Difference between revisions of "WormBase-Caltech Weekly Calls"

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== May 27, 2021 ==
=== 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 ===
== October 14, 2021 ==
* 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 ===
=== WormBase HD YouTube channel has ads ===
* Scheduled for June 22, 2021
* Is there a way to turn them off? Seems like we cannot remove them entirely
* 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
=== Form headers and footers no longer updating ===
== May 20, 2021 ==
* WS version number falls out of date; Juancarlos will manually update
=== 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

Latest revision as of 18:27, 14 October 2021

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October 14, 2021

WormBase HD YouTube channel has ads

  • Is there a way to turn them off? Seems like we cannot remove them entirely

Form headers and footers no longer updating

  • WS version number falls out of date; Juancarlos will manually update