Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
  
 +
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
  
==February 10, 2011==
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[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
*Should we have a Caltech project/site manager? We'll look at the issues to be solved first
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[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
*Todd would like to know more about what's going on at Caltech
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[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
**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?
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[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
*Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
*Bitbucket use
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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
**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
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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
**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
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
**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
 
  
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GoToMeeting link: https://www.gotomeet.me/wormbase1
  
== February 17, 2011 ==
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= 2020 Meetings =
  
Interaction dumping script
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
*Spot check table
 
*Push changes to Git? Yes, to main branch
 
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
Interactions automatically downloaded to FTP every release? Yes
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
*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?
 
  
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
Ranjana - Solar flares causing static on phone? ;)
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
  
Newsletter for new website release? Yes
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== June 4, 2020 ==
*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
 
  
 +
=== Citace (tentative) upload ===
 +
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 +
* Citace upload to Hinxton on Friday, July 10th
  
BioGRID
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=== Caltech reopening ===
*WormBase to BioGRID curation
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* Paul looking to get plan approved
*Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB
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* People that want to come to campus need to watch training video
*Moving towards using WB interaction types
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* Masks available in Paul's lab
*Definitions of our interaction types
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* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
*Rose will propose to BioGRID community
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** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
*Physical interactions - BioGRID has a better format
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* Need to coordinate, maybe make a Google calendar to do so (also Slack)
**break physical interactions away from other interaction types?
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* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
**Kimberly can propose changes to model: YH separate from other interactions?
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* Also, need to submit who you were in contact with for contact tracing
**Physical vs Genetic interactions? keep separate
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* Form is used all week, and hold on to it until asked to be submitted
*We need an interaction ontology, of some sort
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* If someone goes in to the office, they could print several forms for people to pick up in WB offices
*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
 
  
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=== Nameserver ===
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* Nameserver was down
 +
* CIT curators would still like to have a single form to interact with
 +
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 +
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 +
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 +
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
WormBase IWM souvenir?
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=== Alliance SimpleMine ===
*Computer stress ball? with new site address?
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* Any updates? 3.1 feature freeze is tomorrow
*bouncy ball?
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* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
*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
 

Revision as of 00:09, 5 June 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call