Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
 
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
 +
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
  
== September 2, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
  
1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
 
Needed for
 
*AFP community curation
 
*microPublication author tracking for all species
 
*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
 
  
Problems:
 
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
 
*need to do this outside of Alliance
 
  
Action
+
== November 4 2021 ==
*Paul talks to zfin about interest in person pages
 
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
 
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
 
  
Will do
+
=== Migrating Paper Pipeline to Alliance ===
*create biolink model based on current WB postgres/Caltech model
+
*Meeting abstracts
*Adam will add tables when we have them
+
**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
  
2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
 
  
== September 16, 2021 ==
+
== November 11 2021 ==
  
1. CeNGEN enriched genes per cell type data targeted for WS283.
+
=== WS284 upload dates for Caltech ===
 +
* When are files due for the Caltech group?
  
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
+
===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
  
== September 23, 2021 ==
 
  
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
+
== 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

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

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