Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
−
==February 10, 2011==
+
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
−
 
 
−
*Should we have a Caltech project/site manager? We'll look at the issues to be solved first
 
−
 
 
−
*Todd would like to know more about what's going on at Caltech
 
−
**What would Todd like to know about? New ideas, data types?
 
−
**What can we communicate more effectively to Todd?
 
−
 
 
−
*Should we take minutes of Caltech WormBase group meetings and send around?
 
−
 
 
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*Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
 
  
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*Bitbucket use
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[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
−
**How do we see only what pertains to us, individually?
 
−
**Paul: good way to document bugs and fixes, problems/solutions
 
−
**Bitbucket Wiki - does that capture what people want/need to see?
 
−
**Who should Todd follow? What would Todd like to know about?
 
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**Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
 
−
**Should we develop best practices guideline for Bitbucket use?
 
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***Avoid posting topics that are too specific or too vague?
 
−
***What do we want most to get out of Bitbucket?
 
−
**Curation efforts? No
 
  
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*SAB Meeting
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[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
−
**Not much feedback for literature curators
 
−
**User interface stuff took precedence
 
−
**Paul: Testing, spot-checking website for errors
 
−
**Web issues, e-mails from Gary and Oliver
 
  
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*WormBase-wide conference call twice per month
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
−
**First & third Thursday of the month
 
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**Starting next Thursday (2-17) @ 8:30am PST
 
−
**Web redesign meetings on Thursdays will have to be every other week? Do both same day?
 
  
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*Raymond: WormBase mirrors
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
−
**Do we want to implement the Genome Browser for the mirror(s)? If practical
 
−
**It seems as though Caltech mirror has been crashing often
 
−
**Has the Caltech mirror been working for people lately? Yes, more or less
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
−
== February 17, 2011 ==
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
−
Interaction dumping script
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
−
*Spot check table
 
−
*Push changes to Git? Yes, to main branch
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
−
Interactions automatically downloaded to FTP every release? Yes
 
−
*People should check their own curation data
 
−
*Users query frequently?
 
−
*Can WormMart work instead?
 
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*Ruihua - feature can be added
 
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*Todd - good to have pre-defined queries generated automatically
 
−
*Parse/remove predicted interactions (400,000) from others during dump? Yes
 
−
*Paul - Wei Wei wants to help with updates - who should she contact at WB?
 
  
  
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Ranjana - Solar flares causing static on phone? ;)
 
  
 +
= 2020 Meetings =
  
−
Newsletter for new website release? Yes
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
−
*Todd - 5 development milestones
 
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**teleconference with Gary Ruvkun's lab next week
 
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**Go live with Beta version in June (@IWM)
 
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**Go live live with new site in September
 
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**Retire old site at end of year
 
−
**Need outreach, documentation, screencasts
 
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
−
BioGRID
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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*WormBase to BioGRID curation
 
−
*Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB
 
−
*Moving towards using WB interaction types
 
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*Definitions of our interaction types
 
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*Rose will propose to BioGRID community
 
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*Physical interactions - BioGRID has a better format
 
−
**break physical interactions away from other interaction types?
 
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**Kimberly can propose changes to model: YH separate from other interactions?
 
−
**Physical vs Genetic interactions? keep separate
 
−
*We need an interaction ontology, of some sort
 
−
*Who should Wei Wei contact, how to coordinate with Hinxton; getting data from FlyBase and SGD?
 
−
**Automation?
 
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*Interaction pages - explain what the interaction is based on; provenance/reference
 
−
*Gene Orienteer shows data, but user has to link out
 
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
−
WormBase IWM souvenir?
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
−
*Computer stress ball? with new site address?
 
−
*bouncy ball?
 
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*worm rubber band thing?
 
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*Screen shield?
 
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*Complementary iPads? ;)
 
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*Antifungal socks? wristbands?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
−
SPELL
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
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*new data doesn't load; problem runnning search engine; can load it on athena, not generalizable problem?
 
