Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
== June 3, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
=== Reserving meeting rooms ===
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* Raymond encountering challenges with setting up regular meeting room reservations in Chen building
 
* We've been asked to make reservations one week in advance
 
* Need to use a room if we reserve it
 
  
=== Summer student(s) ===
+
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
* Anatomy function project with Raymond
 
* Many types of anatomy function data submitted via AFP
 
  
== June 10, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
  
=== Variation-Gene Associations ===
 
*Some QC on AFP-extracted data led to the realization that at least some of the 'tm' variations aren't associated with genes on tazendra
 
*https://github.com/WormBase/author-first-pass/issues/204
 
*https://github.com/WormBase/website/issues/8262
 
*It looks like non-manually asserted variation-gene associations will be generated via the VEP pipeline during the build, so Caltech would need to get this information from each WB release
 
  
=== Confirm WS282 Upload Dates ===
 
*July 6th?
 
*Data freeze/upload date on the release schedule is July 12th
 
  
=== CenGen bar plots ===
+
== November 4 2021 ==
*Initially discussed to have the bar plot images going in as image data
+
 
*CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.  
+
=== Migrating Paper Pipeline to Alliance ===
*They can provide the underlying data and have the WB team generate interactive plots for each gene
+
*Meeting abstracts
*Sibyl said that this is feasible and we could: 1. bring the data files in OR 2. call the CenGen API on the fly
+
**Continuing to review what we have and standardize bibliographic info before we migrate
*The first approach may be more work but better in the long run as we store the data
+
**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
*Will ping Hinxton and see how they can integrate the data
+
**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

Latest revision as of 17:51, 18 November 2021

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2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

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2020 Meetings

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