload directly from Quicktime
  • Can capture tutorials in response to user requests as well as for upcoming IWM Workshops
  • YouTube account name: outreach@wormbase.org

Next citace upload

  • By 10am on Friday June 21st, 2013


  • Slowly progressing at core development side
  • Raymond & Juancarlos working on incorporation of AMIGO2 into WormBase
  • Eventually we will embed AMIGO2 features into WormBase pages

May 16, 2013

New server

  • Raymond ordered a new server computer
  • Should be able to support services currently run on older hardware (e.g. Spica)
  • Will (physically) live in the server room
  • 2 cpus, 64 GB RAM
  • Name? WormBase? WormBase 1?

WormMine Tutorial

  • Next Wednesday, May 22, 2013 12pm
  • Additional tutorial Friday at 2pm


  • Problem: many genes are in intermine only as UniProt IDs from the GO Gene Association File (GAF)
  • We either want to:
    • 1. Remove these (UniProt-based) gene entries entirely OR
    • 2. Keep the gene entries, change the UniProt IDs to WBGene IDs, and pull in the "Assigned By" field from the GO GAF to appropriately attribute UniProt as the source for relevant GO Annotations
  • GO pipeline still in flux, so we will have to wait until that is settled before we establish a long term pipeline for this
  • GO Policy: Every MOD is responsible for their respective organism's GAF
  • We rely on Protein-to-GO annotation/mapping followed by Protein-to-Gene mapping

March 24, 2013


  • Giveaways - designed, planning the order now
  • Workshops - in progress
  • Posters
    • Each of our posters gets a designated place during one of three sessions
    • Room for two posters at the WormBase booth
  • Post-meeting? Lunch on Sunday?

Release Schedule

  • Timeline proposal by Karen
  • Upload can happen as early as models are frozen
  • Need time to test data with models
  • Need to allow time for errors/mistakes
  • 3 days between models freeze and upload?
    • Freeze models on Thursday morning (Pacific time), test for ~3 working days, upload data by Tuesday morning (Pacific time)


  • JD has been giving tutorials
  • Not intuitive, learning curve
  • Infinite nested loops from cross-references
  • Users will need to rely heavily on query templates and lists
  • Once a user has a basic understanding of certain Intermine procedures, many other queries are possible
  • We are generating many GitHub issues now; JD will have to triage
  • How do we best indicate priority of issues? IWM milestone?
  • JD may be willing to take in new tags for existing data types, but is unlikely to accept any new data types
  • YouTube video tutorials

Historical genes

  • Interaction and Gene_regulation OA dumpers working OK
  • Can follow documentation on Interaction Wiki page

Web Resources section for WormBook

  • How to break up descriptions of WormBase for a WormBook chapter?
  • Gene Function, Ontology use, screenshots

May 30, 2013

IWM Posters

  • Format, printing
    • Meeting poster size limit is 3'8" x 3'8" (44" x 44" OR 111.8cm x 111.8cm)
    • EBI wants to print A0 format (slightly smaller width- but too long by 2 inches)
    • Seeing if we can get high quality fabric printing ("flag") at reasonable cost
    • Could offer EBI team to print here (in CA), but may be logistically difficult
  • Function poster: many topics, need to design effectively

Google Summer of Code

  • We have a student; working on a WormBase App

Upload & Release Schedule

  • Plan now is to freeze models on Thursday, upload data on following Tuesday
  • What is the next Freeze/Upload date?
  • Build team needs ~3 weeks after model freeze

Worm Nobel Lectures

  • Can we store/provide lectures as PDFs and videos via WormBook and/or WormBase?
  • Lecture videos on WormBase TV? Need copyright info, permissions
  • Link out to the videos?