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]]
 +
 +
 +
== 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
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
== February 13, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
=== ?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
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
=== Genotype OA ===
 +
* Will put documentation [[Genotype|here]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
=== WB All-Hands Meeting ===
 +
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
 +
* Any thoughts at this point?  Still need to discuss with Hinxton, Toronto.
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
== February 20, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
 
  
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
+
== February 27, 2020 ==
  
 +
=== WB Project meeting ===
 +
* Early May (~May 7th, 8th)
 +
* Discussion topics:
 +
** Creating more transparency/communication in the Alliance DQM data submission process for QC
 +
*** Can there be a landing page for all uploaded files to check?
 +
*** JSON or TSV, etc.?
  
== December 5, 2019 ==
+
=== Genotype ===
 +
* [[Genotype|Genotype Wiki page]] updated
 +
* Will start building Genotype OA
  
=== New interaction Venn diagram tool ===
+
=== Outreach inbox ===
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
+
* 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
* Venn diagram shows how various interactors have multiple interaction types with a common focus gene
+
* Many are bounced emails messages
* For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
+
* 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.
* Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
 
* Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
 
* Request: could there be a toggle to include/exclude high-throughput interactions?
 
* Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
 
* Request: Change the wording "Browse selection" to something like "View/analyze gene list"
 
* Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?
 
  
=== New round of phenotype requests ===
+
=== New nameserver issues ===
* GMail really throttling email sending
+
* Many variations and strains getting submitted to new nameserver are not making it into the OA/Postgres
* Chris will reach out to Google/GMail to see if we can:
+
* Should be getting dumped nightly to Postgres, but something seems to be wrong
** A) get a clear explanation about what their restrictions are and how they work and
+
* Ranjana added a list of strains last week, but still doesn't see them in the OA
** B) see if we can get a paid plan to help expedite the email process (see how much cost)
+
* Daniela has been using the old CGI to add in new variation objects to Postgres
 +
* These objects are coming up when querying the nameserver, but not showing up in OA
  
=== Aligning interaction data with GO and GO-CAM ===
+
=== GO CAM/Noctua modeling ===
* The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
+
* Should be major improvements in Noctua in place after recent hackathon
* Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
+
* Would be good to make a big push on curating models; e.g. signalling pathways that act somewhat differently in different cell types (in same organism) and in different organisms (e.g. Wnt signaling)
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
 
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
 
* Chris and Kimberly will meet to discuss further
 
  
=== Short SObA talk at Alliance meeting ===
+
=== SObA ===
* Raymond prepared to give short talk on SObA to the Alliance group
+
* Raymond working on writing paper
 +
* While reviewing pipeline, Raymond encountered some issues
 +
* Seth suggested using Docker
 +
* Raymond wants to go through and explain the development pipeline from the beginning
  
=== Single cell data visualization tool ===
+
=== Alaska ===
* Eduardo will present to Paul's lab meeting tomorrow
+
* Stalled; no word from Joseph
* Will discuss at Alliance expression working group pre-meeting
 

Latest revision as of 20:01, 27 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


February 27, 2020

WB Project meeting

  • Early May (~May 7th, 8th)
  • Discussion topics:
    • Creating more transparency/communication in the Alliance DQM data submission process for QC
      • Can there be a landing page for all uploaded files to check?
      • JSON or TSV, etc.?

Genotype

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.

New nameserver issues

  • Many variations and strains getting submitted to new nameserver are not making it into the OA/Postgres
  • Should be getting dumped nightly to Postgres, but something seems to be wrong
  • Ranjana added a list of strains last week, but still doesn't see them in the OA
  • Daniela has been using the old CGI to add in new variation objects to Postgres
  • These objects are coming up when querying the nameserver, but not showing up in OA

GO CAM/Noctua modeling

  • Should be major improvements in Noctua in place after recent hackathon
  • Would be good to make a big push on curating models; e.g. signalling pathways that act somewhat differently in different cell types (in same organism) and in different organisms (e.g. Wnt signaling)

SObA

  • Raymond working on writing paper
  • While reviewing pipeline, Raymond encountered some issues
  • Seth suggested using Docker
  • Raymond wants to go through and explain the development pipeline from the beginning

Alaska

  • Stalled; no word from Joseph