Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchm (→March 11, 2021) |
m (→March 11, 2021) |
||
Line 63: | Line 63: | ||
** We will link to the CeNGEN homepage wherever appropriate | ** We will link to the CeNGEN homepage wherever appropriate | ||
* All else will depend on Eduardo's tools for single cell expression data | * All else will depend on Eduardo's tools for single cell expression data | ||
+ | * Display solutions can be used for Alliance single-cell data in general | ||
+ | * May want to consider future use cases, e.g. mutant-vs-WT expression, chemical/drug-induced expression, etc. | ||
=== Chen building access === | === Chen building access === |
Revision as of 19:43, 11 March 2021
Contents
Previous Years
2021 Meetings
March 4, 2021
Webinar Monday
- Juancarlos can send a reminder email; he just needs the text for the body of the email message
- Can we send the webinar reminder to WB staff? Cannot use staff@wormbase.org to register
- Raymond will try to remember to forward to staff
Neural Network (NN) evaluation
- Kimberly (and other curators) looking through NN results
- Had previously prevented LOW scoring SVMs(?) from being sent to authors
- We need an agreed upon protocol for evaluation
- To avoid bias, we should randomly sample papers; usually will find negatives; how do we represent high, medium and low-scoring papers in the set without making curators review >> 100 papers?
- Michael will come up with protocol and send around list of papers for each data type (in Google Doc)
- Perhaps evaluation should happen on non-curated, newer papers
March 11, 2021
Spreadsheet for Data not in ACEDB
- Magdalena/Hinxton would like to know how much data at Caltech doesn't get into ACEDB
- Sheet here: https://docs.google.com/spreadsheets/d/1VcFykdyBcoMBvYliem8tnch5Q2VDMImL6EqlcEBCU-s/edit?usp=sharing
- We want to pull everything into the Alliance eventually, but maybe not everything needs to be harmonized
- We should evaluate existing forms and fields/tables for whether they need to be harmonized or can stay as is
CeNGEN To Dos
- Daniela, Wen, Valerio, Eduardo, Raymond met with CeNGEN
- Want to add JBrowse track for promoters(?)
- Three things:
- CeNGEN will provide histograms that we can put on each gene page, similar to modENCODE plots (do they provide static images or data that we process and display as histograms?)
- Their tool can assess "enriched" genes by cell type (enriched vs. neurons or vs. all cell types; not just housekeeping genes); these can be sent to WB -> SObA and enrichment analysis
- We will link to the CeNGEN homepage wherever appropriate
- All else will depend on Eduardo's tools for single cell expression data
- Display solutions can be used for Alliance single-cell data in general
- May want to consider future use cases, e.g. mutant-vs-WT expression, chemical/drug-induced expression, etc.
Chen building access
- You'll need an ID with RFID?
- help.caltech.edu -> request type Card Office
- It will be ready and wait for you at the Reddoor cafe.