Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
= 2021 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
== April 2, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
=== Community phenotype requests ===
+
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
* March 9-28
 
* 2,548 emails went out; 89 bounced; 6 resent; 13 backup; 2,478 successful emails
 
* 361 annotations overall
 
* 48 papers requested received curation (2% response rate)
 
* 53 distinct papers overall (5 papers without request)
 
* 53 distinct persons overall
 
  
=== Community curation volunteers ===
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
 
* 14 volunteers so far, all have been assigned a WBPerson ID
 
* Chris will set up a webinar tutorial in the coming week or two
 
  
=== AFP pipeline ===
+
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
* Will resend email requests to authors that haven't already responded
 
* May also send out for older papers
 
* May work with people to help
 
* Does the old AFP form still work? It should
 
* If someone has a link to the old form, they won't get one for the new form
 
* Maybe could set up an automatic redirect from the old form to the new form
 
* Received many submissions recently (>20% response rate)
 
  
=== Ontology Annotator ===
+
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
* Need to work on Genotype OA dumper
 
* Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
 
* Ampersands (&) are also problematic for object names in the OA
 
** 20237  | Is[Pgcy-5::daf-2a::venus; Punc-122::mCherry]                          | 2014-10-08 10:32:45.874519-07
 
** 20239  | Ex[Pgcy-5::casy-1::venus; Pgcy-5::aman-2::mCherry; Punc-122::mCherry] | 2014-10-08 10:45:23.202362-07
 
** 20238  | Is[Pgcy-5::daf-2c::venus; Punc-122::mCherry]                          | 2014-10-08 10:38:19.859078-07
 
** 25249  | Ex[Prheb-1::rheb-1::GFP; unc-119(+]                                  | 2018-06-29 10:16:40.784295-07
 
** 16283  | [hlh-13::GFP;unc-119(+)]                                             | 2013-02-07 17:43:22.384819-08
 
** 26131  | Ex[pedc-3EDC-3::DsRed;pRF4]                                           | 2019-08-14 08:44:49.91063-07
 
  
=== Use Slack More ===
 
* Slack is a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication
 
  
  
== April 9, 2020 ==
+
== November 4 2021 ==
  
=== Volunteer curators ===
+
=== Migrating Paper Pipeline to Alliance ===
* Have sent out emails to schedule tutorials
+
*Meeting abstracts
* Chris had one tutorial with Michael Davies (Alyson Ashe's lab) yesterday
+
**Continuing to review what we have and standardize bibliographic info before we migrate
* One already scheduled for next Monday with Wilber and Stephanie from Paul's lab
+
**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
* Two others already scheduled for next Tuesday with Lina Dahlberg and Colin Dolphin
+
**We can always respond to individual requests to add old meeting abstracts if they arise
  
===TAGC is virtual (4.22-25.2020)===
 
FYI in case you missed it
 
*You still have to register (it's free), if you hadn't before
 
https://genetics-gsa.org/tagc-2020/registration/
 
  
===summer students??===
+
== 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