Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
(497 intermediate revisions by 12 users not shown)
Line 18: Line 18:
  
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
 +
= 2020 Meetings =
  
−
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
−
 
 
−
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
−
 
 
−
== April 4, 2019 ==
 
  
−
=== Paul's Biocuration Keynote ===
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
−
* At Biocuration keynote, Paul S. will talk about web forms, including Author First Pass form
 
−
* Can someone send Paul the latest AFP form location and documentation
 
−
* Will also discuss the future of micropublications
 
  
−
=== IWM Swag ===
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
−
* Stickers vs. screen cloths
 
−
* Daniela had contacted Jessie to make new graphic; she's interested, but do we still need a new graphic?
 
−
* Plan was to make ~2,000 screen cloths (4x4 inch or 6x6 inch?)
 
−
** As for design would be nice to have new design
 
−
** Gary had made cartoon for community curation (proposal might be offensive to some)
 
−
* Include water bottles for special contributors? In addition to shot glasses?
 
−
* Turn around time? ~ 1 month; designs done in April; submit request by mid-May at latest
 
−
* Worm in apple graphic? Dragon worm cartooon? Maybe some variation on it?
 
−
** We can ask Jessie if she can draw up a couple quick sketch ideas
 
  
−
=== Collaborators tool ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
−
* Juancarlos worked on a tool to extract WBPerson collaborators
 
−
* WB staff generally had ~100 collaborators, Paul S has 670
 
−
* Distinguish between collaborators and coauthors? Manual (self reported) vs. automatic associations?
 
−
* Make modification to ACEDB model?
 
−
* Maybe 'collaborators' should be restricted to the laboratory level?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
−
== April 11, 2019 ==
 
  
−
=== Canadian C. elegans meeting ===
+
== June 4, 2020 ==
−
the "Canadian C. elegans meeting” that will follow the 2019 annual conference of the Canadian Society for Molecular Biosciences. The CSMB conference is held at Université de Montréal on June 2-5, 2019 and will focus on Model systems in cancer research (https://www.fourwav.es/view/1174/info/). The C. elegans conference will be held at the CHUM Research Center in downtown Montréal on Thursday June 6, 2019, and will offer opportunities for both oral and poster presentations. The schedule is not finalized yet but it should start around 8:30am and end around 6pm, followed by an apero in a nearby pub. The costs of registrations will depend on the number of participants but will be between 35 and 50 $ per person (it will cover the costs of lunch, coffee break and logistics).
 
−
* Karen may be able to go; she will contact Kimberly for any pertinent information
 
  
−
=== Feedback from small RNA meeting April 3-5, 2019 ===
+
=== Citace (tentative) upload ===
−
* Future meeting invitations and summer workshop?
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
−
* Dustin Updike - in Maine - interested in running a summer workshop for students
+
* Citace upload to Hinxton on Friday, July 10th
−
** Maybe one or two week-long (5-10 days); unconfirmed
 
−
** Wen followed up with him: WormBase curator could attend and present on JBrowse, scientific writing, micropublications
 
−
** Hopefully they can cover travel costs of WB curators
 
−
** Dustin will get back to us about details as they emerge
 
−
* Julie Claycomb interested in having WB curator at Toronto's worm meeting
 
  
−
=== New SVM approach ===
+
=== Caltech reopening ===
−
* Michael will send around paper list with new and old results in the same file
+
* Paul looking to get plan approved
−
* Raymond looked at his data types; at first glance thinks there may be quite a few false positives and false negatives
+
* People that want to come to campus need to watch training video
−
* Can represent new SVM scores as histograms, presumably produce Gaussian curves, can we accept the overlap in distribution tails?
+
* Masks available in Paul's lab
−
* Old thresholds were not necessarily gold standards, probably somewhat arbitrarily chosen initially; we can use the old metrics to roughly choose a new set of corresponding thresholds for the new SVM scores
+
* 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
  
−
=== IWM workshop ===
+
=== Nameserver ===
−
* On Saturday of meeting
+
* 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
  
−
=== NIH workshop on Trustworthiness ===
+
=== Alliance SimpleMine ===
−
* Chris attended on Monday and Tuesday
+
* Any updates? 3.1 feature freeze is tomorrow
−
* Not quite clear that there is or will be any mandate from funders; just encouragement
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
−
* Chris will review briefly at next site-wide call
 
−
* Karen: This is something the data commons really wants
 
−
** Maybe just need to make sure that the Alliance meets these requirements going forward, not so much for WormBase (?)
 

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
Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls&oldid=35405"