Difference between revisions of "WBConfCall 2016.05.19-Agenda and Minutes"

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=Agenda=
 
=Agenda=
 
== modENCODE tracks for G/Jbrowse ==
 
== modENCODE tracks for G/Jbrowse ==
* A number of users (the latest being Victor Ambrose) have observed/complained that features in the modENCODE tracks are not appearing exactly where they should.
+
* A number of users (the latest being Victor Ambros) have observed/complained that features in the modENCODE tracks are not appearing exactly where they should.
 
* This is because the tracks are on WBcel215 coords.
 
* This is because the tracks are on WBcel215 coords.
* They need to be remapped to WBcel235 coords. Can hinxton help with this?  
+
* They need to be remapped to WBcel235 coords. Can hinxton help with this?
 +
* would that help: [[Converting_Coordinates_between_releases]]?
  
 
== WS255 ==
 
== WS255 ==
* upload date: 29th of June?
+
* upload date: 29th of July?
  
== Pending Help Desk Issue ==
+
== Pending Help Desk Issues ==
* https://github.com/WormBase/website/issues/4817 How can I switch off the auto-suggestion/auto-correction in the search box? 16th May
 
 
* https://github.com/WormBase/website/issues/4818 Could you please tell me if it is possible to get the Caenorhabditis elegans Protein Stats? 16th May (Todd?)  
 
* https://github.com/WormBase/website/issues/4818 Could you please tell me if it is possible to get the Caenorhabditis elegans Protein Stats? 16th May (Todd?)  
* https://github.com/WormBase/website/issues/4809 I was requesting gene location info via curl. Can this be closed?
 
 
* https://github.com/WormBase/website/issues/4813 I have a long list of genes with sequence ID. 14th May. Pending with user
 
* https://github.com/WormBase/website/issues/4813 I have a long list of genes with sequence ID. 14th May. Pending with user
 +
 +
=Minutes=
 +
== modENCODE tracks for G/Jbrowse ==
 +
KH: current coordinates are based on the previous version of assembly. Need to be remapped, a task which has been pending last couple of years. Been deprioritised because it's a massive task.
 +
 +
PWS: Mike Cherry has money to remap. Could he do it? He has new modENCODE DCC.
 +
 +
KH: When it finished first time around, we took responsibility for data.
 +
The realignment is a massive job OR remap coord using mapping pipeline. The problem is that Hinxton don’t have data.
 +
If they (Hinxton) have data, they could use cluster to remap.
 +
 +
SC: could be done. Doesn’t know where orig GFFs are. Could write script to dump out.
 +
 +
PK: is this the highest value data? We can’t take control of all data for ever. Is this important enough? We could make old data available as legacy. This data is 4 years old, but is it still valuabl?
 +
 +
modENCODE site display: old assembly with old annotation.
 +
 +
SC: makes sense to map forward. Massive project.
 +
 +
PK: Is it sustainable?
 +
 +
PWS : We could ask Mike Cherry. Or we could get some of their money.
 +
 +
'''Action''': Kev to ask Mike (cc PWS) and report back.
 +
 +
If they say no, we do it ourselves.
 +
 +
== WS255 ==
 +
* Upload is Friday 1st July
 +
* Models frozen 3 weeks prior to upload - Friday 10th June
 +
 +
== Pending Help Desk Issues ==
 +
* We do not go back to WS4!
 +
* FTP goes back to 100 (and randomly WS77).
 +
* '''Action''': MAT to respond
 +
 +
== AOB ==
 +
*Progress Report
 +
**OICR pending. Scott and Sibyl will send draft to PWS by 20th May
 +
** Hinxton - done
 +
** Most of CalTech - done
 +
** MAT to send to PWS by 20th May
 +
** Deadline is 26th May, but must be in place well before then
 +
 +
*Fraqmine = Simple Mine
 +
** http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/simplemine.cgi
 +
** Layout needs to be changed before Todd making available

Latest revision as of 16:25, 19 May 2016

Agenda

modENCODE tracks for G/Jbrowse

  • A number of users (the latest being Victor Ambros) have observed/complained that features in the modENCODE tracks are not appearing exactly where they should.
  • This is because the tracks are on WBcel215 coords.
  • They need to be remapped to WBcel235 coords. Can hinxton help with this?
  • would that help: Converting_Coordinates_between_releases?

WS255

  • upload date: 29th of July?

Pending Help Desk Issues

Minutes

modENCODE tracks for G/Jbrowse

KH: current coordinates are based on the previous version of assembly. Need to be remapped, a task which has been pending last couple of years. Been deprioritised because it's a massive task.

PWS: Mike Cherry has money to remap. Could he do it? He has new modENCODE DCC.

KH: When it finished first time around, we took responsibility for data. The realignment is a massive job OR remap coord using mapping pipeline. The problem is that Hinxton don’t have data. If they (Hinxton) have data, they could use cluster to remap.

SC: could be done. Doesn’t know where orig GFFs are. Could write script to dump out.

PK: is this the highest value data? We can’t take control of all data for ever. Is this important enough? We could make old data available as legacy. This data is 4 years old, but is it still valuabl?

modENCODE site display: old assembly with old annotation.

SC: makes sense to map forward. Massive project.

PK: Is it sustainable?

PWS : We could ask Mike Cherry. Or we could get some of their money.

Action: Kev to ask Mike (cc PWS) and report back.

If they say no, we do it ourselves.

WS255

  • Upload is Friday 1st July
  • Models frozen 3 weeks prior to upload - Friday 10th June

Pending Help Desk Issues

  • We do not go back to WS4!
  • FTP goes back to 100 (and randomly WS77).
  • Action: MAT to respond

AOB

  • Progress Report
    • OICR pending. Scott and Sibyl will send draft to PWS by 20th May
    • Hinxton - done
    • Most of CalTech - done
    • MAT to send to PWS by 20th May
    • Deadline is 26th May, but must be in place well before then