Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[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 ===
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Eduardo and Valerio will give an update on single cell analysis and visualization tools
 
  
 +
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
== May 13, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
=== Textpresso supplement ===
+
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
* Due Monday
 
* Michael working with Paul S
 
  
=== AWS credits ===
+
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
* 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
 
  
 +
== November 4 2021 ==
  
== May 20, 2021 ==
+
=== Migrating Paper Pipeline to Alliance ===
 +
*Meeting abstracts
 +
**Continuing to review what we have and standardize bibliographic info before we migrate
 +
**QC checks highlight some older abstracts with little-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
 +
**We can always respond to individual requests to add old meeting abstracts if they arise
  
=== 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 ===
+
== November 11 2021 ==
* 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 ===
+
=== WS284 upload dates for Caltech ===
* Student will work with Raymond, Kimberly to do anatomy function & Noctua/GO-CAM curation on dauer development
+
* When are files due for the Caltech group?
* 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 ===
+
===Minutes===
* Valerio looking into AI-ready format input
+
*WS284 upload-Better to upload before the holidays or in Jan 2022
* Looking into applying to neural circuits
+
*Wen will contact Paul D/Hinxton to find out when the WS284 models will be released
  
  
 +
== November 18 2021 ==
 +
Proposal for upgrading tanzendra/mangolassi computing resources
 +
1. Move them to Chen. (done)
 +
  monitor stability of network
  
== May 27, 2021 ==
+
Old hardware and out of support OS (Ubuntu 14.04)
  
=== CeNGEN data ===
+
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
* CeNGEN project wants to generate expression displays like our FPKM plots (made by Gary Williams)
+
  (use Valerio's local server/desktop)
* Can we generate plots like these with this new data?
+
 
 +
3. Establish a local file server for storage and download access (PDFs, dump files)
 +
 
 +
4. Run dockerized services from AWS
 +
 
 +
5. Continuous development and integration locally -> AWS
 +
 
 +
===Commercial antibodies===
 +
* Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
 +
* TODO: Contact TAIR and see if they including commercial antibodies and if  they charge companies  (Daniela sent a message on slack). Tanya: We have not charged for placing the links but have strongly encouraged a corporate subscription for the two companies.
 +
* This can be an  Alliance project. Need to contact companies and see who is interested (need to have a  price in mind for that).
 +
* Can pilot text mining for commercial antibodies
 +
* GeneCards charges for inclusion of commercial reagents on their website: "Companies that wish to provide deep links to their products (e.g. reagents, assays, antibodies, clones, etc) in the Services and other relevant sections of GeneCards, should contact sales@lifemapsc.com." From https://www.genecards.org/Guide/FAQ

Latest revision as of 17:51, 18 November 2021

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2016 Meetings

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2018 Meetings

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2021 Meetings

January

February

March

April

May

June

July

August

September

October


November 4 2021

Migrating Paper Pipeline to Alliance

  • Meeting abstracts
    • Continuing to review what we have and standardize bibliographic info before we migrate
    • QC checks highlight some older abstracts with little-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
    • We can always respond to individual requests to add old meeting abstracts if they arise


November 11 2021

WS284 upload dates for Caltech

  • When are files due for the Caltech group?

Minutes

  • WS284 upload-Better to upload before the holidays or in Jan 2022
  • Wen will contact Paul D/Hinxton to find out when the WS284 models will be released


November 18 2021

Proposal for upgrading tanzendra/mangolassi computing resources

1. Move them to Chen. (done)
  monitor stability of network
Old hardware and out of support OS (Ubuntu 14.04)
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
  (use Valerio's local server/desktop)
3. Establish a local file server for storage and download access (PDFs, dump files)
4. Run dockerized services from AWS
5. Continuous development and integration locally -> AWS

Commercial antibodies

  • Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
  • TODO: Contact TAIR and see if they including commercial antibodies and if they charge companies (Daniela sent a message on slack). Tanya: We have not charged for placing the links but have strongly encouraged a corporate subscription for the two companies.
  • This can be an Alliance project. Need to contact companies and see who is interested (need to have a price in mind for that).
  • Can pilot text mining for commercial antibodies
  • GeneCards charges for inclusion of commercial reagents on their website: "Companies that wish to provide deep links to their products (e.g. reagents, assays, antibodies, clones, etc) in the Services and other relevant sections of GeneCards, should contact sales@lifemapsc.com." From https://www.genecards.org/Guide/FAQ