Difference between revisions of "WBConfCall 2022.03.17-Agenda and Minutes"
From WormBaseWiki
Jump to navigationJump to search(7 intermediate revisions by 2 users not shown) | |||
Line 6: | Line 6: | ||
- Hinxton are in touch with her to scope out the size and timing of the work.[MZ] | - 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 === | === BioCyc-WB Links === | ||
Line 13: | Line 29: | ||
** [https://docs.google.com/document/d/1E88K6t2lY2UODy9l3gf9v5AnikZKvoHmyK-krAsvVX8/ Minutes] | ** [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 Waterson single cell embryo data === | ||
Line 20: | Line 41: | ||
* 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 | * 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? | * 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
Contents
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:
- 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
- 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
- Here it is: https://github.com/WormBase/website/issues/8572 Display BioCyc pathway images at WB
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
- Priority one is to get the images in that we already sent to us (Raymond)
- 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