Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[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 =
 +
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
== February 6, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
=== Worcester Area Worm Meeting talk ===
 +
* Confirmed for December 2020 or February 2021
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
=== Alaska software ===
 +
* 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
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
== February 13, 2020 ==
  
 +
=== 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
  
== June 6, 2019 ==
+
=== ?Genotype class model ===
 +
* [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
  
=== New SObA graphs ===
+
=== Genotype OA ===
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
+
* Will put documentation [[Genotype|here]]
  
=== Phenotype association file format ===
+
=== WB All-Hands Meeting ===
* May be best to leave the format as is
+
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
* There are problems; paper IDs keep switching columns
+
* Any thoughts at this point?  Still need to discuss with Hinxton, Toronto.
* Would need to revisit the reasoning for why we do it that way
 
* When will the Alliance produce a similar/replacement file? Not sure
 
  
=== Phenotype requests ===
 
* Sent out 1140 emails on May 30
 
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
 
* 21 papers flagged as not having phenotypes
 
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
 
  
 +
== February 20, 2020 ==
  
== June 13, 2019 ==
+
=== Genotype ===
 +
* 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
  
=== IWM ===
+
=== VC2010 assembly genes ===
* Coordinating transportation of swag boxes to Pauley Pavilion
+
* WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
* Workshop on Saturday June 22, from 1pm to 2:30pm
+
* How to best handle these "extra" genes?
* Saturday morning micropublication breakfast 7:30 - 8:30am
+
* We could make different species entries that specify the assembly version
* Workshop
 
** Presenters: it may be best to present as use cases rather than a research project
 
** Chris will cover SimpleMine for Wen
 
** Chris: won't do live demo; only screenshots, maybe some video
 
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
 

Latest revision as of 17:37, 20 February 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 6, 2020

Worcester Area Worm Meeting talk

  • Confirmed for December 2020 or February 2021

Alaska software

  • 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


February 13, 2020

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

  • Proposal
  • Can aim to implement for WS277 but may have to wait until WS278

Genotype OA

  • Will put documentation here

WB All-Hands Meeting

  • Doodle poll
  • Any thoughts at this point? Still need to discuss with Hinxton, Toronto.


February 20, 2020

Genotype

  • 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

  • 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