WormBase-Caltech Weekly Calls April 2013

From WormBaseWiki
Jump to navigationJump to search

April 4, 2013

IWM 2013

  • Abstracts for posters (6 posters total)
  • WormBase booth with desks and poster space
    • How is the space going to be configured?
    • Will there be enough space?
  • Projector? Need space to project
  • Standing tables instead of desks

IWM Promotional ideas

  • Recycle ideas/items
  • See what we have in stock
  • Temporary tattoos?
  • SPlit cost with GSA?
  • Mugs?
  • Triangular worm pick/pencil grip

Expression pattern, personal communication

  • Can we include expression patterns from WormBook?
    • Original report from paper by Chris Li et al
    • Conflicting neuropeptide expression pattern from Oliver Hobert & Cori Bargmann in WormBook
  • How do we handle? Can we put description in WormBase?
  • Normally we don't curate from reviews
  • Best to contact Chris Li, check with her about expression pattern
  • Amend/Edit expression pattern as appropriate

Function, Human Disease poster

  • "Gene Function & Dysfunction"
  • Concise description
  • GO terms
  • Phenotypes (RNAi- and variation-based)
  • Anatomy: Site of Action and Anatomy Function

Variation list

  • Handling large number of variations in OA
  • Generating list of variations likely to be attributed with phenotypes
  • Table maker vs Scripts?
  • Variation data from GeneAce, how frequently updated? Real time?
  • Get new variations from Variation Name Server, not GeneAce
  • Is it worth trying to get daily updates?
  • Name Server: get Variation & Gene info from
  • Propose adding the Variation-Gene connections to Name Server
  • Can we (Caltech) mirror/copy GeneAce locally? Fire wall issues
  • Store MySQL databases on the cloud? Bypass fire walls? Maybe for long term plan

April 11, 2013

IWM abstracts

  • Deadline tomorrow
  • Topics to place posters under? Database, biological topics?
  • Registration
    • What's the status?
    • Karen made a Google doc, but asked us to hold off on filling out info until she talks to Mary Alvarez

Upload coming up

  • Wen preparing mid-build
  • Wen pushing Citace Minus fixes

Dead gene handling

  • Historical_gene tag has been added to appropriate models
  • Chris will work with Juancarlos to sort out OA dumping scripts for Gene_regulation and Interaction OAs
  • Chris will work with web team to sort out web display issues
  • Chris will write up a template describing all the changes that need to be made


  • Raymond setup FTP directory for Wen
  • If anyone wants an FTP folder, we can do that
  • Would exist on caltech.wormbase.org on Canopus
  • Spica: WS237 was having problems
    • Couple of issues with Spica: older hardware, using older operating system (Red Hat)
    • ACEDB software problem
      • Possible but difficult to upgrade ACEDB software
      • Not yet resolved issue with XACE or AcePerl, but AceDiff is resolved
    • WS237 had a data problem
      • Raymond re-installed WS database
  • Mac issues: key mapping (e.g. Alt+F4)
    • Solution? Use virtual machine?
    • VMWare has Fusion; apparently works fairly well
    • Mac users could install, for example, Ubuntu with Fusion and run ACEDB on Ubuntu
    • Raymond is confident in providing support for this approach
  • Running ACEDB remotely is possible, but probably not a long-term, robust, or sustainable solution
  • Note: ACEDB needs to be built from source; binary images don't work

April 25, 2013

IWM Meeting

  • Posters and talk(s)
  • We may not be able to get booth space to accommodate all (6) posters AND a projection screen
  • Todd and Chris will discuss with Anne Marie Mahoney

Upload Schedule

  • Need better upload/release schedule
  • Add more events: Citace testing?
  • Strict vs flexible timeline?
  • Proposed timeline on Time Glider app: Karen's proposal

WormBase You Tube Channel

  • Abby and Todd looking into this now
  • Macs running OSX Lion or higher have a good screen capture functionality with Quicktime (for free)
  • We can prepare videos with content for the upcoming workshops

Capturing curation pipeline documentation on GitHub WormBase curation repository

  • Store scripts for OA dumping scripts, for example
  • Can keep links to relevant Wiki pages
  • Curators should be the ultimate manager of scripts, working with Juancarlos to make any required changes
  • Karen will work out a procedure for "Gitifying" her curation pipelines and will share what worked with other curators