−
*OS was not complete with an update; try again
 
−
*two virtual machines working back and forth for support
 
−
*how often is SPELL being used? log?; had 6-7 users within two weeks complaining of SPELL problems
 
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*Todd - can send Google analytic tool to put at bottom of page
 
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*Wen - SPELL testing server; official and mirror; want a separate testing server for new releases; mirror on athena (Wen's working machine); Raymond says don't want to attract users to that machine; WB's running SPELL on altair; heavily loaded and has had problems; relying on athena may be problematic
 
−
*maybe we need analysis of all of our machines to see big picture; can we consolidate machines; make use of ones we have? If not we can get another machine.
 
−
*what type of machine do we need?
 
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*Log of all machines with purchase date and functionality?
 
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*Linux vs Mac curators? athena development machine;
 
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*how much power do the scripts need? can check
 
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*may not be appropriate as official server if main machine goes down
 
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*WB and athena can run SPELL server, but not others. security problems?
 
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*prefer work machine is readily re-bootable; reconfigure software easily without affecting other things that people rely on
 
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*need 10GB space; 4GB memory? SPELL production server; want it stable for outside world; hardware designed for that purpose; farm it out to IMSS?
 
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*complexity of the application; Linux can run multiple applications; caprica has SVM production and WormMart; understand demand of the application; requirements; development vs running scripts, how often? Efficient use of machines. Have 2 computers, getting a third; for WormMart need power; traffic suddenly increased yesterday; monitor traffic; not much personal experience with server maintenance; cluster needs lots of expertise
 
−
*building official sever of SPELL at OICR? Yes
 
  
  
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WormMart
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==August 6th, 2020==
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*with WormMart and WormBase, people just want to know if it's down, just to know to lessen frustration; Official statement from dev team
 
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*WormMart - we give users testing url; can we just change WormBase link to that testing server?
 
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*going to change HTML to update users with most recent information; discuss with Lincoln, 5 datasets on testing server; remaining 3 datasets. if WormMart not working, put a message on main site
 
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*it doesn't look good to have a link to a tool linked from a production server; if we don't trust the data we shouldn't put it up.
 
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*would like to keep the html page as a testing server; could modify page
 
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*if WormMart is working OK but not perfect, that's OK; Comment in the banner
 
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*the html page is a useful tool to get feedback from users
 
  
 +
===Experimental conditions data flow into Alliance===
 +
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
 +
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
 +
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
 +
*So for data flow into Alliance:
 +
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
 +
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
 +
* How do we handle genetic sex? Part of condition?
 +
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
 +
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
  
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== February 24, 2011 ==
 
  
−
CIT Computer Survey - done
+
== August 13, 2020 ==
  
−
CD/DVD burner not working (Wen)
+
=== Species in Postgres and ACEDB/Datomic ===
 +
* Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
 +
* Want to be sure that what gets dumped aligns with species loaded into ACEDB
 +
* Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
 +
* We currently have multiple Postgres tables for storing species lists:
 +
** pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
 +
** obo_name_ncbitaxonid
 +
** obo_name_taxon (original, smaller list)
 +
** h_pap_species_index (history for pap_species_index)
 +
* How do species get loaded into ACEDB? Dumps from Postgres? Which table(s)?
 +
* WS277 has 7,906 species (1,936 have no NCBI Taxon ID)
 +
* Kimberly has occasionally uploaded a species.ace file in the context of GO curation; but Hinxton otherwise handles it; should ask them
 +
* New species are associated with paper objects, but otherwise no additional data for those species come from Caltech
 +
* It might be useful to have species pages in WB that at least list papers for which we have species associations, maybe include other information?
  
−
Build Scripts:
+
=== WS279 Citace upload ===
−
*run @ OICR
+
* When is it happening? Not sure; not on release schedule right now
−
*dynamic/static files
 
−
*problem: no one takes care of them
 
−
*curators should claim them and take care of them
 
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**Gene interaction dump script claimed by Raymond and Xiaodong
 
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**256 interaction objects empty (should not be); emptied during build?
 
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*Monitor usage with new site
 
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*Files (like FASTA, GFF) should be immediately available to users
 
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*Page that links to the scripts (FTP)
 
−
*Need to define what we should have (common datasets)
 
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**Example: Table with all genes, RNAi phenotype, genetic phenotype, etc.
 
