WormBase-Caltech Weekly Calls February 2011

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February 10, 2011

  • Should we have a Caltech project/site manager? We'll look at the issues to be solved first
  • Todd would like to know more about what's going on at Caltech
    • What would Todd like to know about? New ideas, data types?
    • What can we communicate more effectively to Todd?
  • Should we take minutes of Caltech WormBase group meetings and send around?
  • Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
  • Bitbucket use
    • How do we see only what pertains to us, individually?
    • Paul: good way to document bugs and fixes, problems/solutions
    • Bitbucket Wiki - does that capture what people want/need to see?
    • Who should Todd follow? What would Todd like to know about?
    • Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
    • Should we develop best practices guideline for Bitbucket use?
      • Avoid posting topics that are too specific or too vague?
      • What do we want most to get out of Bitbucket?
    • Curation efforts? No
  • SAB Meeting
    • Not much feedback for literature curators
    • User interface stuff took precedence
    • Paul: Testing, spot-checking website for errors
    • Web issues, e-mails from Gary and Oliver
  • WormBase-wide conference call twice per month
    • First & third Thursday of the month
    • Starting next Thursday (2-17) @ 8:30am PST
    • Web redesign meetings on Thursdays will have to be every other week? Do both same day?
  • Raymond: WormBase mirrors
    • Do we want to implement the Genome Browser for the mirror(s)? If practical
    • It seems as though Caltech mirror has been crashing often
    • Has the Caltech mirror been working for people lately? Yes, more or less

February 17, 2011

Interaction dumping script

  • Spot check table
  • Push changes to Git? Yes, to main branch

Interactions automatically downloaded to FTP every release? Yes

  • People should check their own curation data
  • Users query frequently?
  • Can WormMart work instead?
  • Ruihua - feature can be added
  • Todd - good to have pre-defined queries generated automatically
  • Parse/remove predicted interactions (400,000) from others during dump? Yes
  • Paul - Wei Wei wants to help with updates - who should she contact at WB?

Ranjana - Solar flares causing static on phone? ;)

Newsletter for new website release? Yes

  • Todd - 5 development milestones
    • teleconference with Gary Ruvkun's lab next week
    • Go live with Beta version in June (@IWM)
    • Go live live with new site in September
    • Retire old site at end of year
    • Need outreach, documentation, screencasts


  • WormBase to BioGRID curation
  • Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB
  • Moving towards using WB interaction types
  • Definitions of our interaction types
  • Rose will propose to BioGRID community
  • Physical interactions - BioGRID has a better format
    • break physical interactions away from other interaction types?
    • Kimberly can propose changes to model: YH separate from other interactions?
    • Physical vs Genetic interactions? keep separate
  • We need an interaction ontology, of some sort
  • Who should Wei Wei contact, how to coordinate with Hinxton; getting data from FlyBase and SGD?
    • Automation?
  • Interaction pages - explain what the interaction is based on; provenance/reference
  • Gene Orienteer shows data, but user has to link out

WormBase IWM souvenir?

  • Computer stress ball? with new site address?
  • bouncy ball?
  • worm rubber band thing?
  • Screen shield?
  • Complementary iPads? ;)
  • Antifungal socks? wristbands?


  • new data doesn't load; problem runnning search engine; can load it on athena, not generalizable problem?
  • OS was not complete with an update; try again
  • two virtual machines working back and forth for support
  • how often is SPELL being used? log?; had 6-7 users within two weeks complaining of SPELL problems
  • Todd - can send Google analytic tool to put at bottom of page
  • Wen - SPELL testing server; official and mirror; want a separate testing server for new releases; mirror on athena (Wen's working machine); Raymond says don't want to attract users to that machine; WB's running SPELL on altair; heavily loaded and has had problems; relying on athena may be problematic
  • maybe we need analysis of all of our machines to see big picture; can we consolidate machines; make use of ones we have? If not we can get another machine.
  • what type of machine do we need?
  • Log of all machines with purchase date and functionality?
  • Linux vs Mac curators? athena development machine;
  • how much power do the scripts need? can check
  • may not be appropriate as official server if main machine goes down
  • WB and athena can run SPELL server, but not others. security problems?
  • prefer work machine is readily re-bootable; reconfigure software easily without affecting other things that people rely on
  • need 10GB space; 4GB memory? SPELL production server; want it stable for outside world; hardware designed for that purpose; farm it out to IMSS?
  • complexity of the application; Linux can run multiple applications; caprica has SVM production and WormMart; understand demand of the application; requirements; development vs running scripts, how often? Efficient use of machines. Have 2 computers, getting a third; for WormMart need power; traffic suddenly increased yesterday; monitor traffic; not much personal experience with server maintenance; cluster needs lots of expertise
  • building official sever of SPELL at OICR? Yes


  • with WormMart and WormBase, people just want to know if it's down, just to know to lessen frustration; Official statement from dev team
  • WormMart - we give users testing url; can we just change WormBase link to that testing server?
  • going to change HTML to update users with most recent information; discuss with Lincoln, 5 datasets on testing server; remaining 3 datasets. if WormMart not working, put a message on main site
  • it doesn't look good to have a link to a tool linked from a production server; if we don't trust the data we shouldn't put it up.
  • would like to keep the html page as a testing server; could modify page
  • if WormMart is working OK but not perfect, that's OK; Comment in the banner
  • the html page is a useful tool to get feedback from users

February 24, 2011

CIT Computer Survey - done

CD/DVD burner not working (Wen)

Build Scripts:

  • run @ OICR
  • dynamic/static files
  • problem: no one takes care of them
  • curators should claim them and take care of them
    • Gene interaction dump script claimed by Raymond and Xiaodong
    • 256 interaction objects empty (should not be); emptied during build?
  • Monitor usage with new site
  • Files (like FASTA, GFF) should be immediately available to users
  • Page that links to the scripts (FTP)
  • Need to define what we should have (common datasets)
    • Example: Table with all genes, RNAi phenotype, genetic phenotype, etc.
    • How many genes have been knocked out by RNAi?, etc.
    • Metrics table on each species: #genes, #chromosomes, etc.
  • Curators think about what data should be available
  • Modifying existing script is easier than making new one
  • Gary Williams already generates RNAi-phenotype-gene connections?

Snehal work half-time at WormBase?

  • Will interview
  • UI testing?
  • Curation? GO? Phenotype?
  • Start April 15th - 8 months? (Sept.) maybe longer
  • Focus on particular papers?

Physical Interaction model

  • Have been discussing with Rose at BioGRID
  • Y2H, CoIPs, Pull downs, etc.
  • Store physical interactions in WB outside of GO curation
  • Data model
    • YH model vs Interaction model
    • Physical interaction tag in current interaction model unused
    • Generalize YH model -> physical interaction model
    • Add experiment types
    • Issue: what do we do with existing physical interaction tag in interaction model?
    • Split out different interaction types into individual classes?
    • Separate into physical, genetic, predicted classes? Textpresso?
    • Create separate classes for each experimental type? (Y2H, CoIP, etc.)
    • XREF Interaction to Physical interaction, Genetic interaction
    • Goal is for cleanliness and completeness
    • How to capture experimental-specific info in curation and database?
    • Suppress Y2H import from BioGRID?
    • Keep interaction models as they are?
    • All curators: Review interaction models to see what they want on the curation end