Difference between revisions of "WormBase-Caltech Weekly Calls"

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==June 11, 2009==
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= Previous Years =
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*Discussion of allele-paper connections
 
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**Jolene has a Textpresso-based pipeline for identifying alleles in papers
 
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**Alleles get associated with a paper if there is phenotypic or molecular data
 
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**List of all alleles associated with a paper could possibly be passed on to Sanger for subsequent connection
 
  
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*Discussion of gene-paper connections
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[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
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**What criteria should be used for associating genes with papers?
 
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**Currently being associated manually by a curator during first-pass
 
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**Could Textpresso be harnessed for this task?
 
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**There are different evidences attached to gene-paper connections
 
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**Genes associated with a paper via Textpresso searches could be presented to the first-pass curator for approval in the first-pass form
 
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**Need to fix current abstract-gene associating script to include proteins (e.g. PIE-1)
 
  
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*Incorporate a customized Textpresso query on WormBase object pages so users could look for additional info if they want
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[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
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**Data type curator could help design a useful query
 
  
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*Other gene-object connections
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[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
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**Develop a canned query for all objects that should be associated with the gene page
 
  
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*Worm Meeting
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[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
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**Pre-meeting - meeting rooms?
 
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**Pre-meeting - practice talks for WormBase workshop
 
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**Storage for swag - pavillion should be okay
 
  
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==June 18, 2009==
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[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
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*Worm Meeting and Pre-Meeting
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[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
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**WormBase Help Desk Schedule - set for worm meeting
 
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**Wen may need help carrying boxes of swag
 
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**Do any Sanger or WashU people need rides to UCLA?
 
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**Mary Alvarez is working on finding rooms for the pre-meeting
 
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**Be prepared to report on curation status of your data type and what we might need
 
  
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*Author contact information on first-pass form
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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
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**email goes to the first email address found by Textpresso
 
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**Raymond - we do care where this data comes from
 
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**Erich - can we send it to the designated corresponding author
 
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**first-pass curation could capture the corresponding author
 
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**if the email didn't go to the corresponding author, it may affect our response rate
 
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**two-stage approach proposal
 
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***respond to Bernard - we'll try to find corresponding author in the future and add his name to the comments field for now
 
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***going forward, how best to determine corresponding author?
 
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***keep track of IP address from which the data was sent?
 
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***add text to email saying that authors may include their contact information in the comments box, if they wish
 
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***Raymond will proof-read papers to check on corresponding author designation and email addresses
 
  
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*Zfin visit - PATO progress, worth looking at
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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
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**Erich noted no genome browser - what is the issue?
 
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**Their experience with getting figures from journals might be helpful.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
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==February 10, 2011==
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
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*Should we have a Caltech project/site manager? We'll look at the issues to be solved first
 
  
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*Todd would like to know more about what's going on at Caltech
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GoToMeeting link: https://www.gotomeet.me/wormbase1
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**What would Todd like to know about? New ideas, data types?
 
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**What can we communicate more effectively to Todd?
 
  
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*Should we take minutes of Caltech WormBase group meetings and send around?
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= 2020 Meetings =
  
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*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_January_2020|January]]
  
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*Bitbucket use
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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**How do we see only what pertains to us, individually?
 
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**Paul: good way to document bugs and fixes, problems/solutions
 
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**Bitbucket Wiki - does that capture what people want/need to see?
 
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**Who should Todd follow? What would Todd like to know about?
 
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**Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
 
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**Should we develop best practices guideline for Bitbucket use?
 
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***Avoid posting topics that are too specific or too vague?
 
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***What do we want most to get out of Bitbucket?
 
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**Curation efforts? No
 
  
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*SAB Meeting
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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**Not much feedback for literature curators
 
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**User interface stuff took precedence
 
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**Paul: Testing, spot-checking website for errors
 
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**Web issues, e-mails from Gary and Oliver
 
  
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*WormBase-wide conference call twice per month
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
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**First & third Thursday of the month
 
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**Starting next Thursday (2-17) @ 8:30am PST
 
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**Web redesign meetings on Thursdays will have to be every other week? Do both same day?
 
  
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*Raymond: WormBase mirrors
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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**Do we want to implement the Genome Browser for the mirror(s)? If practical
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**It seems as though Caltech mirror has been crashing often
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**Has the Caltech mirror been working for people lately? Yes, more or less
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== June 4, 2020 ==
 +
 
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=== Citace (tentative) upload ===
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* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
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* Citace upload to Hinxton on Friday, July 10th
 +
 
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=== Caltech reopening ===
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* Paul looking to get plan approved
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* People that want to come to campus need to watch training video
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* Masks available in Paul's lab
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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
 +
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
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* 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 ===
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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
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* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
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* Hinxton is pulling in CGC strains, how often?
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* Caltech could possibly get a block of IDs
 +
 
 +
=== Alliance SimpleMine ===
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* Any updates? 3.1 feature freeze is tomorrow
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* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call

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
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