Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
==January 11th, 2019==
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
===WB workshop at IWM 2019===
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
Here's a draft, need to finalize as Jan 15th is the deadline
 
<pre style="white-space: pre-wrap;
 
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Possible Title 1: Data in WormBase and how to query it
 
Possible Title 2: WormBase 2019 - Data, Tools and Community Curation
 
This workshop will be an interactive session with users in order to discuss the types of data in WormBase and how to query them using the right tools.  We will discuss recent changes to WormBase community annotation forms and how to use them to contribute data to WormBase.  We will also present updates to ParaSite, a portal to parasitic worm genomic data, and how to find cross-species data at the Alliance of Genome Research.
 
  
1:00 pm 
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
Keep your widgets open: a wealth of gene-related data on the gene page
 
(This will be a quick walk-through of the gene page for orienting Users before we jump into the tools; can point to data related to Gene function, expression and disease models) - Ranjana Kishore
 
     
 
1:10 pm 
 
Use the right tool for the right data:
 
Get simple lists using SimpleMine - Wen Chen
 
Tissue enrichment analysis tools - Kimberly Van Auken
 
Tools for RNA seq data - Wen Chen
 
Get batch gene data using the WormBase Ontology Browser - Raymond Lee
 
Get the big picture: visualize annotations using the SOBA tool -Raymond Lee
 
     
 
1.50 pm  WormBase ParaSite: Exploring lots of genomes - Kevin Howe
 
  
2.00 pm  Find cross-species data at the Alliance of Genome Research - Chris Grove
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
2.10 pm  Be a Community Curator: submit your data to WormBase - Daniela Raciti
+
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
2.10-2.30pm. Open forum for questions
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
</pre>
 
  
=== Finalize Protege tutorial time ===
+
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
* Best final options:
 
** Wed, Jan 16th, 1pm Pacific/4pm Eastern
 
** Thurs, Jan 17th, 11am Pacific/2pm Eastern
 
** Thurs, Jan 17th, 1pm Pacific/4pm Eastern
 
* Propose we go with Wed, Jan 16th, 1pm Pacific/4pm Eastern
 
  
== January 3, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
  
=== WS270 Citace upload ===
 
* Next Tuesday, Jan 8th, 10am Pacific
 
  
=== Gene descriptions ===
 
* Valerio generated new files to ignore/filter-out problematic genes
 
* Still need to validate new pipeline
 
* Barring any major issues, will submit new files for WS270 (can load old files if needed)
 
* Maybe should define a test set (random sample) to test each release? Already have a test set
 
  
=== Protege Tutorial ===
+
== November 4 2021 ==
* Doodle poll open: https://doodle.com/poll/kn49rd3rggymn68g
+
 
* Please fill out poll if you are interested in attending; have responses from Kimberly and Gary S.
+
=== 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

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