Difference between revisions of "WBConfCall 2022.03.17-Agenda and Minutes"

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* Julie Ahringer asking for a genome-wide mapping of all Ahringer RNAi clones (sjj_* and sjj2_* ?PCR_Product objects) to identify, according to our primary and secondary RNAi mapping criteria, which genes are predicted to be knocked down by each clone
 
* Julie Ahringer asking for a genome-wide mapping of all Ahringer RNAi clones (sjj_* and sjj2_* ?PCR_Product objects) to identify, according to our primary and secondary RNAi mapping criteria, which genes are predicted to be knocked down by each clone
 +
 +
- Hinxton are in touch with her to scope out the size and timing of the work.[MZ]
 +
 +
===== Minutes =====
 +
Julia Ahringer
 +
* Need to have RNAi objects in database
 +
** Mapping data could be included with the RNAi object or separately.
 +
** Need to come up with an official schema for storing this data
 +
* Deciding on making this a one of or something that we do every release
 +
** Making it for each release is something that would help users as it has come up in many helpdesk tickets over the years (Chris Grove)
 +
** If we show this data we will need to make sure it is clear to the user that the information was generated in-silico
 +
*** This could be made as a Micro Publication to make sure users use the data correctly
 +
** Would entail generating a bolus of mappings between RNA and Gene Targets
 +
 +
Two open tickets:
 +
 +
* https://github.com/WormBase/website/issues/8570 Cells in C. elegans are roughly 3–30 ... (Still not responded to)
 +
* https://github.com/WormBase/website/issues/8571 Add links to single cell tools in "Tools" menu #8571 (since the meeting has been responded to)
 +
 +
=== BioCyc-WB Links ===
 +
* Report back from follow-up meeting last Thursday with Peter Karp:
 +
** BioCyc will make available pathway images that WB will display, initially, on gene and molecule pages
 +
** We'll also have reciprocal links
 +
** [https://docs.google.com/document/d/1E88K6t2lY2UODy9l3gf9v5AnikZKvoHmyK-krAsvVX8/ Minutes]
 +
 +
==== Minutes ====
 +
 +
* Kimberly decided she would create a Ticket for this
 +
** Here it is: https://github.com/WormBase/website/issues/8572  Display BioCyc pathway images at WB
 +
*** BioCyc will create a web service for WB to access C. elegans pathway images, then WB will display the pathways on relevant gene and molecule pages
 +
 +
=== Bob Waterson single cell embryo data ===
 +
 +
* Bob asking if interested in displaying the single cell embryo data from their 2019 Science paper in WormBase
 +
* He has large tables of the tpms per cell type and for the lineage as well as the percent of cells expressing.  * He made graphs of these, not interactive
 +
* Could go in the 'Single cell gene expression graphs' section, where Sibyl put in CenGen Data. https://wormbase.org/species/c_elegans/gene/WBGene00001170#c13--10
 +
* Can Web Team display the Bob's graphs, too?
 +
* if we have the data we can generate a similar graph
 +
* If they offer static images we could bring in as images or the Web Team can display directly on the 'Single cell gene expression graphs' section
 +
* Daniela to talk to Todd and see what is the best way forward
 +
* If we get raw data we can display as CenGen, may  be able to reuse Sibyl's code
 +
* Quickly get static images in is #1 priority
 +
 +
==== Minutes ====
 +
 +
* Assuming Sibyl's code for CenGen can be adapted
 +
** Priority one is to get the images in that we already sent to us (Raymond)
 +
*** Add data (csv files) into a more interactive graph. At first display static data.
 +
*** Start with graphs that have already been generated by Bob
 +
 +
** First action item is to get data already generated by Bob
 +
 +
Ticket has been generated for this work: https://github.com/WormBase/website/issues/8574  Bob Waterson single cell embryo data #8574

Latest revision as of 03:27, 19 March 2022

Agenda

Help Desk

  • Julie Ahringer asking for a genome-wide mapping of all Ahringer RNAi clones (sjj_* and sjj2_* ?PCR_Product objects) to identify, according to our primary and secondary RNAi mapping criteria, which genes are predicted to be knocked down by each clone

- Hinxton are in touch with her to scope out the size and timing of the work.[MZ]

Minutes

Julia Ahringer

  • Need to have RNAi objects in database
    • Mapping data could be included with the RNAi object or separately.
    • Need to come up with an official schema for storing this data
  • Deciding on making this a one of or something that we do every release
    • Making it for each release is something that would help users as it has come up in many helpdesk tickets over the years (Chris Grove)
    • If we show this data we will need to make sure it is clear to the user that the information was generated in-silico
      • This could be made as a Micro Publication to make sure users use the data correctly
    • Would entail generating a bolus of mappings between RNA and Gene Targets

Two open tickets:

BioCyc-WB Links

  • Report back from follow-up meeting last Thursday with Peter Karp:
    • BioCyc will make available pathway images that WB will display, initially, on gene and molecule pages
    • We'll also have reciprocal links
    • Minutes

Minutes

  • Kimberly decided she would create a Ticket for this
    • Here it is: https://github.com/WormBase/website/issues/8572 Display BioCyc pathway images at WB
      • BioCyc will create a web service for WB to access C. elegans pathway images, then WB will display the pathways on relevant gene and molecule pages

Bob Waterson single cell embryo data

  • Bob asking if interested in displaying the single cell embryo data from their 2019 Science paper in WormBase
  • He has large tables of the tpms per cell type and for the lineage as well as the percent of cells expressing. * He made graphs of these, not interactive
  • Could go in the 'Single cell gene expression graphs' section, where Sibyl put in CenGen Data. https://wormbase.org/species/c_elegans/gene/WBGene00001170#c13--10
  • Can Web Team display the Bob's graphs, too?
  • if we have the data we can generate a similar graph
  • If they offer static images we could bring in as images or the Web Team can display directly on the 'Single cell gene expression graphs' section
  • Daniela to talk to Todd and see what is the best way forward
  • If we get raw data we can display as CenGen, may be able to reuse Sibyl's code
  • Quickly get static images in is #1 priority

Minutes

  • Assuming Sibyl's code for CenGen can be adapted
    • Priority one is to get the images in that we already sent to us (Raymond)
      • Add data (csv files) into a more interactive graph. At first display static data.
      • Start with graphs that have already been generated by Bob
    • First action item is to get data already generated by Bob

Ticket has been generated for this work: https://github.com/WormBase/website/issues/8574 Bob Waterson single cell embryo data #8574