Difference between revisions of "WBConfCall 2016.05.19-Agenda and Minutes"
(3 intermediate revisions by 2 users not shown) | |||
Line 7: | Line 7: | ||
== WS255 == | == WS255 == | ||
− | * upload date: 29th of | + | * upload date: 29th of July? |
== Pending Help Desk Issues == | == Pending Help Desk Issues == | ||
− | |||
* 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/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
Contents
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
- 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/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