WormBase-Caltech Weekly Calls

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