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**How many genes have been knocked out by RNAi?, etc.
 
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**Metrics table on each species: #genes, #chromosomes, etc.
 
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*Curators think about what data should be available
 
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*Modifying existing script is easier than making new one
 
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*Gary Williams already generates RNAi-phenotype-gene connections?
 
  
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Snehal work half-time at WormBase?
+
=== SOLR server security (IMSS) ===
−
*Will interview
+
* IMSS network security blocked network on our server due to its open SOLR web access.
−
*UI testing?
+
* Part of AMIGO stack, very old version, drives our ontology browser directly, SObA, Enrichment tools indirectly.
−
*Curation? GO? Phenotype?
+
* Added some firewall/URL filter and IMSS opens up the network (for now). IMSS still gripes about its service is open to the world.
−
*Start April 15th - 8 months? (Sept.) maybe longer
 
−
*Focus on particular papers?
 
  
−
Physical Interaction model
+
=== Alzheimer's disease portal ===
−
*Have been discussing with Rose at BioGRID
+
* Supplement grant awarded to Alliance for an Alzheimer's disease portal
−
*Y2H, CoIPs, Pull downs, etc.
+
* Could involve automated/concise descriptions, interactions, etc.
−
*Store physical interactions in WB outside of GO curation
+
* Could establish useful pipelines that could be reused in other contexts
−
*Data model
 
−
**YH model vs Interaction model
 
−
**Physical interaction tag in current interaction model unused
 
−
**Generalize YH model -> physical interaction model
 
−
**Add experiment types
 
−
**Issue: what do we do with existing physical interaction tag in interaction model?
 
−
**Split out different interaction types into individual classes?
 
−
**Separate into physical, genetic, predicted classes? Textpresso?
 
−
**Create separate classes for each experimental type? (Y2H, CoIP, etc.)
 
−
**XREF Interaction to Physical interaction, Genetic interaction
 
−
**Goal is for cleanliness and completeness
 
−
**How to capture experimental-specific info in curation and database?
 
−
**Suppress Y2H import from BioGRID?
 
−
**Keep interaction models as they are?
 
−
**All curators: Review interaction models to see what they want on the curation end
 

Revision as of 21:01, 13 August 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July


August 6th, 2020

Experimental conditions data flow into Alliance

  • Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
  • We use the WB Molecule CV for Inducers and Modifiers in disease annotation
  • Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
  • So for data flow into Alliance:
    • In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
    • Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
  • How do we handle genetic sex? Part of condition?
    • Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
    • Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex


August 13, 2020

Species in Postgres and ACEDB/Datomic

  • Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
  • Want to be sure that what gets dumped aligns with species loaded into ACEDB
  • Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
  • We currently have multiple Postgres tables for storing species lists:
    • pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
    • obo_name_ncbitaxonid
    • obo_name_taxon (original, smaller list)
    • h_pap_species_index (history for pap_species_index)
  • How do species get loaded into ACEDB? Dumps from Postgres? Which table(s)?
  • WS277 has 7,906 species (1,936 have no NCBI Taxon ID)
  • Kimberly has occasionally uploaded a species.ace file in the context of GO curation; but Hinxton otherwise handles it; should ask them
  • New species are associated with paper objects, but otherwise no additional data for those species come from Caltech
  • It might be useful to have species pages in WB that at least list papers for which we have species associations, maybe include other information?

WS279 Citace upload

  • When is it happening? Not sure; not on release schedule right now

SOLR server security (IMSS)

  • IMSS network security blocked network on our server due to its open SOLR web access.
  • Part of AMIGO stack, very old version, drives our ontology browser directly, SObA, Enrichment tools indirectly.
  • Added some firewall/URL filter and IMSS opens up the network (for now). IMSS still gripes about its service is open to the world.

Alzheimer's disease portal

  • Supplement grant awarded to Alliance for an Alzheimer's disease portal
  • Could involve automated/concise descriptions, interactions, etc.
  • Could establish useful pipelines that could be reused in other contexts
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