Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
(233 intermediate revisions by 11 users not shown)
Line 18: Line 18:
  
 
[[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 =
  
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
 
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
== November 7, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
=== WS275 Citace upload ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* Maybe Nov 22 upload to Hinxton
 
* CIT curators upload to Spica on Tues Nov 19
 
  
=== ?Genotype class ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
 
* Several classes have a "Genotype" tag with text entry
 
** Strain
 
** 2_point_data
 
** Pos_neg_data
 
** Multi_pt_data
 
** RNAi
 
** Phenotype_info
 
** Mass_spec_experiment (no data as of WS273)
 
** Condition
 
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
 
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
 
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
 
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
 
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
 
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
 
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
 
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
 
** Reference to parent strain, like "Parent strain is AG359"
 
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
 
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
 
  
=== Gene comparison SObA ===
 
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 
  
 +
== June 4, 2020 ==
  
== November 14, 2019 ==
+
=== Citace (tentative) upload ===
 +
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 +
* Citace upload to Hinxton on Friday, July 10th
  
=== TAGC meeting ===
+
=== Caltech reopening ===
* The Allied Genetics Conference next April (2020) in/near Washington DC
+
* Paul looking to get plan approved
* Abstract deadline is Dec 5th
+
* People that want to come to campus need to watch training video
* Alliance has a shared booth (3 adjacent booths)
+
* Masks available in Paul's lab
* Micropublications will have a booth (Karen and Daniela will attend)
+
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
* Focus will be on highlighting the Alliance
+
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
* Workshop at NLM in days following TAGC about curation at scale (Kimberly attending and chairing session)
+
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
=== Alliance all hands meeting ===
+
=== Nameserver ===
* Lightning talk topics?
+
* Nameserver was down
** Single cell RNA Seq (Eduardo)
+
* CIT curators would still like to have a single form to interact with
** SimpleMine? (Wen)
+
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
** SObA? (Raymond); still working on multi-species SObA
+
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
** Phenotype community curation?
+
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
** Micropublications?
+
* Hinxton is pulling in CGC strains, how often?
** AFP?
+
* Caltech could possibly get a block of IDs
  
=== Alliance general ===
+
=== Alliance SimpleMine ===
* Alliance needs a curation database
+
* Any updates? 3.1 feature freeze is tomorrow
** A curation working group was proposed
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
** What needs to happen to get this going?
 
** Would include text mining tools/resources
 
** Would be good to have something like the curation status form
 
** MODs likely have their own special requirements, but there should probably be at least a common minimal set of features
 
** Variant sequence curation could be a good first start (if all MODs handle their own variant sequence curation) as a common data type
 
* Micropubs pushing data submission forms; might as well house them within the Alliance
 
* Would be good to have a common (or individually relevant) AFP form(s) for all Alliance members
 
** Maybe MOD curators can manage configuration files to indicate what is relevant for their species
 

Revision as of 00:09, 5 June 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

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call