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]]
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
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 +
= 2020 Meetings =
 +
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
  
= 2019 Meetings =
+
== February 6, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
=== Worcester Area Worm Meeting talk ===
 +
* Confirmed for December 2020 or February 2021
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
=== 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_March_2019|March]]
 
  
== April 4, 2019 ==
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== February 13, 2020 ==
  
=== Paul's Biocuration Keynote ===
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=== Alliance Literature Group ===
* At Biocuration keynote, Paul S. will talk about web forms, including Author First Pass form
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* Held first meeting on Monday, February 10th
* Can someone send Paul the latest AFP form location and documentation
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* Regular meetings will be on Tuesdays at 10am/1pm/6pm
* Will also discuss the future of micropublications
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* 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
  
=== IWM Swag ===
+
=== ?Genotype class model ===
* Stickers vs. screen cloths
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* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
* Daniela had contacted Jessie to make new graphic; she's interested, but do we still need a new graphic?
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* Can aim to implement for WS277 but may have to wait until WS278
* 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 ===
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=== Genotype OA ===
* Juancarlos worked on a tool to extract WBPerson collaborators
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* Will put documentation [[Genotype|here]]
* 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?
 
  
== April 11, 2019 ==
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=== WB All-Hands Meeting ===
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* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
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* Any thoughts at this point?  Still need to discuss with Hinxton, Toronto.
  
=== Canadian C. elegans meeting ===
 
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).
 
  
 +
== February 20, 2020 ==
  
=== Feedback from small RNA meeting Apilr 3-5, 2019 ===
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=== 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
  
Future meeting invitations and summer workshop?
+
=== 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

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