Difference between revisions of "Issues-9/10/2013"

From WormBaseWiki
Jump to navigationJump to search
 
(One intermediate revision by the same user not shown)
Line 10: Line 10:
 
== Joachim ==
 
== Joachim ==
 
=== GFF3 ===
 
=== GFF3 ===
 +
* emailed KH - GFF3 of c_elegans
 +
** can't display all features in segmented features
 +
** certain features - gbrowse needs label on lowest tier (heirarchy)
 +
** new gff3 with proper names and backtrack on sources/types
 +
** going through config files one by one - gff2/misconfigured tracks
  
 
=== Visualizations ===
 
=== Visualizations ===
Line 16: Line 21:
 
* #885 -RNASeq expression feature request Hinxton Webteam UI-data display
 
* #885 -RNASeq expression feature request Hinxton Webteam UI-data display
 
* prototype?
 
* prototype?
 +
 +
*installed Ruby and R on new server - went really well
 +
** new versions
 +
** in principle set up, fill in api to show graphs
  
 
=== Current Issues ===
 
=== Current Issues ===
Line 24: Line 33:
 
* #909 - Standardize GBrowse configuration (when possible) gbrowse Webteam
 
* #909 - Standardize GBrowse configuration (when possible) gbrowse Webteam
 
* #910 -Test GFF3 and update species still using Bio::DB::GFF to Bio::DB::SeqFeature::Store administration gbrowse Webteam
 
* #910 -Test GFF3 and update species still using Bio::DB::GFF to Bio::DB::SeqFeature::Store administration gbrowse Webteam
 +
 +
 +
* #1724 - Update FTP site with bioproject ids
 +
* #1718 - Genelet tracks in gbrowse
 +
** probably db connections
  
 
== JD ==
 
== JD ==
Line 29: Line 43:
 
=== Current Issues ===
 
=== Current Issues ===
 
* #741- lineage browser
 
* #741- lineage browser
 +
** implementing LS suggestions
 
* #1647 - sequence summary addition
 
* #1647 - sequence summary addition
 
** change the label to just 'Pseudogene'?
 
** change the label to just 'Pseudogene'?
 +
** just about done
 
* #1082 - transposon family summary pages
 
* #1082 - transposon family summary pages
 +
** about done - just link to transposon page
 
* #1602 - sequence summary
 
* #1602 - sequence summary
 
* #1511 - remove links to non-curated species strains
 
* #1511 - remove links to non-curated species strains
 +
 +
=== Intermine ===
 +
* recreated test suite - limited to mapping files
 +
** reads mapping files, tests if records for each field, if it's filled in
  
 
= WS239 =
 
= WS239 =
Line 39: Line 60:
 
** gbrowse
 
** gbrowse
 
** website
 
** website
 +
*** suggest to TH - keep it as it is, change for 240
 
* Cytoscape upgrade
 
* Cytoscape upgrade
 +
** Karen & Chris requested legend changes
  
 
= Other =
 
= Other =

Latest revision as of 14:57, 10 September 2013

All meetings: WebDev Issues Meetings

Tuesday Sept 10th, 10:30am, 5th floor NE Boardroom

wb-dev -> dev.wormbase.org

Is anything not working?

Current issues

Joachim

GFF3

  • emailed KH - GFF3 of c_elegans
    • can't display all features in segmented features
    • certain features - gbrowse needs label on lowest tier (heirarchy)
    • new gff3 with proper names and backtrack on sources/types
    • going through config files one by one - gff2/misconfigured tracks

Visualizations

Website:Visualization_Library_Assessment Website:Visualization_with_ggplot2_of_the_R-Project

  • #885 -RNASeq expression feature request Hinxton Webteam UI-data display
  • prototype?
  • installed Ruby and R on new server - went really well
    • new versions
    • in principle set up, fill in api to show graphs

Current Issues

Under Testing - anything left to be done

  • #1586 - Bug Report: the URLs in the Downloads widget of... HelpDesk Webteam UI-data display Under testing

WS239

  • #909 - Standardize GBrowse configuration (when possible) gbrowse Webteam
  • #910 -Test GFF3 and update species still using Bio::DB::GFF to Bio::DB::SeqFeature::Store administration gbrowse Webteam


  • #1724 - Update FTP site with bioproject ids
  • #1718 - Genelet tracks in gbrowse
    • probably db connections

JD

Current Issues

  • #741- lineage browser
    • implementing LS suggestions
  • #1647 - sequence summary addition
    • change the label to just 'Pseudogene'?
    • just about done
  • #1082 - transposon family summary pages
    • about done - just link to transposon page
  • #1602 - sequence summary
  • #1511 - remove links to non-curated species strains

Intermine

  • recreated test suite - limited to mapping files
    • reads mapping files, tests if records for each field, if it's filled in

WS239

  • GFF3
    • gbrowse
    • website
      • suggest to TH - keep it as it is, change for 240
  • Cytoscape upgrade
    • Karen & Chris requested legend changes

Other