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]]
  
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
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= 2021 Meetings =
  
= 2019 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
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[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
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[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
 
  
  
== November 7, 2019 ==
+
== November 4 2021 ==
  
=== WS275 Citace upload ===
+
=== Migrating Paper Pipeline to Alliance ===
* Maybe Nov 22 upload to Hinxton
+
*Meeting abstracts
* CIT curators upload to Spica on Tues Nov 19
+
**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
  
=== ?Genotype class ===
+
 
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
== November 11 2021 ==
* Several classes have a "Genotype" tag with text entry
+
 
** Strain
+
=== WS284 upload dates for Caltech ===
** 2_point_data
+
* When are files due for the Caltech group?
** Pos_neg_data
+
 
** Multi_pt_data
+
===Minutes===
** RNAi
+
*WS284 upload-Better to upload before the holidays or in Jan 2022
** Phenotype_info
+
*Wen will contact Paul D/Hinxton to find out when the WS284 models will be released
** Mass_spec_experiment (no data as of WS273)
+
 
** Condition
+
 
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
+
== November 18 2021 ==
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
+
Proposal for upgrading tanzendra/mangolassi computing resources
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
+
1. Move them to Chen. (done)
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
+
  monitor stability of network
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
+
 
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
+
Old hardware and out of support OS (Ubuntu 14.04)
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
+
 
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
+
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
** Reference to parent strain, like "Parent strain is AG359"
+
  (use Valerio's local server/desktop)
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
+
 
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
+
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