Version 6 (modified by val_wood, 9 years ago) (diff)


(March 18 2013)


Outstanding Action items

New action items from February

New Agenda Items


  • We are now showing version 31 from 19 December (324 fully curated publications)
    • V32 was skipped because version 31 hasn't gone live (330 fully curated publications)
    • V33 (7th March) (535 fully curated publications) is on stage

File formats and repositories for HTP data

  • Proteomics (Dieter Wolfe)
  • Transcriptomics/RNA seq
  • Poly A sites (Juan Mata) Bam files?

We want to put dome documentation up about what users need to do

Updates from various Areas

Website update from Mark

  • Present the stats for the difference between the stage site now and the live site as it was when we were having trouble.
    • Talk about the use of (Starter pack is $7.50 per month and can select 3 locations by country (US has 5 of those locations) (25 listed), actual location not listed.)
    • See if it is possible to set something up in Cambridge.
    • Looking at converting the python Selenium tests into Java and then working on expanding the tests that are run.
  • Got the data on Thursday (7th March). I had started working on the ontology db and loading that so they could get the release to us. I have been able to perform the updates and reload the core and ontology

a couple of times to fix a few bugs. v33 is now on the test genomebrowser. I have initiated the Drupal server to rebuild the JSON cache. I have also rebuilt the ontology database. If everything is working and the stats look fine we should be able to start to push through to dev on Tuesday and then hopefully on to live on Wednesday.

  • Given the manual run through that I have just done; Val and Kim are you happy going forward with the timeline that I'll take the latest release on the 1st Monday of the Month and then go for release on the third Monday? This gives two weeks for the updates and then do the release on a Monday rather than a Friday?
  • After going through a full release manually I have noted down the procedure I followed, along with subsequent updates. This now needs to be formalised and packed in an automated fashion along with regression testing. My target is to focus on this after the release and hopefully have a pipeline ready for the next meeting.
  • With automation I need to work on the dumping scripts for the stats. These should come in soon after having the main pipeline generated and then I can just plumb them in accordingly.

This discussion will probably cover many of the items below:

  • update on speed and page loading
  • Update on regularity of updates
  • Progress implementing the RNA/protein expression data from Sam's paper
    • (now tabled for V 34, need to load into Chado and get display on gene page sorted)
  • Update on gene name synching (e.g. why is mre11 still called rad32…was changed in early November?)
  • Update on providing files for download
    • At present files are not consistent with version (out of date). Lots of outstanding helpdesk tickets related to this
  • synchronicity issues


Curation Update

  • triage
  • * approved sessions up from 535

  • session management and help finishing for Canto (in progress) COMPLTETE TEST AND UPDATE

Phenotype Ontology

  • ???? phenotype terms
  • anything else

Chado loading

  • anything to report ?

Curation tool

  • anything to report?

Review next priorities & progress

Current jira status:

  • Data download files
  • Other data hosting

Meetings Attended Upcoming UPDATE

  • 28 Feb-1 March GO cell cycle ontology content meeting ( GO and Jacky Hayles)
  • March 20-22 BYG 2 posters submitted: Antonia (community curation), Midori (phenotypes)
  • April 7-10 ISB, 4 posters submitted: Val (Annotation QC, general PomBase), Antonia (community curation), Midori (phenotypes) Mark might want to attend, at least poster sessions?
    • April 10-13 GO meeting is immediately after this meeting, Mark should attend the software sessions

  • Pombe meeting, still need to decide what to do about PomBase/GO/curation demo


Attachments (1)

Download all attachments as: .zip