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
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= 2021 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== March 5, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
=== WormBase curation ===
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Tim Schedl: WB needs to do more curation for phenotype and variation
 
* Doing community curation, but not fast enough
 
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 
  
=== Alaksa ===
+
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
* Joesph may be able to meet with Raymond
 
* How can the tool be maintained? If it can't it needs to be pulled
 
  
=== Single cell expression tool ===
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* Tool is here: http://de.wormcells.com/
 
* What do we need to consider for pulling into WormBase?
 
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
 
** Would want it to be in sync with WormBase releases
 
** May not need to reprocess with every release with current (small-ish) data set
 
* Fully integrated tool versus an embedded tool?
 
  
=== Name service updates ===
+
[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
 
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
 
  
 +
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
  
== March 12, 2020 ==
 
  
=== Cancelled meetings ===
 
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
 
* We should start doing online advertisement for micropublications with webinars
 
  
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
+
== November 4 2021 ==
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
 
* Valerio would like to add these to Postgres to keep a more central repository of them
 
* Chris would still like to be able to readily update/edit the content of those lists
 
  
* Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
+
=== 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
  
=== Updates on Alaska ===
 
  
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
+
== November 11 2021 ==
The future plan is to move the platform to Google colab to reduce maintainance work.
 
  
==Nameservice discussion==
+
=== WS284 upload dates for Caltech ===
*Getting a token has worked for Chris and Ranjana
+
* When are files due for the Caltech group?
*Karen and Daniela need to get tokens
 
  
==Noctua GO-CAM updates==
+
===Minutes===
*Noctua is a production tool available for annotations right now
+
*WS284 upload-Better to upload before the holidays or in Jan 2022
*Create as many interconnected models and make available for curators is the ongoing goal
+
*Wen will contact Paul D/Hinxton to find out when the WS284 models will be released
*Reactome models are in the process of being imported
 
*Real time validation messages as curation is being done, is being worked on
 
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
 
  
  
== March 19, 2020 ==
+
== November 18 2021 ==
 +
Proposal for upgrading tanzendra/mangolassi computing resources
 +
1. Move them to Chen. (done)
 +
  monitor stability of network
  
=== Citace Upload ===
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Old hardware and out of support OS (Ubuntu 14.04)
* Tuesday, March 31st
 
  
=== Latest ACEDB ===
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2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
+
  (use Valerio's local server/desktop)
  
=== Storing email addresses/persons to omit from requests ===
+
3. Establish a local file server for storage and download access (PDFs, dump files)
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
 
  
=== Mailing lists ===
+
4. Run dockerized services from AWS
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
 
  
 +
5. Continuous development and integration locally -> AWS
  
==March 26th==
+
===Commercial antibodies===
===Community curation===
+
* Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
+
* 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.
* Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
+
* This can be an  Alliance project. Need to contact companies and see who is interested (need to have a  price in mind for that).
* Blog about phenotype form to make people generally aware
+
* Can pilot text mining for commercial antibodies
* Could the phenotype form be adapted for other species? Possibly but depends on:
+
* 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
** Whether genotypes could be loaded and recognized
 
 
 
=== AFP for older papers ===
 
* Discussed recently
 
* Many (all?) Old papers have already gone through the old AFP pipeline
 
* Need to check what has already been curated
 
 
 
=== Omit form ===
 
* http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi
 
* Can view, add, or edit persons, email addresses, and IP addresses to omit from email requests (and IP addresses to block)
 
 
 
=== Problems accessing Textpresso Central ===
 
* Ranjana had noticed that the server was acting slow
 
* Unknown problem; hard to pin down
 
* Definitely a Caltech network system
 
* Issue for past couple of weeks
 
* May be able to ask Caltech IMSS for a diagnostic analysis
 
* Bad switch? Maybe; there is an unused switch that could be used to test
 
** Maybe should dedicate an ethernet socket to the server(s) (avoiding switch altogether)
 
* Tazendra is good, mangolassi seems to have had some trouble recently as well
 
* All on subnet 52; Raymond has been monitoring and seems to be working well; could suggest a local (e.g. computer-specific, switch-specific) issue
 
 
 
=== Automated concise pathway descriptions? ===
 
* Could we generate pathway descriptions based on, for example, GO-CAM models?
 
* Might be straightforward if clear guidelines can be documented (important players/genes, important/central functions/processes)
 

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