WormBase-Caltech Weekly Calls

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June 11, 2009

  • Discussion of allele-paper connections
    • Jolene has a Textpresso-based pipeline for identifying alleles in papers
    • Alleles get associated with a paper if there is phenotypic or molecular data
    • List of all alleles associated with a paper could possibly be passed on to Sanger for subsequent connection
  • Discussion of gene-paper connections
    • What criteria should be used for associating genes with papers?
    • Currently being associated manually by a curator during first-pass
    • Could Textpresso be harnessed for this task?
    • There are different evidences attached to gene-paper connections
    • Genes associated with a paper via Textpresso searches could be presented to the first-pass curator for approval in the first-pass form
    • Need to fix current abstract-gene associating script to include proteins (e.g. PIE-1)
  • Incorporate a customized Textpresso query on WormBase object pages so users could look for additional info if they want
    • Data type curator could help design a useful query
  • Other gene-object connections
    • Develop a canned query for all objects that should be associated with the gene page
  • Worm Meeting
    • Pre-meeting - meeting rooms?
    • Pre-meeting - practice talks for WormBase workshop
    • Storage for swag - pavillion should be okay

June 18, 2009

  • Worm Meeting and Pre-Meeting
    • WormBase Help Desk Schedule - set for worm meeting
    • Wen may need help carrying boxes of swag
    • Do any Sanger or WashU people need rides to UCLA?
    • Mary Alvarez is working on finding rooms for the pre-meeting
    • Be prepared to report on curation status of your data type and what we might need
  • Author contact information on first-pass form
    • email goes to the first email address found by Textpresso
    • Raymond - we do care where this data comes from
    • Erich - can we send it to the designated corresponding author
    • first-pass curation could capture the corresponding author
    • if the email didn't go to the corresponding author, it may affect our response rate
    • two-stage approach proposal
      • respond to Bernard - we'll try to find corresponding author in the future and add his name to the comments field for now
      • going forward, how best to determine corresponding author?
      • keep track of IP address from which the data was sent?
      • add text to email saying that authors may include their contact information in the comments box, if they wish
      • Raymond will proof-read papers to check on corresponding author designation and email addresses
  • Zfin visit - PATO progress, worth looking at
    • Erich noted no genome browser - what is the issue?
    • Their experience with getting figures from journals might be helpful.


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


BioGRID

  • 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?

SPELL

  • 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

WormMart

  • 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
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