Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
== March 5, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
=== WormBase curation ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* 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 ===
 
* 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 ===
+
== June 4, 2020 ==
* 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 ===
+
=== Citace (tentative) upload ===
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* 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
+
* Citace upload to Hinxton on Friday, July 10th
  
 +
=== Caltech reopening ===
 +
* Paul looking to get plan approved
 +
* People that want to come to campus need to watch training video
 +
* Masks available in Paul's lab
 +
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 +
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 +
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
== March 12, 2020 ==
+
=== Nameserver ===
 +
* Nameserver was down
 +
* CIT curators would still like to have a single form to interact with
 +
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 +
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 +
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 +
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
=== Cancelled meetings ===
+
=== Alliance SimpleMine ===
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
+
* Any updates? 3.1 feature freeze is tomorrow
* We should start doing online advertisement for micropublications with webinars
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
 
 
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
 
* 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
 
 
 
=== 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
 
The future plan is to move the platform to Google colab to reduce maintainance work.
 
 
 
==Nameservice discussion==
 
*Getting a token has worked for Chris and Ranjana
 
*Karen and Daniela need to get tokens
 
 
 
==Noctua GO-CAM updates==
 
*Noctua is a production tool available for annotations right now
 
*Create as many interconnected models and make available for curators is the ongoing goal
 
*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 ==
 
 
 
=== Citace Upload ===
 
* Tuesday, March 31st
 
 
 
=== Latest ACEDB ===
 
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
 
 
 
=== Storing email addresses/persons to omit from requests ===
 
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
 
 
 
=== Mailing lists ===
 
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
 
 
 
 
 
==March 26th==
 
===Community curation===
 
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
 
* Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
 
* Blog about phenotype form to make people generally aware
 
* Could the phenotype form be adapted for other species? Possibly but depends on:
 
** 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 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
 

Latest revision as of 00:09, 5 June 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call