Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
m
Line 33: Line 33:
 
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
 
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== May 27, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
 
 
=== Single cell ===
 
* Eduardo and Valerio will give an update on single cell analysis and visualization tools
 
 
 
 
 
== May 13, 2021 ==
 
 
 
=== Textpresso supplement ===
 
* Due Monday
 
* Michael working with Paul S
 
 
 
=== AWS credits ===
 
* Michael and Valerio were awarded AWS credits, more than they can use
 
* Maybe they can be repurposed
 
* Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance
 
 
 
=== Automated gene descriptions ===
 
* Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
 
* Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
 
* May be the focus of an Alliance supplement
 
* We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)
 
 
 
=== IWM 2021 WB Workshop ===
 
* Scheduled for June 22, 2021
 
* Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
 
* Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
 
* Here is the submitted workshop schedule:
 
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
 
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
 
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
 
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
 
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
 
 
 
 
 
== May 20, 2021 ==
 
 
 
=== Ontology updates in OA ===
 
* ODK pipeline is not updating the "date" line in OBO artifacts and thus the ontology is not updating
 
* Need to remove the "date" from the anatomy ontology OBO file header and let the OA script use the "data-version" line instead
 
* Life stage still has "date"; Chris will investigate if there are update issues for life stage
 
* Juancarlos has updated the GO URIs from Kimberly's suggestions; use monthly release URI or ~daily snapshot URIs?
 
** Should probably go with daily snapshots for curation purposes (frequent updating for new/deprecated terms)
 
 
 
=== OA updates for UTF-8 ===
 
* Daniela and Juancarlos have updated OA dumpers (antibody, expression, picture, movie) accordingly
 
* Others need to be updated:
 
** Chris will help with Interaction OA, GeneReg OA, Phenotype OA, RNAi OA
 
** Ranjana will help with Disease, Genotype and Concise OAs
 
** Karen will help with Construct, Transgene, Topic, Molecule OAs
 
* Anatomy function form (Valerio wrote) writes to Postgres; need some updates
 
 
 
=== Student Internship ===
 
* Student will work with Raymond, Kimberly to do anatomy function & Noctua/GO-CAM curation on dauer development
 
* To do anatomy function curation in Noctua, requirements will need to be written out and addressed
 
* Can the anatomy function form write directly into Noctua (eventually)?
 
 
 
=== AI-readiness supplement ===
 
* Valerio looking into AI-ready format input
 
* Looking into applying to neural circuits
 
 
 
 
 
 
 
== May 27, 2021 ==
 
 
 
=== CeNGEN data ===
 
* CeNGEN project wants to generate expression displays like our FPKM plots (made by Gary Williams)
 
* Can we generate plots like these with this new data?
 
* Maybe we can just give the data directly to the web team for display, rather than load all the data into Citace/ACEDB (introducing heavy load to system) and have it pass through the whole build pipeline
 
* Does the CeNGEN data get preferential treatment and display, like 'Featured Data' (at least for the near term)? Or does it get integrated with all other expression data equally? Should discuss with Todd/Webteam
 
* Raymond et al. will communicate with Todd and web team about how to handle the data (will also start a ticket)
 
 
 
=== Help desk AFP request ===
 
* Kimberly will send out the AFP form for the paper when
 
** https://github.com/WormBase/website/issues/8243
 
 
 
=== Single-cell data tools ===
 
* Interactive differential expression, gene abundance histograms, heatmaps & dot plots, swarm plots
 
* Split into two code bases: scdefg and wormcells-viz
 
* wormcells-viz: http://cervino.caltech.edu:3000/
 
* Eduardo has wrangled the data into a standard format (.h5ad) (only 10x data sets)
 
* Interactive differential expression demo: improvement
 
** Now users can choose which aspects to stratify the data by
 

Revision as of 15:29, 3 June 2021