Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
= 2021 Meetings =
  
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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== May 13, 2021 ==
  
 +
=== Textpresso supplement ===
 +
* Due Monday
 +
* Michael working with Paul S
  
== June 4, 2020 ==
+
=== AWS credits ===
 +
* Michael and Valerio were awarded AWS credits, more than they can use
 +
* Maybe they can be repurposed
 +
* Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance
  
=== Citace (tentative) upload ===
+
=== Automated gene descriptions ===
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
+
* Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
* Citace upload to Hinxton on Friday, July 10th
+
* Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
 +
* May be the focus of an Alliance supplement
 +
* We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)
  
=== Caltech reopening ===
+
=== IWM 2021 WB Workshop ===
* Paul looking to get plan approved
+
* Scheduled for June 22, 2021
* People that want to come to campus needs to watch training video
+
* Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
* Masks available in Paul's lab
+
* Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
+
* Here is the submitted workshop schedule:
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
+
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
+
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
+
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
* Also, need to submit who you were in contact with for contact tracing
+
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
* Form is used all week, and hold on to it until asked to be submitted
+
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
* 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
 

Latest revision as of 18:31, 13 May 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April


May 13, 2021

Textpresso supplement

  • Due Monday
  • Michael working with Paul S

AWS credits

  • Michael and Valerio were awarded AWS credits, more than they can use
  • Maybe they can be repurposed
  • Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance

Automated gene descriptions

  • Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
  • Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
  • May be the focus of an Alliance supplement
  • We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)

IWM 2021 WB Workshop

  • Scheduled for June 22, 2021
  • Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
  • Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
  • Here is the submitted workshop schedule:
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A