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]]
  
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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
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= 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]]
  
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
== February 6, 2020 ==
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
=== Worcester Area Worm Meeting talk ===
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
* Confirmed for December 2020 or February 2021
 
  
=== Alaska software ===
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Code developed and maintained by Joseph, but not long term solution
 
* Raymond and Eduardo talked about taking it over
 
* Why have a web application vs. a command-line application?
 
** Wanted to make it easy, but also to capture meta data for WB
 
* Should/will find out from Joseph about how hard it is to maintain the software
 
* Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
 
* Expression working group working with Brian Oliver to have GEO take in more structured meta data
 
* Array Express tried requiring more structured meta data, but authors stopped submitting
 
* May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
 
  
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
== February 13, 2020 ==
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
=== Alliance Literature Group ===
 
* Held first meeting on Monday, February 10th
 
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
 
* Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
 
* Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
 
  
=== ?Genotype class model ===
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== September 2, 2021 ==
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
 
* Can aim to implement for WS277 but may have to wait until WS278
 
  
=== Genotype OA ===
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
* Will put documentation [[Genotype|here]]
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Needed for
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*AFP community curation
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*microPublication author tracking for all species
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*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
=== WB All-Hands Meeting ===
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Problems:
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
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*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
* Any thoughts at this point?  Still need to discuss with Hinxton, Toronto.
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*need to do this outside of Alliance
  
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Action
 +
*Paul talks to zfin about interest in person pages
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*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
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*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
== February 20, 2020 ==
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Will do
 +
*create biolink model based on current WB postgres/Caltech model
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*Adam will add tables when we have them
  
=== Genotype ===
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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.
* We will equate superficially similar/identical genotypes for now
 
* What if labs sequence strains later and find out more?
 
* Labs will have to report strains and their sequence and we back-curate accordingly
 
  
=== VC2010 assembly genes ===
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== September 16, 2021 ==
* WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
 
* How to best handle these "extra" genes?
 
* We could make different species entries that specify the assembly version
 
  
 +
1. CeNGEN enriched genes per cell type data targeted for WS283.
  
== February 27, 2020 ==
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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.
 
 
=== Genotype ===
 
* [[Genotype|Genotype Wiki page]] updated
 
 
 
=== Outreach inbox ===
 
* 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
 
* Many are bounced emails messages
 
* Do we want a common place to track bad/bouncing email addresses? We need to distinguish addresses that bounce for policy/SPAM reasons versus those that are likely outdated or no longer in use.
 

Latest revision as of 16:04, 16 September 2021

Previous Years

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2011 Meetings

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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.