Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== April 1, 2021 ==
 
  
=== Antibodies ===
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== May 13, 2021 ==
* Alignment of the antibody class to Alliance:
 
** Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
 
*** Other animal is sometimes used for older annotations, e.g. authors say that the antibodies were raised both  in rats and rabbits. Standard practice would create 2 records, one for the rat antibody and one for the rabbit.
 
*** Possible pseudonym was used when  a curator was not able to unambiguously assign a previous antibody to a record. (we have a Other name -synonym- tag to capture unambiguous ones). When moving to remarks we can keep a controlled vocabulary for easy future parsing, e.g. “possible_pseudonym:”
 
** Antigen field: currently separated into Protein, peptide, and other_antigen (e.g.: homogenate of early C.elegans embryos, sperm). Propose to use just one antigen field to capture antigen info.
 
  
All changes proposed above were approved by the group
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=== Textpresso supplement ===
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* Due Monday
 +
* Michael working with Paul S
  
=== textpress-dev clean up ===
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=== AWS credits ===
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
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* Michael and Valerio were awarded AWS credits, more than they can use
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
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* Maybe they can be repurposed
* Direct access may be possible via Caltech VPN
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* Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance
* Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines
 
  
=== Braun servers ===
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=== Automated gene descriptions ===
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
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* Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
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* Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
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* May be the focus of an Alliance supplement
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* We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)
 +
 
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=== IWM 2021 WB Workshop ===
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* Scheduled for June 22, 2021
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* Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
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* Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
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* Here is the submitted workshop schedule:
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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
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12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
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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
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12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A

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