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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
== May 13, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
=== Textpresso supplement ===
 +
* Due Monday
 +
* Michael working with Paul S
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
=== 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)
  
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+
=== IWM 2021 WB Workshop ===
 
+
* Scheduled for June 22, 2021
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
+
* 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:
== October 1, 2020 ==
+
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
=== Gene association file formats on FTP ===
+
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
+
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
* Our association files have format "*.wb"; is this useful or necessary?
+
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
* Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
 
* We could add a README file and/or convert to the new [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md GAF 2.2 format] which would have a more expressive file header and possibly column headers(?)
 
** File headers could possibly link to the format specification page
 
 
 
=== Phenotype association file idiosyncrasy ===
 
* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
 
* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
 
* When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
 
* However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
 
** This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
 
* Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
 
* With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
 
* Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
 
 
 
=== Server space in Chen Building ===
 
* It looks like that we will not have a specific space for server computers.
 
 
 
 
 
== October 8, 2020 ==
 
 
 
=== Webinar Announcement ===
 
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
 
* Caltech zoom allows 300 attendees.
 

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