Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(57 intermediate revisions by 8 users not shown)
Line 35: Line 35:
 
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
== June 3, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
=== Reserving meeting rooms ===
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* Raymond encountering challenges with setting up regular meeting room reservations in Chen building
 
* We've been asked to make reservations one week in advance
 
* Need to use a room if we reserve it
 
  
=== Summer student(s) ===
 
* Anatomy function project with Raymond
 
* Many types of anatomy function data submitted via AFP
 
  
== June 10, 2021 ==
+
== September 2, 2021 ==
  
=== Variation-Gene Associations ===
+
1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
*Some QC on AFP-extracted data led to the realization that at least some of the 'tm' variations aren't associated with genes on tazendra
+
Needed for
*https://github.com/WormBase/author-first-pass/issues/204
+
*AFP community curation
*https://github.com/WormBase/website/issues/8262
+
*microPublication author tracking for all species
*It looks like non-manually asserted variation-gene associations will be generated via the VEP pipeline during the build, so Caltech would need to get this information from each WB release
+
*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
=== Confirm WS282 Upload Dates ===
+
Problems:
*July 6th?
+
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
*Data freeze/upload date on the release schedule is July 12th
+
*need to do this outside of Alliance
 +
 
 +
Action
 +
*Paul talks to zfin about interest in person pages
 +
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
 +
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
 +
 
 +
Will do
 +
*create biolink model based on current WB postgres/Caltech model
 +
*Adam will add tables when we have them
 +
 
 +
2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
 +
 
 +
== September 16, 2021 ==
 +
 
 +
1. CeNGEN enriched genes per cell type data targeted for WS283.
 +
 
 +
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
 +
 
 +
== September 23, 2021 ==
 +
 
 +
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
 +
* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
 +
* Update the WB page on citing WormBase
 +
 
 +
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
 +
 
 +
3. Server room in Braun power down for no apparent reason. Reset.

Latest revision as of 18:17, 23 September 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

June

July

August


September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.