Difference between revisions of "WBConfCall 2013.10.17-Agenda and Minutes"

From WormBaseWiki
Jump to navigationJump to search
 
(23 intermediate revisions by 2 users not shown)
Line 14: Line 14:
 
* when?
 
* when?
 
* where?
 
* where?
 +
 +
== Release Themes ==
 +
* protein folding / pathways WS241
 +
* ncRNA / specific ncRNAs (lincRNA/snoRNAs) WS242
  
 
= Minutes =
 
= Minutes =
 +
== WormMine ==
 +
* 5.3 days build time, checkpoints used to resume
 +
** 2d14h for build without sequence generation
 +
** 2d7h to generate dna sequences from located features
 +
* sequences for proteins and genomic features for all species except C.sp 5 and C.sp.11
 +
* richer classes to query (example RNAi, etc.)
 +
* link to JDs wiki:
 +
* CDS locations not included in WS239
 +
 +
JD's announcement email:
 +
 +
WormMine WS239 is now up for testing:
 +
 +
Please find the new WormMine build here:
 +
http://206.108.125.174:8080/wormmine/begin.do
 +
 +
Data changes from WS238:
 +
* genomic fasta, protein fasta, genes from gff3, transcripts from gff3 has been expanded to represent all species in wormbase (besides any of the "sp" species)
 +
* the fields of data for each Ace type has been expanded.  Wiki has been updated: http://wiki.wormbase.org/index.php/WormMine#Data_contained_in_WormMine
 +
* RNAi included
 +
* CDS locations have been temporarily omitted due to them being loaded incorrectly in the last build.
 +
 +
Build released to curators for testing, will be pushed to production once approved.
 +
 +
== URLs / URIs ==
 +
* current: flatfile in the github repository (problem: wrong formatted commits)
 +
* future: potentially an update form/site
 +
* proposal: remove the URLs from database (to make it clear the repository is the canonical source)
 +
* proposal: remove the URL_constructor from model
 +
 +
== ABM ==
 +
* early next year
 +
* Hinxton
 +
 +
== Nameserver ==
 +
* JSON dumper too slow
 +
* delay between GeneAce <=> NameDB synch
 +
* make sure that NameDB <=> GeneAce is synched weekly
 +
* proposal: do a nightly JSON dump
 +
* proposal: put the database on the cloud
 +
 +
== InterMine ==
 +
* call for letter of support for their new funding cycle
 +
 +
== Themed Curation ==
 +
* collaborate to curate the protein folding pathways for WS241
 +
** potentially comparative analysis across species
  
 
= Curation Focus ideas for themed releases =
 
= Curation Focus ideas for themed releases =

Latest revision as of 16:32, 17 October 2013

Agenda

WormMine WS239

  • maybe JD can give an overview of the new things
  • Thoughts, reactions?

database URL/URIs

  • where should we store these?
    • acedb + website flat file
    • website flat file only with only database name and description stored in acedb
  • can there be an easier way to update the URL/URIs on the web

ABM 2014

  • when?
  • where?

Release Themes

  • protein folding / pathways WS241
  • ncRNA / specific ncRNAs (lincRNA/snoRNAs) WS242

Minutes

WormMine

  • 5.3 days build time, checkpoints used to resume
    • 2d14h for build without sequence generation
    • 2d7h to generate dna sequences from located features
  • sequences for proteins and genomic features for all species except C.sp 5 and C.sp.11
  • richer classes to query (example RNAi, etc.)
  • link to JDs wiki:
  • CDS locations not included in WS239

JD's announcement email:

WormMine WS239 is now up for testing:

Please find the new WormMine build here: http://206.108.125.174:8080/wormmine/begin.do

Data changes from WS238:

  • genomic fasta, protein fasta, genes from gff3, transcripts from gff3 has been expanded to represent all species in wormbase (besides any of the "sp" species)
  • the fields of data for each Ace type has been expanded. Wiki has been updated: http://wiki.wormbase.org/index.php/WormMine#Data_contained_in_WormMine
  • RNAi included
  • CDS locations have been temporarily omitted due to them being loaded incorrectly in the last build.

Build released to curators for testing, will be pushed to production once approved.

URLs / URIs

  • current: flatfile in the github repository (problem: wrong formatted commits)
  • future: potentially an update form/site
  • proposal: remove the URLs from database (to make it clear the repository is the canonical source)
  • proposal: remove the URL_constructor from model

ABM

  • early next year
  • Hinxton

Nameserver

  • JSON dumper too slow
  • delay between GeneAce <=> NameDB synch
  • make sure that NameDB <=> GeneAce is synched weekly
  • proposal: do a nightly JSON dump
  • proposal: put the database on the cloud

InterMine

  • call for letter of support for their new funding cycle

Themed Curation

  • collaborate to curate the protein folding pathways for WS241
    • potentially comparative analysis across species

Curation Focus ideas for themed releases

ncRNAs

  • we could add ncRNAs to the other non-cores from other databases (Hinxton) and look through literature (CalTech)